anno_start	anno_end	anno_text	entity_type	sentence	section
0	26	Ribosome biogenesis factor	protein_type	Ribosome biogenesis factor Tsr3 is the aminocarboxypropyl transferase responsible for 18S rRNA hypermodification in yeast and humans	TITLE
27	31	Tsr3	protein	Ribosome biogenesis factor Tsr3 is the aminocarboxypropyl transferase responsible for 18S rRNA hypermodification in yeast and humans	TITLE
39	69	aminocarboxypropyl transferase	protein_type	Ribosome biogenesis factor Tsr3 is the aminocarboxypropyl transferase responsible for 18S rRNA hypermodification in yeast and humans	TITLE
86	94	18S rRNA	chemical	Ribosome biogenesis factor Tsr3 is the aminocarboxypropyl transferase responsible for 18S rRNA hypermodification in yeast and humans	TITLE
116	121	yeast	taxonomy_domain	Ribosome biogenesis factor Tsr3 is the aminocarboxypropyl transferase responsible for 18S rRNA hypermodification in yeast and humans	TITLE
126	132	humans	species	Ribosome biogenesis factor Tsr3 is the aminocarboxypropyl transferase responsible for 18S rRNA hypermodification in yeast and humans	TITLE
44	54	eukaryotic	taxonomy_domain	The chemically most complex modification in eukaryotic rRNA is the conserved hypermodified nucleotide N1-methyl-N3-aminocarboxypropyl-pseudouridine (m1acp3Ψ) located next to the P-site tRNA on the small subunit 18S rRNA.	ABSTRACT
55	59	rRNA	chemical	The chemically most complex modification in eukaryotic rRNA is the conserved hypermodified nucleotide N1-methyl-N3-aminocarboxypropyl-pseudouridine (m1acp3Ψ) located next to the P-site tRNA on the small subunit 18S rRNA.	ABSTRACT
67	76	conserved	protein_state	The chemically most complex modification in eukaryotic rRNA is the conserved hypermodified nucleotide N1-methyl-N3-aminocarboxypropyl-pseudouridine (m1acp3Ψ) located next to the P-site tRNA on the small subunit 18S rRNA.	ABSTRACT
77	90	hypermodified	protein_state	The chemically most complex modification in eukaryotic rRNA is the conserved hypermodified nucleotide N1-methyl-N3-aminocarboxypropyl-pseudouridine (m1acp3Ψ) located next to the P-site tRNA on the small subunit 18S rRNA.	ABSTRACT
91	101	nucleotide	chemical	The chemically most complex modification in eukaryotic rRNA is the conserved hypermodified nucleotide N1-methyl-N3-aminocarboxypropyl-pseudouridine (m1acp3Ψ) located next to the P-site tRNA on the small subunit 18S rRNA.	ABSTRACT
102	147	N1-methyl-N3-aminocarboxypropyl-pseudouridine	chemical	The chemically most complex modification in eukaryotic rRNA is the conserved hypermodified nucleotide N1-methyl-N3-aminocarboxypropyl-pseudouridine (m1acp3Ψ) located next to the P-site tRNA on the small subunit 18S rRNA.	ABSTRACT
149	156	m1acp3Ψ	chemical	The chemically most complex modification in eukaryotic rRNA is the conserved hypermodified nucleotide N1-methyl-N3-aminocarboxypropyl-pseudouridine (m1acp3Ψ) located next to the P-site tRNA on the small subunit 18S rRNA.	ABSTRACT
178	184	P-site	site	The chemically most complex modification in eukaryotic rRNA is the conserved hypermodified nucleotide N1-methyl-N3-aminocarboxypropyl-pseudouridine (m1acp3Ψ) located next to the P-site tRNA on the small subunit 18S rRNA.	ABSTRACT
185	189	tRNA	chemical	The chemically most complex modification in eukaryotic rRNA is the conserved hypermodified nucleotide N1-methyl-N3-aminocarboxypropyl-pseudouridine (m1acp3Ψ) located next to the P-site tRNA on the small subunit 18S rRNA.	ABSTRACT
211	219	18S rRNA	chemical	The chemically most complex modification in eukaryotic rRNA is the conserved hypermodified nucleotide N1-methyl-N3-aminocarboxypropyl-pseudouridine (m1acp3Ψ) located next to the P-site tRNA on the small subunit 18S rRNA.	ABSTRACT
6	26	S-adenosylmethionine	chemical	While S-adenosylmethionine was identified as the source of the aminocarboxypropyl (acp) group more than 40 years ago the enzyme catalyzing the acp transfer remained elusive.	ABSTRACT
63	81	aminocarboxypropyl	chemical	While S-adenosylmethionine was identified as the source of the aminocarboxypropyl (acp) group more than 40 years ago the enzyme catalyzing the acp transfer remained elusive.	ABSTRACT
83	86	acp	chemical	While S-adenosylmethionine was identified as the source of the aminocarboxypropyl (acp) group more than 40 years ago the enzyme catalyzing the acp transfer remained elusive.	ABSTRACT
143	146	acp	chemical	While S-adenosylmethionine was identified as the source of the aminocarboxypropyl (acp) group more than 40 years ago the enzyme catalyzing the acp transfer remained elusive.	ABSTRACT
61	65	Tsr3	protein	Here we identify the cytoplasmic ribosome biogenesis protein Tsr3 as the responsible enzyme in yeast and human cells.	ABSTRACT
95	100	yeast	taxonomy_domain	Here we identify the cytoplasmic ribosome biogenesis protein Tsr3 as the responsible enzyme in yeast and human cells.	ABSTRACT
105	110	human	species	Here we identify the cytoplasmic ribosome biogenesis protein Tsr3 as the responsible enzyme in yeast and human cells.	ABSTRACT
25	29	Tsr3	protein	In functionally impaired Tsr3-mutants, a reduced level of acp modification directly correlates with increased 20S pre-rRNA accumulation.	ABSTRACT
30	37	mutants	protein_state	In functionally impaired Tsr3-mutants, a reduced level of acp modification directly correlates with increased 20S pre-rRNA accumulation.	ABSTRACT
58	61	acp	chemical	In functionally impaired Tsr3-mutants, a reduced level of acp modification directly correlates with increased 20S pre-rRNA accumulation.	ABSTRACT
110	122	20S pre-rRNA	chemical	In functionally impaired Tsr3-mutants, a reduced level of acp modification directly correlates with increased 20S pre-rRNA accumulation.	ABSTRACT
4	21	crystal structure	evidence	The crystal structure of archaeal Tsr3 homologs revealed the same fold as in SPOUT-class RNA-methyltransferases but a distinct SAM binding mode.	ABSTRACT
25	33	archaeal	taxonomy_domain	The crystal structure of archaeal Tsr3 homologs revealed the same fold as in SPOUT-class RNA-methyltransferases but a distinct SAM binding mode.	ABSTRACT
34	38	Tsr3	protein	The crystal structure of archaeal Tsr3 homologs revealed the same fold as in SPOUT-class RNA-methyltransferases but a distinct SAM binding mode.	ABSTRACT
77	111	SPOUT-class RNA-methyltransferases	protein_type	The crystal structure of archaeal Tsr3 homologs revealed the same fold as in SPOUT-class RNA-methyltransferases but a distinct SAM binding mode.	ABSTRACT
127	143	SAM binding mode	site	The crystal structure of archaeal Tsr3 homologs revealed the same fold as in SPOUT-class RNA-methyltransferases but a distinct SAM binding mode.	ABSTRACT
12	28	SAM binding mode	site	This unique SAM binding mode explains why Tsr3 transfers the acp and not the methyl group of SAM to its substrate.	ABSTRACT
42	46	Tsr3	protein	This unique SAM binding mode explains why Tsr3 transfers the acp and not the methyl group of SAM to its substrate.	ABSTRACT
61	64	acp	chemical	This unique SAM binding mode explains why Tsr3 transfers the acp and not the methyl group of SAM to its substrate.	ABSTRACT
93	96	SAM	chemical	This unique SAM binding mode explains why Tsr3 transfers the acp and not the methyl group of SAM to its substrate.	ABSTRACT
14	18	Tsr3	protein	Structurally, Tsr3 therefore represents a novel class of acp transferase enzymes.	ABSTRACT
57	72	acp transferase	protein_type	Structurally, Tsr3 therefore represents a novel class of acp transferase enzymes.	ABSTRACT
0	10	Eukaryotic	taxonomy_domain	Eukaryotic ribosome biogenesis is highly complex and requires a large number of non-ribosomal proteins and small non-coding RNAs in addition to ribosomal RNAs (rRNAs) and proteins.	INTRO
107	128	small non-coding RNAs	chemical	Eukaryotic ribosome biogenesis is highly complex and requires a large number of non-ribosomal proteins and small non-coding RNAs in addition to ribosomal RNAs (rRNAs) and proteins.	INTRO
144	158	ribosomal RNAs	chemical	Eukaryotic ribosome biogenesis is highly complex and requires a large number of non-ribosomal proteins and small non-coding RNAs in addition to ribosomal RNAs (rRNAs) and proteins.	INTRO
160	165	rRNAs	chemical	Eukaryotic ribosome biogenesis is highly complex and requires a large number of non-ribosomal proteins and small non-coding RNAs in addition to ribosomal RNAs (rRNAs) and proteins.	INTRO
7	17	eukaryotic	taxonomy_domain	During eukaryotic ribosome biogenesis several dozens of rRNA nucleotides become chemically modified.	INTRO
56	60	rRNA	chemical	During eukaryotic ribosome biogenesis several dozens of rRNA nucleotides become chemically modified.	INTRO
61	72	nucleotides	chemical	During eukaryotic ribosome biogenesis several dozens of rRNA nucleotides become chemically modified.	INTRO
18	22	rRNA	chemical	The most abundant rRNA modifications are methylations at the 2′-OH ribose moieties and isomerizations of uridine residues to pseudouridine, catalyzed by small nucleolar ribonucleoprotein particles (snoRNPs).	INTRO
41	53	methylations	ptm	The most abundant rRNA modifications are methylations at the 2′-OH ribose moieties and isomerizations of uridine residues to pseudouridine, catalyzed by small nucleolar ribonucleoprotein particles (snoRNPs).	INTRO
67	73	ribose	chemical	The most abundant rRNA modifications are methylations at the 2′-OH ribose moieties and isomerizations of uridine residues to pseudouridine, catalyzed by small nucleolar ribonucleoprotein particles (snoRNPs).	INTRO
105	112	uridine	chemical	The most abundant rRNA modifications are methylations at the 2′-OH ribose moieties and isomerizations of uridine residues to pseudouridine, catalyzed by small nucleolar ribonucleoprotein particles (snoRNPs).	INTRO
125	138	pseudouridine	chemical	The most abundant rRNA modifications are methylations at the 2′-OH ribose moieties and isomerizations of uridine residues to pseudouridine, catalyzed by small nucleolar ribonucleoprotein particles (snoRNPs).	INTRO
153	196	small nucleolar ribonucleoprotein particles	complex_assembly	The most abundant rRNA modifications are methylations at the 2′-OH ribose moieties and isomerizations of uridine residues to pseudouridine, catalyzed by small nucleolar ribonucleoprotein particles (snoRNPs).	INTRO
198	205	snoRNPs	complex_assembly	The most abundant rRNA modifications are methylations at the 2′-OH ribose moieties and isomerizations of uridine residues to pseudouridine, catalyzed by small nucleolar ribonucleoprotein particles (snoRNPs).	INTRO
13	16	18S	chemical	In addition, 18S and 25S (yeast)/ 28S (humans) rRNAs contain several base modifications catalyzed by site-specific and snoRNA-independent enzymes.	INTRO
21	24	25S	chemical	In addition, 18S and 25S (yeast)/ 28S (humans) rRNAs contain several base modifications catalyzed by site-specific and snoRNA-independent enzymes.	INTRO
26	31	yeast	taxonomy_domain	In addition, 18S and 25S (yeast)/ 28S (humans) rRNAs contain several base modifications catalyzed by site-specific and snoRNA-independent enzymes.	INTRO
34	37	28S	chemical	In addition, 18S and 25S (yeast)/ 28S (humans) rRNAs contain several base modifications catalyzed by site-specific and snoRNA-independent enzymes.	INTRO
39	45	humans	species	In addition, 18S and 25S (yeast)/ 28S (humans) rRNAs contain several base modifications catalyzed by site-specific and snoRNA-independent enzymes.	INTRO
47	52	rRNAs	chemical	In addition, 18S and 25S (yeast)/ 28S (humans) rRNAs contain several base modifications catalyzed by site-specific and snoRNA-independent enzymes.	INTRO
119	125	snoRNA	chemical	In addition, 18S and 25S (yeast)/ 28S (humans) rRNAs contain several base modifications catalyzed by site-specific and snoRNA-independent enzymes.	INTRO
3	27	Saccharomyces cerevisiae	species	In Saccharomyces cerevisiae 18S rRNA contains four base methylations, two acetylations and a single 3-amino-3-carboxypropyl (acp) modification, whereas six base methylations are present in the 25S rRNA.	INTRO
28	36	18S rRNA	chemical	In Saccharomyces cerevisiae 18S rRNA contains four base methylations, two acetylations and a single 3-amino-3-carboxypropyl (acp) modification, whereas six base methylations are present in the 25S rRNA.	INTRO
56	68	methylations	ptm	In Saccharomyces cerevisiae 18S rRNA contains four base methylations, two acetylations and a single 3-amino-3-carboxypropyl (acp) modification, whereas six base methylations are present in the 25S rRNA.	INTRO
74	86	acetylations	ptm	In Saccharomyces cerevisiae 18S rRNA contains four base methylations, two acetylations and a single 3-amino-3-carboxypropyl (acp) modification, whereas six base methylations are present in the 25S rRNA.	INTRO
100	123	3-amino-3-carboxypropyl	chemical	In Saccharomyces cerevisiae 18S rRNA contains four base methylations, two acetylations and a single 3-amino-3-carboxypropyl (acp) modification, whereas six base methylations are present in the 25S rRNA.	INTRO
125	128	acp	chemical	In Saccharomyces cerevisiae 18S rRNA contains four base methylations, two acetylations and a single 3-amino-3-carboxypropyl (acp) modification, whereas six base methylations are present in the 25S rRNA.	INTRO
161	173	methylations	ptm	In Saccharomyces cerevisiae 18S rRNA contains four base methylations, two acetylations and a single 3-amino-3-carboxypropyl (acp) modification, whereas six base methylations are present in the 25S rRNA.	INTRO
193	201	25S rRNA	chemical	In Saccharomyces cerevisiae 18S rRNA contains four base methylations, two acetylations and a single 3-amino-3-carboxypropyl (acp) modification, whereas six base methylations are present in the 25S rRNA.	INTRO
9	15	humans	species	While in humans the 18S rRNA base modifications are highly conserved, only three of the yeast base modifications catalyzed by ScRrp8/HsNML, ScRcm1/HsNSUN5 and ScNop2/HsNSUN1 are preserved in the corresponding human 28S rRNA.	INTRO
20	28	18S rRNA	chemical	While in humans the 18S rRNA base modifications are highly conserved, only three of the yeast base modifications catalyzed by ScRrp8/HsNML, ScRcm1/HsNSUN5 and ScNop2/HsNSUN1 are preserved in the corresponding human 28S rRNA.	INTRO
52	68	highly conserved	protein_state	While in humans the 18S rRNA base modifications are highly conserved, only three of the yeast base modifications catalyzed by ScRrp8/HsNML, ScRcm1/HsNSUN5 and ScNop2/HsNSUN1 are preserved in the corresponding human 28S rRNA.	INTRO
88	93	yeast	taxonomy_domain	While in humans the 18S rRNA base modifications are highly conserved, only three of the yeast base modifications catalyzed by ScRrp8/HsNML, ScRcm1/HsNSUN5 and ScNop2/HsNSUN1 are preserved in the corresponding human 28S rRNA.	INTRO
126	132	ScRrp8	protein	While in humans the 18S rRNA base modifications are highly conserved, only three of the yeast base modifications catalyzed by ScRrp8/HsNML, ScRcm1/HsNSUN5 and ScNop2/HsNSUN1 are preserved in the corresponding human 28S rRNA.	INTRO
133	138	HsNML	protein	While in humans the 18S rRNA base modifications are highly conserved, only three of the yeast base modifications catalyzed by ScRrp8/HsNML, ScRcm1/HsNSUN5 and ScNop2/HsNSUN1 are preserved in the corresponding human 28S rRNA.	INTRO
140	146	ScRcm1	protein	While in humans the 18S rRNA base modifications are highly conserved, only three of the yeast base modifications catalyzed by ScRrp8/HsNML, ScRcm1/HsNSUN5 and ScNop2/HsNSUN1 are preserved in the corresponding human 28S rRNA.	INTRO
147	154	HsNSUN5	protein	While in humans the 18S rRNA base modifications are highly conserved, only three of the yeast base modifications catalyzed by ScRrp8/HsNML, ScRcm1/HsNSUN5 and ScNop2/HsNSUN1 are preserved in the corresponding human 28S rRNA.	INTRO
159	165	ScNop2	protein	While in humans the 18S rRNA base modifications are highly conserved, only three of the yeast base modifications catalyzed by ScRrp8/HsNML, ScRcm1/HsNSUN5 and ScNop2/HsNSUN1 are preserved in the corresponding human 28S rRNA.	INTRO
166	173	HsNSUN1	protein	While in humans the 18S rRNA base modifications are highly conserved, only three of the yeast base modifications catalyzed by ScRrp8/HsNML, ScRcm1/HsNSUN5 and ScNop2/HsNSUN1 are preserved in the corresponding human 28S rRNA.	INTRO
209	214	human	species	While in humans the 18S rRNA base modifications are highly conserved, only three of the yeast base modifications catalyzed by ScRrp8/HsNML, ScRcm1/HsNSUN5 and ScNop2/HsNSUN1 are preserved in the corresponding human 28S rRNA.	INTRO
215	223	28S rRNA	chemical	While in humans the 18S rRNA base modifications are highly conserved, only three of the yeast base modifications catalyzed by ScRrp8/HsNML, ScRcm1/HsNSUN5 and ScNop2/HsNSUN1 are preserved in the corresponding human 28S rRNA.	INTRO
0	13	Ribosomal RNA	chemical	Ribosomal RNA modifications have been suggested to optimize ribosome function, although in most cases this remains to be clearly established.	INTRO
35	38	RNA	chemical	They might contribute to increased RNA stability by providing additional hydrogen bonds (pseudouridines), improved base stacking (pseudouridines and base methylations) or an increased resistance against hydrolysis (ribose methylations).	INTRO
73	87	hydrogen bonds	bond_interaction	They might contribute to increased RNA stability by providing additional hydrogen bonds (pseudouridines), improved base stacking (pseudouridines and base methylations) or an increased resistance against hydrolysis (ribose methylations).	INTRO
89	103	pseudouridines	chemical	They might contribute to increased RNA stability by providing additional hydrogen bonds (pseudouridines), improved base stacking (pseudouridines and base methylations) or an increased resistance against hydrolysis (ribose methylations).	INTRO
115	128	base stacking	bond_interaction	They might contribute to increased RNA stability by providing additional hydrogen bonds (pseudouridines), improved base stacking (pseudouridines and base methylations) or an increased resistance against hydrolysis (ribose methylations).	INTRO
130	144	pseudouridines	chemical	They might contribute to increased RNA stability by providing additional hydrogen bonds (pseudouridines), improved base stacking (pseudouridines and base methylations) or an increased resistance against hydrolysis (ribose methylations).	INTRO
149	166	base methylations	ptm	They might contribute to increased RNA stability by providing additional hydrogen bonds (pseudouridines), improved base stacking (pseudouridines and base methylations) or an increased resistance against hydrolysis (ribose methylations).	INTRO
215	234	ribose methylations	ptm	They might contribute to increased RNA stability by providing additional hydrogen bonds (pseudouridines), improved base stacking (pseudouridines and base methylations) or an increased resistance against hydrolysis (ribose methylations).	INTRO
14	18	rRNA	chemical	Most modified rRNA nucleotides cluster in the vicinity of the decoding or the peptidyl transferase center, suggesting an influence on ribosome functionality and stability.	INTRO
19	30	nucleotides	chemical	Most modified rRNA nucleotides cluster in the vicinity of the decoding or the peptidyl transferase center, suggesting an influence on ribosome functionality and stability.	INTRO
62	70	decoding	site	Most modified rRNA nucleotides cluster in the vicinity of the decoding or the peptidyl transferase center, suggesting an influence on ribosome functionality and stability.	INTRO
78	105	peptidyl transferase center	site	Most modified rRNA nucleotides cluster in the vicinity of the decoding or the peptidyl transferase center, suggesting an influence on ribosome functionality and stability.	INTRO
11	15	rRNA	chemical	Defects of rRNA modification enzymes often lead to disturbed ribosome biogenesis or functionally impaired ribosomes, although the lack of individual rRNA modifications often has no or only a slight influence on the cell.	INTRO
149	153	rRNA	chemical	Defects of rRNA modification enzymes often lead to disturbed ribosome biogenesis or functionally impaired ribosomes, although the lack of individual rRNA modifications often has no or only a slight influence on the cell.	INTRO
59	80	loop capping helix 31	structure_element	The chemically most complex modification is located in the loop capping helix 31 of 18S rRNA (Supplementary Figure S1B).	INTRO
84	92	18S rRNA	chemical	The chemically most complex modification is located in the loop capping helix 31 of 18S rRNA (Supplementary Figure S1B).	INTRO
8	15	uridine	residue_name	There a uridine (U1191 in yeast) is modified to 1-methyl-3-(3-amino-3-carboxypropyl)-pseudouridine (m1acp3Ψ, Figure 1A).	INTRO
17	22	U1191	residue_name_number	There a uridine (U1191 in yeast) is modified to 1-methyl-3-(3-amino-3-carboxypropyl)-pseudouridine (m1acp3Ψ, Figure 1A).	INTRO
26	31	yeast	taxonomy_domain	There a uridine (U1191 in yeast) is modified to 1-methyl-3-(3-amino-3-carboxypropyl)-pseudouridine (m1acp3Ψ, Figure 1A).	INTRO
48	98	1-methyl-3-(3-amino-3-carboxypropyl)-pseudouridine	chemical	There a uridine (U1191 in yeast) is modified to 1-methyl-3-(3-amino-3-carboxypropyl)-pseudouridine (m1acp3Ψ, Figure 1A).	INTRO
100	107	m1acp3Ψ	chemical	There a uridine (U1191 in yeast) is modified to 1-methyl-3-(3-amino-3-carboxypropyl)-pseudouridine (m1acp3Ψ, Figure 1A).	INTRO
55	62	hamster	taxonomy_domain	This base modification was first described in 1968 for hamster cells and is conserved in eukaryotes.	INTRO
76	88	conserved in	protein_state	This base modification was first described in 1968 for hamster cells and is conserved in eukaryotes.	INTRO
89	99	eukaryotes	taxonomy_domain	This base modification was first described in 1968 for hamster cells and is conserved in eukaryotes.	INTRO
5	18	hypermodified	protein_state	This hypermodified nucleotide, which is located at the P-site tRNA, is synthesized in three steps beginning with the snR35 H/ACA snoRNP guided conversion of uridine into pseudouridine.	INTRO
19	29	nucleotide	chemical	This hypermodified nucleotide, which is located at the P-site tRNA, is synthesized in three steps beginning with the snR35 H/ACA snoRNP guided conversion of uridine into pseudouridine.	INTRO
55	61	P-site	site	This hypermodified nucleotide, which is located at the P-site tRNA, is synthesized in three steps beginning with the snR35 H/ACA snoRNP guided conversion of uridine into pseudouridine.	INTRO
62	66	tRNA	chemical	This hypermodified nucleotide, which is located at the P-site tRNA, is synthesized in three steps beginning with the snR35 H/ACA snoRNP guided conversion of uridine into pseudouridine.	INTRO
117	122	snR35	chemical	This hypermodified nucleotide, which is located at the P-site tRNA, is synthesized in three steps beginning with the snR35 H/ACA snoRNP guided conversion of uridine into pseudouridine.	INTRO
123	128	H/ACA	structure_element	This hypermodified nucleotide, which is located at the P-site tRNA, is synthesized in three steps beginning with the snR35 H/ACA snoRNP guided conversion of uridine into pseudouridine.	INTRO
129	135	snoRNP	complex_assembly	This hypermodified nucleotide, which is located at the P-site tRNA, is synthesized in three steps beginning with the snR35 H/ACA snoRNP guided conversion of uridine into pseudouridine.	INTRO
157	164	uridine	chemical	This hypermodified nucleotide, which is located at the P-site tRNA, is synthesized in three steps beginning with the snR35 H/ACA snoRNP guided conversion of uridine into pseudouridine.	INTRO
170	183	pseudouridine	chemical	This hypermodified nucleotide, which is located at the P-site tRNA, is synthesized in three steps beginning with the snR35 H/ACA snoRNP guided conversion of uridine into pseudouridine.	INTRO
32	61	SPOUT-class methyltransferase	protein_type	In a second step, the essential SPOUT-class methyltransferase Nep1/Emg1 modifies the pseudouridine to N1-methylpseudouridine.	INTRO
62	66	Nep1	protein	In a second step, the essential SPOUT-class methyltransferase Nep1/Emg1 modifies the pseudouridine to N1-methylpseudouridine.	INTRO
67	71	Emg1	protein	In a second step, the essential SPOUT-class methyltransferase Nep1/Emg1 modifies the pseudouridine to N1-methylpseudouridine.	INTRO
85	98	pseudouridine	chemical	In a second step, the essential SPOUT-class methyltransferase Nep1/Emg1 modifies the pseudouridine to N1-methylpseudouridine.	INTRO
102	124	N1-methylpseudouridine	chemical	In a second step, the essential SPOUT-class methyltransferase Nep1/Emg1 modifies the pseudouridine to N1-methylpseudouridine.	INTRO
0	11	Methylation	ptm	Methylation can only occur once pseudouridylation has taken place, as the latter reaction generates the substrate for the former.	INTRO
32	49	pseudouridylation	ptm	Methylation can only occur once pseudouridylation has taken place, as the latter reaction generates the substrate for the former.	INTRO
10	13	acp	chemical	The final acp modification leading to N1-methyl-N3-aminocarboxypropyl-pseudouridine occurs late during 40S biogenesis in the cytoplasm, while the two former reactions are taking place in the nucleolus and nucleus, and is independent from pseudouridylation or methylation.	INTRO
38	83	N1-methyl-N3-aminocarboxypropyl-pseudouridine	chemical	The final acp modification leading to N1-methyl-N3-aminocarboxypropyl-pseudouridine occurs late during 40S biogenesis in the cytoplasm, while the two former reactions are taking place in the nucleolus and nucleus, and is independent from pseudouridylation or methylation.	INTRO
103	106	40S	complex_assembly	The final acp modification leading to N1-methyl-N3-aminocarboxypropyl-pseudouridine occurs late during 40S biogenesis in the cytoplasm, while the two former reactions are taking place in the nucleolus and nucleus, and is independent from pseudouridylation or methylation.	INTRO
238	255	pseudouridylation	ptm	The final acp modification leading to N1-methyl-N3-aminocarboxypropyl-pseudouridine occurs late during 40S biogenesis in the cytoplasm, while the two former reactions are taking place in the nucleolus and nucleus, and is independent from pseudouridylation or methylation.	INTRO
51	71	S-adenosylmethionine	chemical	Both the methyl and the acp group are derived from S-adenosylmethionine (SAM), but the enzyme responsible for acp modification remained elusive for more than 40 years.	INTRO
73	76	SAM	chemical	Both the methyl and the acp group are derived from S-adenosylmethionine (SAM), but the enzyme responsible for acp modification remained elusive for more than 40 years.	INTRO
110	113	acp	chemical	Both the methyl and the acp group are derived from S-adenosylmethionine (SAM), but the enzyme responsible for acp modification remained elusive for more than 40 years.	INTRO
0	4	Tsr3	protein	Tsr3 is necessary for acp modification of 18S rRNA in yeast and human. (A) Hypermodified nucleotide m1acp3Ψ is synthesized in three steps: pseudouridylation catalyzed by snoRNP35, N1-methylation catalyzed by methyltransferase Nep1 and N3-acp modification catalyzed by Tsr3.	FIG
22	25	acp	chemical	Tsr3 is necessary for acp modification of 18S rRNA in yeast and human. (A) Hypermodified nucleotide m1acp3Ψ is synthesized in three steps: pseudouridylation catalyzed by snoRNP35, N1-methylation catalyzed by methyltransferase Nep1 and N3-acp modification catalyzed by Tsr3.	FIG
42	50	18S rRNA	chemical	Tsr3 is necessary for acp modification of 18S rRNA in yeast and human. (A) Hypermodified nucleotide m1acp3Ψ is synthesized in three steps: pseudouridylation catalyzed by snoRNP35, N1-methylation catalyzed by methyltransferase Nep1 and N3-acp modification catalyzed by Tsr3.	FIG
54	59	yeast	taxonomy_domain	Tsr3 is necessary for acp modification of 18S rRNA in yeast and human. (A) Hypermodified nucleotide m1acp3Ψ is synthesized in three steps: pseudouridylation catalyzed by snoRNP35, N1-methylation catalyzed by methyltransferase Nep1 and N3-acp modification catalyzed by Tsr3.	FIG
64	69	human	species	Tsr3 is necessary for acp modification of 18S rRNA in yeast and human. (A) Hypermodified nucleotide m1acp3Ψ is synthesized in three steps: pseudouridylation catalyzed by snoRNP35, N1-methylation catalyzed by methyltransferase Nep1 and N3-acp modification catalyzed by Tsr3.	FIG
75	88	Hypermodified	protein_state	Tsr3 is necessary for acp modification of 18S rRNA in yeast and human. (A) Hypermodified nucleotide m1acp3Ψ is synthesized in three steps: pseudouridylation catalyzed by snoRNP35, N1-methylation catalyzed by methyltransferase Nep1 and N3-acp modification catalyzed by Tsr3.	FIG
89	99	nucleotide	chemical	Tsr3 is necessary for acp modification of 18S rRNA in yeast and human. (A) Hypermodified nucleotide m1acp3Ψ is synthesized in three steps: pseudouridylation catalyzed by snoRNP35, N1-methylation catalyzed by methyltransferase Nep1 and N3-acp modification catalyzed by Tsr3.	FIG
100	107	m1acp3Ψ	chemical	Tsr3 is necessary for acp modification of 18S rRNA in yeast and human. (A) Hypermodified nucleotide m1acp3Ψ is synthesized in three steps: pseudouridylation catalyzed by snoRNP35, N1-methylation catalyzed by methyltransferase Nep1 and N3-acp modification catalyzed by Tsr3.	FIG
139	156	pseudouridylation	ptm	Tsr3 is necessary for acp modification of 18S rRNA in yeast and human. (A) Hypermodified nucleotide m1acp3Ψ is synthesized in three steps: pseudouridylation catalyzed by snoRNP35, N1-methylation catalyzed by methyltransferase Nep1 and N3-acp modification catalyzed by Tsr3.	FIG
170	178	snoRNP35	complex_assembly	Tsr3 is necessary for acp modification of 18S rRNA in yeast and human. (A) Hypermodified nucleotide m1acp3Ψ is synthesized in three steps: pseudouridylation catalyzed by snoRNP35, N1-methylation catalyzed by methyltransferase Nep1 and N3-acp modification catalyzed by Tsr3.	FIG
180	194	N1-methylation	ptm	Tsr3 is necessary for acp modification of 18S rRNA in yeast and human. (A) Hypermodified nucleotide m1acp3Ψ is synthesized in three steps: pseudouridylation catalyzed by snoRNP35, N1-methylation catalyzed by methyltransferase Nep1 and N3-acp modification catalyzed by Tsr3.	FIG
208	225	methyltransferase	protein_type	Tsr3 is necessary for acp modification of 18S rRNA in yeast and human. (A) Hypermodified nucleotide m1acp3Ψ is synthesized in three steps: pseudouridylation catalyzed by snoRNP35, N1-methylation catalyzed by methyltransferase Nep1 and N3-acp modification catalyzed by Tsr3.	FIG
226	230	Nep1	protein	Tsr3 is necessary for acp modification of 18S rRNA in yeast and human. (A) Hypermodified nucleotide m1acp3Ψ is synthesized in three steps: pseudouridylation catalyzed by snoRNP35, N1-methylation catalyzed by methyltransferase Nep1 and N3-acp modification catalyzed by Tsr3.	FIG
238	241	acp	chemical	Tsr3 is necessary for acp modification of 18S rRNA in yeast and human. (A) Hypermodified nucleotide m1acp3Ψ is synthesized in three steps: pseudouridylation catalyzed by snoRNP35, N1-methylation catalyzed by methyltransferase Nep1 and N3-acp modification catalyzed by Tsr3.	FIG
268	272	Tsr3	protein	Tsr3 is necessary for acp modification of 18S rRNA in yeast and human. (A) Hypermodified nucleotide m1acp3Ψ is synthesized in three steps: pseudouridylation catalyzed by snoRNP35, N1-methylation catalyzed by methyltransferase Nep1 and N3-acp modification catalyzed by Tsr3.	FIG
50	73	14C-incorporation assay	experimental_method	The asterisk indicates the C1-atom labeled in the 14C-incorporation assay.	FIG
4	11	RP-HPLC	experimental_method	(B) RP-HPLC elution profile of yeast 18S rRNA nucleosides.	FIG
12	27	elution profile	evidence	(B) RP-HPLC elution profile of yeast 18S rRNA nucleosides.	FIG
31	36	yeast	taxonomy_domain	(B) RP-HPLC elution profile of yeast 18S rRNA nucleosides.	FIG
37	45	18S rRNA	chemical	(B) RP-HPLC elution profile of yeast 18S rRNA nucleosides.	FIG
46	57	nucleosides	chemical	(B) RP-HPLC elution profile of yeast 18S rRNA nucleosides.	FIG
0	13	Hypermodified	protein_state	Hypermodified m1acp3Ψ elutes at 7.4 min (wild type, left profile) and is missing in Δtsr3 (middle profile) and Δnep1 Δnop6 mutants (right profile).	FIG
14	21	m1acp3Ψ	chemical	Hypermodified m1acp3Ψ elutes at 7.4 min (wild type, left profile) and is missing in Δtsr3 (middle profile) and Δnep1 Δnop6 mutants (right profile).	FIG
41	50	wild type	protein_state	Hypermodified m1acp3Ψ elutes at 7.4 min (wild type, left profile) and is missing in Δtsr3 (middle profile) and Δnep1 Δnop6 mutants (right profile).	FIG
84	89	Δtsr3	mutant	Hypermodified m1acp3Ψ elutes at 7.4 min (wild type, left profile) and is missing in Δtsr3 (middle profile) and Δnep1 Δnop6 mutants (right profile).	FIG
111	122	Δnep1 Δnop6	mutant	Hypermodified m1acp3Ψ elutes at 7.4 min (wild type, left profile) and is missing in Δtsr3 (middle profile) and Δnep1 Δnop6 mutants (right profile).	FIG
4	11	14C-acp	chemical	(C) 14C-acp labeling of 18S rRNAs.	FIG
24	33	18S rRNAs	chemical	(C) 14C-acp labeling of 18S rRNAs.	FIG
0	9	Wild type	protein_state	Wild type (WT) and plasmid encoded 18S rRNA (U1191U) show the 14C-acp signal, whereas the 14C-acp signal is missing in the U1191A mutant plasmid encoded 18S rRNA (U1191A) and Δtsr3 mutants (Δtsr3).	FIG
11	13	WT	protein_state	Wild type (WT) and plasmid encoded 18S rRNA (U1191U) show the 14C-acp signal, whereas the 14C-acp signal is missing in the U1191A mutant plasmid encoded 18S rRNA (U1191A) and Δtsr3 mutants (Δtsr3).	FIG
35	43	18S rRNA	chemical	Wild type (WT) and plasmid encoded 18S rRNA (U1191U) show the 14C-acp signal, whereas the 14C-acp signal is missing in the U1191A mutant plasmid encoded 18S rRNA (U1191A) and Δtsr3 mutants (Δtsr3).	FIG
45	51	U1191U	mutant	Wild type (WT) and plasmid encoded 18S rRNA (U1191U) show the 14C-acp signal, whereas the 14C-acp signal is missing in the U1191A mutant plasmid encoded 18S rRNA (U1191A) and Δtsr3 mutants (Δtsr3).	FIG
62	69	14C-acp	chemical	Wild type (WT) and plasmid encoded 18S rRNA (U1191U) show the 14C-acp signal, whereas the 14C-acp signal is missing in the U1191A mutant plasmid encoded 18S rRNA (U1191A) and Δtsr3 mutants (Δtsr3).	FIG
90	97	14C-acp	chemical	Wild type (WT) and plasmid encoded 18S rRNA (U1191U) show the 14C-acp signal, whereas the 14C-acp signal is missing in the U1191A mutant plasmid encoded 18S rRNA (U1191A) and Δtsr3 mutants (Δtsr3).	FIG
123	129	U1191A	mutant	Wild type (WT) and plasmid encoded 18S rRNA (U1191U) show the 14C-acp signal, whereas the 14C-acp signal is missing in the U1191A mutant plasmid encoded 18S rRNA (U1191A) and Δtsr3 mutants (Δtsr3).	FIG
130	136	mutant	protein_state	Wild type (WT) and plasmid encoded 18S rRNA (U1191U) show the 14C-acp signal, whereas the 14C-acp signal is missing in the U1191A mutant plasmid encoded 18S rRNA (U1191A) and Δtsr3 mutants (Δtsr3).	FIG
153	161	18S rRNA	chemical	Wild type (WT) and plasmid encoded 18S rRNA (U1191U) show the 14C-acp signal, whereas the 14C-acp signal is missing in the U1191A mutant plasmid encoded 18S rRNA (U1191A) and Δtsr3 mutants (Δtsr3).	FIG
163	169	U1191A	mutant	Wild type (WT) and plasmid encoded 18S rRNA (U1191U) show the 14C-acp signal, whereas the 14C-acp signal is missing in the U1191A mutant plasmid encoded 18S rRNA (U1191A) and Δtsr3 mutants (Δtsr3).	FIG
175	180	Δtsr3	mutant	Wild type (WT) and plasmid encoded 18S rRNA (U1191U) show the 14C-acp signal, whereas the 14C-acp signal is missing in the U1191A mutant plasmid encoded 18S rRNA (U1191A) and Δtsr3 mutants (Δtsr3).	FIG
190	195	Δtsr3	mutant	Wild type (WT) and plasmid encoded 18S rRNA (U1191U) show the 14C-acp signal, whereas the 14C-acp signal is missing in the U1191A mutant plasmid encoded 18S rRNA (U1191A) and Δtsr3 mutants (Δtsr3).	FIG
21	37	ethidium bromide	chemical	Upper lanes show the ethidium bromide staining of the 18S rRNAs for quantification.	FIG
54	63	18S rRNAs	chemical	Upper lanes show the ethidium bromide staining of the 18S rRNAs for quantification.	FIG
82	107	Primer extension analysis	experimental_method	All samples were loaded on the gel with two different amounts of 5 and 10 μl. (D) Primer extension analysis of acp modification in yeast 18S rRNA (right gel) including a sequencing ladder (left gel).	FIG
111	114	acp	chemical	All samples were loaded on the gel with two different amounts of 5 and 10 μl. (D) Primer extension analysis of acp modification in yeast 18S rRNA (right gel) including a sequencing ladder (left gel).	FIG
131	136	yeast	taxonomy_domain	All samples were loaded on the gel with two different amounts of 5 and 10 μl. (D) Primer extension analysis of acp modification in yeast 18S rRNA (right gel) including a sequencing ladder (left gel).	FIG
137	145	18S rRNA	chemical	All samples were loaded on the gel with two different amounts of 5 and 10 μl. (D) Primer extension analysis of acp modification in yeast 18S rRNA (right gel) including a sequencing ladder (left gel).	FIG
40	44	1191	residue_number	The primer extension stop at nucleotide 1191 is missing exclusively in Δtsr3 mutants and Δtsr3 Δsnr35 recombinants.	FIG
71	76	Δtsr3	mutant	The primer extension stop at nucleotide 1191 is missing exclusively in Δtsr3 mutants and Δtsr3 Δsnr35 recombinants.	FIG
89	101	Δtsr3 Δsnr35	mutant	The primer extension stop at nucleotide 1191 is missing exclusively in Δtsr3 mutants and Δtsr3 Δsnr35 recombinants.	FIG
4	29	Primer extension analysis	experimental_method	(E) Primer extension analysis of human 18S rRNA after siRNA knockdown of HsNEP1/EMG1 (541, 542 and 543) and HsTSR3 (544 and 545) (right gel), including a sequencing ladder (left gel).	FIG
33	38	human	species	(E) Primer extension analysis of human 18S rRNA after siRNA knockdown of HsNEP1/EMG1 (541, 542 and 543) and HsTSR3 (544 and 545) (right gel), including a sequencing ladder (left gel).	FIG
39	47	18S rRNA	chemical	(E) Primer extension analysis of human 18S rRNA after siRNA knockdown of HsNEP1/EMG1 (541, 542 and 543) and HsTSR3 (544 and 545) (right gel), including a sequencing ladder (left gel).	FIG
54	69	siRNA knockdown	experimental_method	(E) Primer extension analysis of human 18S rRNA after siRNA knockdown of HsNEP1/EMG1 (541, 542 and 543) and HsTSR3 (544 and 545) (right gel), including a sequencing ladder (left gel).	FIG
73	79	HsNEP1	protein	(E) Primer extension analysis of human 18S rRNA after siRNA knockdown of HsNEP1/EMG1 (541, 542 and 543) and HsTSR3 (544 and 545) (right gel), including a sequencing ladder (left gel).	FIG
80	84	EMG1	protein	(E) Primer extension analysis of human 18S rRNA after siRNA knockdown of HsNEP1/EMG1 (541, 542 and 543) and HsTSR3 (544 and 545) (right gel), including a sequencing ladder (left gel).	FIG
108	114	HsTSR3	protein	(E) Primer extension analysis of human 18S rRNA after siRNA knockdown of HsNEP1/EMG1 (541, 542 and 543) and HsTSR3 (544 and 545) (right gel), including a sequencing ladder (left gel).	FIG
72	78	siRNAs	chemical	The primer extension arrest is reduced in HTC116 cells transfected with siRNAs 544 and 545.	FIG
18	23	siRNA	chemical	The efficiency of siRNA mediated HsTSR3 repression correlates with the primer extension signals (see Supplementary Figure S2A).	FIG
33	39	HsTSR3	protein	The efficiency of siRNA mediated HsTSR3 repression correlates with the primer extension signals (see Supplementary Figure S2A).	FIG
71	95	primer extension signals	evidence	The efficiency of siRNA mediated HsTSR3 repression correlates with the primer extension signals (see Supplementary Figure S2A).	FIG
11	14	acp	chemical	Only a few acp transferring enzymes have been characterized until now.	INTRO
27	37	wybutosine	chemical	During the biosynthesis of wybutosine, a tricyclic nucleoside present in eukaryotic and archaeal phenylalanine tRNA, Tyw2 (Trm12 in yeast) transfers an acp group from SAM to an acidic carbon atom.	INTRO
51	61	nucleoside	chemical	During the biosynthesis of wybutosine, a tricyclic nucleoside present in eukaryotic and archaeal phenylalanine tRNA, Tyw2 (Trm12 in yeast) transfers an acp group from SAM to an acidic carbon atom.	INTRO
73	83	eukaryotic	taxonomy_domain	During the biosynthesis of wybutosine, a tricyclic nucleoside present in eukaryotic and archaeal phenylalanine tRNA, Tyw2 (Trm12 in yeast) transfers an acp group from SAM to an acidic carbon atom.	INTRO
88	96	archaeal	taxonomy_domain	During the biosynthesis of wybutosine, a tricyclic nucleoside present in eukaryotic and archaeal phenylalanine tRNA, Tyw2 (Trm12 in yeast) transfers an acp group from SAM to an acidic carbon atom.	INTRO
97	110	phenylalanine	chemical	During the biosynthesis of wybutosine, a tricyclic nucleoside present in eukaryotic and archaeal phenylalanine tRNA, Tyw2 (Trm12 in yeast) transfers an acp group from SAM to an acidic carbon atom.	INTRO
111	115	tRNA	chemical	During the biosynthesis of wybutosine, a tricyclic nucleoside present in eukaryotic and archaeal phenylalanine tRNA, Tyw2 (Trm12 in yeast) transfers an acp group from SAM to an acidic carbon atom.	INTRO
117	121	Tyw2	protein	During the biosynthesis of wybutosine, a tricyclic nucleoside present in eukaryotic and archaeal phenylalanine tRNA, Tyw2 (Trm12 in yeast) transfers an acp group from SAM to an acidic carbon atom.	INTRO
123	128	Trm12	protein	During the biosynthesis of wybutosine, a tricyclic nucleoside present in eukaryotic and archaeal phenylalanine tRNA, Tyw2 (Trm12 in yeast) transfers an acp group from SAM to an acidic carbon atom.	INTRO
132	137	yeast	taxonomy_domain	During the biosynthesis of wybutosine, a tricyclic nucleoside present in eukaryotic and archaeal phenylalanine tRNA, Tyw2 (Trm12 in yeast) transfers an acp group from SAM to an acidic carbon atom.	INTRO
152	155	acp	chemical	During the biosynthesis of wybutosine, a tricyclic nucleoside present in eukaryotic and archaeal phenylalanine tRNA, Tyw2 (Trm12 in yeast) transfers an acp group from SAM to an acidic carbon atom.	INTRO
167	170	SAM	chemical	During the biosynthesis of wybutosine, a tricyclic nucleoside present in eukaryotic and archaeal phenylalanine tRNA, Tyw2 (Trm12 in yeast) transfers an acp group from SAM to an acidic carbon atom.	INTRO
0	8	Archaeal	taxonomy_domain	Archaeal Tyw2 has a structure very similar to Rossmann-fold (class I) RNA-methyltransferases, but its distinctive SAM-binding mode enables the transfer of the acp group instead of the methyl group of the cofactor.	INTRO
9	13	Tyw2	protein	Archaeal Tyw2 has a structure very similar to Rossmann-fold (class I) RNA-methyltransferases, but its distinctive SAM-binding mode enables the transfer of the acp group instead of the methyl group of the cofactor.	INTRO
20	29	structure	evidence	Archaeal Tyw2 has a structure very similar to Rossmann-fold (class I) RNA-methyltransferases, but its distinctive SAM-binding mode enables the transfer of the acp group instead of the methyl group of the cofactor.	INTRO
46	92	Rossmann-fold (class I) RNA-methyltransferases	protein_type	Archaeal Tyw2 has a structure very similar to Rossmann-fold (class I) RNA-methyltransferases, but its distinctive SAM-binding mode enables the transfer of the acp group instead of the methyl group of the cofactor.	INTRO
114	130	SAM-binding mode	site	Archaeal Tyw2 has a structure very similar to Rossmann-fold (class I) RNA-methyltransferases, but its distinctive SAM-binding mode enables the transfer of the acp group instead of the methyl group of the cofactor.	INTRO
159	162	acp	chemical	Archaeal Tyw2 has a structure very similar to Rossmann-fold (class I) RNA-methyltransferases, but its distinctive SAM-binding mode enables the transfer of the acp group instead of the methyl group of the cofactor.	INTRO
8	11	acp	chemical	Another acp modification has been described in the diphtamide biosynthesis pathway, where an acp group is transferred from SAM to the carbon atom of a histidine residue of eukaryotic translation elongation factor 2 by use of a radical mechanism.	INTRO
51	61	diphtamide	chemical	Another acp modification has been described in the diphtamide biosynthesis pathway, where an acp group is transferred from SAM to the carbon atom of a histidine residue of eukaryotic translation elongation factor 2 by use of a radical mechanism.	INTRO
93	96	acp	chemical	Another acp modification has been described in the diphtamide biosynthesis pathway, where an acp group is transferred from SAM to the carbon atom of a histidine residue of eukaryotic translation elongation factor 2 by use of a radical mechanism.	INTRO
123	126	SAM	chemical	Another acp modification has been described in the diphtamide biosynthesis pathway, where an acp group is transferred from SAM to the carbon atom of a histidine residue of eukaryotic translation elongation factor 2 by use of a radical mechanism.	INTRO
151	160	histidine	residue_name	Another acp modification has been described in the diphtamide biosynthesis pathway, where an acp group is transferred from SAM to the carbon atom of a histidine residue of eukaryotic translation elongation factor 2 by use of a radical mechanism.	INTRO
172	182	eukaryotic	taxonomy_domain	Another acp modification has been described in the diphtamide biosynthesis pathway, where an acp group is transferred from SAM to the carbon atom of a histidine residue of eukaryotic translation elongation factor 2 by use of a radical mechanism.	INTRO
183	214	translation elongation factor 2	protein_type	Another acp modification has been described in the diphtamide biosynthesis pathway, where an acp group is transferred from SAM to the carbon atom of a histidine residue of eukaryotic translation elongation factor 2 by use of a radical mechanism.	INTRO
53	58	yeast	taxonomy_domain	In a recent bioinformatic study, the uncharacterized yeast gene YOR006c was predicted to be involved in ribosome biogenesis.	INTRO
64	71	YOR006c	gene	In a recent bioinformatic study, the uncharacterized yeast gene YOR006c was predicted to be involved in ribosome biogenesis.	INTRO
6	22	highly conserved	protein_state	It is highly conserved among eukaryotes and archaea (Supplementary Figure S1A) and its deletion leads to an accumulation of the 20S pre-rRNA precursor of 18S rRNA, suggesting an influence on D-site cleavage during the maturation of the small ribosomal subunit.	INTRO
29	39	eukaryotes	taxonomy_domain	It is highly conserved among eukaryotes and archaea (Supplementary Figure S1A) and its deletion leads to an accumulation of the 20S pre-rRNA precursor of 18S rRNA, suggesting an influence on D-site cleavage during the maturation of the small ribosomal subunit.	INTRO
44	51	archaea	taxonomy_domain	It is highly conserved among eukaryotes and archaea (Supplementary Figure S1A) and its deletion leads to an accumulation of the 20S pre-rRNA precursor of 18S rRNA, suggesting an influence on D-site cleavage during the maturation of the small ribosomal subunit.	INTRO
128	140	20S pre-rRNA	chemical	It is highly conserved among eukaryotes and archaea (Supplementary Figure S1A) and its deletion leads to an accumulation of the 20S pre-rRNA precursor of 18S rRNA, suggesting an influence on D-site cleavage during the maturation of the small ribosomal subunit.	INTRO
154	162	18S rRNA	chemical	It is highly conserved among eukaryotes and archaea (Supplementary Figure S1A) and its deletion leads to an accumulation of the 20S pre-rRNA precursor of 18S rRNA, suggesting an influence on D-site cleavage during the maturation of the small ribosomal subunit.	INTRO
191	197	D-site	site	It is highly conserved among eukaryotes and archaea (Supplementary Figure S1A) and its deletion leads to an accumulation of the 20S pre-rRNA precursor of 18S rRNA, suggesting an influence on D-site cleavage during the maturation of the small ribosomal subunit.	INTRO
15	22	YOR006C	gene	On this basis, YOR006C was renamed ‘Twenty S rRNA accumulation 3′ (TSR3).	INTRO
36	64	Twenty S rRNA accumulation 3	protein	On this basis, YOR006C was renamed ‘Twenty S rRNA accumulation 3′ (TSR3).	INTRO
67	71	TSR3	protein	On this basis, YOR006C was renamed ‘Twenty S rRNA accumulation 3′ (TSR3).	INTRO
93	101	18S rRNA	chemical	However, its function remained unclear although recently a putative nuclease function during 18S rRNA maturation was predicted.	INTRO
18	22	Tsr3	protein	Here, we identify Tsr3 as the long-sought acp transferase that catalyzes the last step in the biosynthesis of the hypermodified nucleotide m1acp3Ψ in yeast and human cells.	INTRO
42	57	acp transferase	protein_type	Here, we identify Tsr3 as the long-sought acp transferase that catalyzes the last step in the biosynthesis of the hypermodified nucleotide m1acp3Ψ in yeast and human cells.	INTRO
114	127	hypermodified	protein_state	Here, we identify Tsr3 as the long-sought acp transferase that catalyzes the last step in the biosynthesis of the hypermodified nucleotide m1acp3Ψ in yeast and human cells.	INTRO
128	138	nucleotide	chemical	Here, we identify Tsr3 as the long-sought acp transferase that catalyzes the last step in the biosynthesis of the hypermodified nucleotide m1acp3Ψ in yeast and human cells.	INTRO
139	146	m1acp3Ψ	chemical	Here, we identify Tsr3 as the long-sought acp transferase that catalyzes the last step in the biosynthesis of the hypermodified nucleotide m1acp3Ψ in yeast and human cells.	INTRO
150	155	yeast	taxonomy_domain	Here, we identify Tsr3 as the long-sought acp transferase that catalyzes the last step in the biosynthesis of the hypermodified nucleotide m1acp3Ψ in yeast and human cells.	INTRO
160	165	human	species	Here, we identify Tsr3 as the long-sought acp transferase that catalyzes the last step in the biosynthesis of the hypermodified nucleotide m1acp3Ψ in yeast and human cells.	INTRO
18	41	catalytically defective	protein_state	Furthermore using catalytically defective mutants of yeast Tsr3 we demonstrated that the acp modification is required for 18S rRNA maturation.	INTRO
53	58	yeast	taxonomy_domain	Furthermore using catalytically defective mutants of yeast Tsr3 we demonstrated that the acp modification is required for 18S rRNA maturation.	INTRO
59	63	Tsr3	protein	Furthermore using catalytically defective mutants of yeast Tsr3 we demonstrated that the acp modification is required for 18S rRNA maturation.	INTRO
89	92	acp	chemical	Furthermore using catalytically defective mutants of yeast Tsr3 we demonstrated that the acp modification is required for 18S rRNA maturation.	INTRO
122	130	18S rRNA	chemical	Furthermore using catalytically defective mutants of yeast Tsr3 we demonstrated that the acp modification is required for 18S rRNA maturation.	INTRO
18	36	crystal structures	evidence	Surprisingly, the crystal structures of archaeal homologs revealed that Tsr3 is structurally similar to the SPOUT-class RNA methyltransferases.	INTRO
40	48	archaeal	taxonomy_domain	Surprisingly, the crystal structures of archaeal homologs revealed that Tsr3 is structurally similar to the SPOUT-class RNA methyltransferases.	INTRO
72	76	Tsr3	protein	Surprisingly, the crystal structures of archaeal homologs revealed that Tsr3 is structurally similar to the SPOUT-class RNA methyltransferases.	INTRO
108	142	SPOUT-class RNA methyltransferases	protein_type	Surprisingly, the crystal structures of archaeal homologs revealed that Tsr3 is structurally similar to the SPOUT-class RNA methyltransferases.	INTRO
55	70	acp transferase	protein_type	In contrast, the only other structurally characterized acp transferase enzyme Tyw2 belongs to the Rossmann-fold class of methyltransferase proteins.	INTRO
78	82	Tyw2	protein	In contrast, the only other structurally characterized acp transferase enzyme Tyw2 belongs to the Rossmann-fold class of methyltransferase proteins.	INTRO
98	147	Rossmann-fold class of methyltransferase proteins	protein_type	In contrast, the only other structurally characterized acp transferase enzyme Tyw2 belongs to the Rossmann-fold class of methyltransferase proteins.	INTRO
97	100	SAM	chemical	Interestingly, the two structurally very different enzymes use similar strategies in binding the SAM-cofactor in order to ensure that in contrast to methyltransferases the acp and not the methyl group of SAM is transferred to the substrate.	INTRO
149	167	methyltransferases	protein_type	Interestingly, the two structurally very different enzymes use similar strategies in binding the SAM-cofactor in order to ensure that in contrast to methyltransferases the acp and not the methyl group of SAM is transferred to the substrate.	INTRO
172	175	acp	chemical	Interestingly, the two structurally very different enzymes use similar strategies in binding the SAM-cofactor in order to ensure that in contrast to methyltransferases the acp and not the methyl group of SAM is transferred to the substrate.	INTRO
204	207	SAM	chemical	Interestingly, the two structurally very different enzymes use similar strategies in binding the SAM-cofactor in order to ensure that in contrast to methyltransferases the acp and not the methyl group of SAM is transferred to the substrate.	INTRO
0	4	Tsr3	protein	Tsr3 is the enzyme responsible for 18S rRNA acp modification in yeast and humans	RESULTS
35	43	18S rRNA	chemical	Tsr3 is the enzyme responsible for 18S rRNA acp modification in yeast and humans	RESULTS
44	47	acp	chemical	Tsr3 is the enzyme responsible for 18S rRNA acp modification in yeast and humans	RESULTS
64	69	yeast	taxonomy_domain	Tsr3 is the enzyme responsible for 18S rRNA acp modification in yeast and humans	RESULTS
74	80	humans	species	Tsr3 is the enzyme responsible for 18S rRNA acp modification in yeast and humans	RESULTS
4	17	S. cerevisiae	species	The S. cerevisiae 18S rRNA acp transferase was identified in a systematic genetic screen where numerous deletion mutants from the EUROSCARF strain collection (www.euroscarf.de) were analyzed by HPLC for alterations in 18S rRNA base modifications.	RESULTS
18	42	18S rRNA acp transferase	protein_type	The S. cerevisiae 18S rRNA acp transferase was identified in a systematic genetic screen where numerous deletion mutants from the EUROSCARF strain collection (www.euroscarf.de) were analyzed by HPLC for alterations in 18S rRNA base modifications.	RESULTS
194	198	HPLC	experimental_method	The S. cerevisiae 18S rRNA acp transferase was identified in a systematic genetic screen where numerous deletion mutants from the EUROSCARF strain collection (www.euroscarf.de) were analyzed by HPLC for alterations in 18S rRNA base modifications.	RESULTS
218	226	18S rRNA	chemical	The S. cerevisiae 18S rRNA acp transferase was identified in a systematic genetic screen where numerous deletion mutants from the EUROSCARF strain collection (www.euroscarf.de) were analyzed by HPLC for alterations in 18S rRNA base modifications.	RESULTS
8	13	Δtsr3	mutant	For the Δtsr3 deletion strain the HPLC elution profile of 18S rRNA nucleosides (Figure 1B) was very similar to that of the pseudouridine-N1 methyltransferase mutant Δnep1, where a shoulder at ∼ 7.4 min elution time was missing in the elution profile.	RESULTS
34	54	HPLC elution profile	evidence	For the Δtsr3 deletion strain the HPLC elution profile of 18S rRNA nucleosides (Figure 1B) was very similar to that of the pseudouridine-N1 methyltransferase mutant Δnep1, where a shoulder at ∼ 7.4 min elution time was missing in the elution profile.	RESULTS
58	66	18S rRNA	chemical	For the Δtsr3 deletion strain the HPLC elution profile of 18S rRNA nucleosides (Figure 1B) was very similar to that of the pseudouridine-N1 methyltransferase mutant Δnep1, where a shoulder at ∼ 7.4 min elution time was missing in the elution profile.	RESULTS
67	78	nucleosides	chemical	For the Δtsr3 deletion strain the HPLC elution profile of 18S rRNA nucleosides (Figure 1B) was very similar to that of the pseudouridine-N1 methyltransferase mutant Δnep1, where a shoulder at ∼ 7.4 min elution time was missing in the elution profile.	RESULTS
123	157	pseudouridine-N1 methyltransferase	protein_type	For the Δtsr3 deletion strain the HPLC elution profile of 18S rRNA nucleosides (Figure 1B) was very similar to that of the pseudouridine-N1 methyltransferase mutant Δnep1, where a shoulder at ∼ 7.4 min elution time was missing in the elution profile.	RESULTS
158	164	mutant	protein_state	For the Δtsr3 deletion strain the HPLC elution profile of 18S rRNA nucleosides (Figure 1B) was very similar to that of the pseudouridine-N1 methyltransferase mutant Δnep1, where a shoulder at ∼ 7.4 min elution time was missing in the elution profile.	RESULTS
165	170	Δnep1	mutant	For the Δtsr3 deletion strain the HPLC elution profile of 18S rRNA nucleosides (Figure 1B) was very similar to that of the pseudouridine-N1 methyltransferase mutant Δnep1, where a shoulder at ∼ 7.4 min elution time was missing in the elution profile.	RESULTS
55	61	ESI-MS	experimental_method	As previously reported this shoulder was identified by ESI-MS as corresponding to m1acp3Ψ.	RESULTS
82	89	m1acp3Ψ	chemical	As previously reported this shoulder was identified by ESI-MS as corresponding to m1acp3Ψ.	RESULTS
49	52	acp	chemical	In order to directly analyze the presence of the acp modification of nucleotide 1191 we used an in vivo14C incorporation assay with 1-14C-methionine.	RESULTS
69	79	nucleotide	chemical	In order to directly analyze the presence of the acp modification of nucleotide 1191 we used an in vivo14C incorporation assay with 1-14C-methionine.	RESULTS
80	84	1191	residue_number	In order to directly analyze the presence of the acp modification of nucleotide 1191 we used an in vivo14C incorporation assay with 1-14C-methionine.	RESULTS
96	126	in vivo14C incorporation assay	experimental_method	In order to directly analyze the presence of the acp modification of nucleotide 1191 we used an in vivo14C incorporation assay with 1-14C-methionine.	RESULTS
132	148	1-14C-methionine	chemical	In order to directly analyze the presence of the acp modification of nucleotide 1191 we used an in vivo14C incorporation assay with 1-14C-methionine.	RESULTS
12	15	acp	chemical	Whereas the acp labeling of 18S rRNA was clearly present in the wild type strain no radioactive labeling could be observed in a Δtsr3 strain (Figure 1C).	RESULTS
28	36	18S rRNA	chemical	Whereas the acp labeling of 18S rRNA was clearly present in the wild type strain no radioactive labeling could be observed in a Δtsr3 strain (Figure 1C).	RESULTS
64	73	wild type	protein_state	Whereas the acp labeling of 18S rRNA was clearly present in the wild type strain no radioactive labeling could be observed in a Δtsr3 strain (Figure 1C).	RESULTS
128	133	Δtsr3	mutant	Whereas the acp labeling of 18S rRNA was clearly present in the wild type strain no radioactive labeling could be observed in a Δtsr3 strain (Figure 1C).	RESULTS
44	54	18S U1191A	mutant	No radioactive labeling was detected in the 18S U1191A mutant which served as a control for the specificity of the 14C-aminocarboxypropyl incorporation.	RESULTS
55	61	mutant	protein_state	No radioactive labeling was detected in the 18S U1191A mutant which served as a control for the specificity of the 14C-aminocarboxypropyl incorporation.	RESULTS
115	137	14C-aminocarboxypropyl	chemical	No radioactive labeling was detected in the 18S U1191A mutant which served as a control for the specificity of the 14C-aminocarboxypropyl incorporation.	RESULTS
30	33	acp	chemical	As previously shown, only the acp but none of the other modifications at U1191 of yeast 18S rRNA blocks reverse transcriptase activity.	RESULTS
73	78	U1191	residue_name_number	As previously shown, only the acp but none of the other modifications at U1191 of yeast 18S rRNA blocks reverse transcriptase activity.	RESULTS
82	87	yeast	taxonomy_domain	As previously shown, only the acp but none of the other modifications at U1191 of yeast 18S rRNA blocks reverse transcriptase activity.	RESULTS
88	96	18S rRNA	chemical	As previously shown, only the acp but none of the other modifications at U1191 of yeast 18S rRNA blocks reverse transcriptase activity.	RESULTS
30	33	acp	chemical	Therefore the presence of the acp modification can be directly assessed by primer extension.	RESULTS
75	91	primer extension	experimental_method	Therefore the presence of the acp modification can be directly assessed by primer extension.	RESULTS
11	20	wild-type	protein_state	Indeed, in wild-type yeast a strong primer extension stop signal occurred at position 1192.	RESULTS
21	26	yeast	taxonomy_domain	Indeed, in wild-type yeast a strong primer extension stop signal occurred at position 1192.	RESULTS
36	64	primer extension stop signal	evidence	Indeed, in wild-type yeast a strong primer extension stop signal occurred at position 1192.	RESULTS
86	90	1192	residue_number	Indeed, in wild-type yeast a strong primer extension stop signal occurred at position 1192.	RESULTS
18	23	Δtsr3	mutant	In contrast, in a Δtsr3 mutant no primer extension stop signal was present at this position.	RESULTS
24	30	mutant	protein_state	In contrast, in a Δtsr3 mutant no primer extension stop signal was present at this position.	RESULTS
18	24	Δsnr35	mutant	As expected, in a Δsnr35 deletion preventing pseudouridylation and N1-methylation (resulting in acp3U) as well as in a Δnep1 deletion strain where pseudouridine is not methylated (resulting in acp3Ψ) a primer extension stop signal of similar intensity as in the wild type was observed.	RESULTS
25	33	deletion	experimental_method	As expected, in a Δsnr35 deletion preventing pseudouridylation and N1-methylation (resulting in acp3U) as well as in a Δnep1 deletion strain where pseudouridine is not methylated (resulting in acp3Ψ) a primer extension stop signal of similar intensity as in the wild type was observed.	RESULTS
45	62	pseudouridylation	ptm	As expected, in a Δsnr35 deletion preventing pseudouridylation and N1-methylation (resulting in acp3U) as well as in a Δnep1 deletion strain where pseudouridine is not methylated (resulting in acp3Ψ) a primer extension stop signal of similar intensity as in the wild type was observed.	RESULTS
67	81	N1-methylation	ptm	As expected, in a Δsnr35 deletion preventing pseudouridylation and N1-methylation (resulting in acp3U) as well as in a Δnep1 deletion strain where pseudouridine is not methylated (resulting in acp3Ψ) a primer extension stop signal of similar intensity as in the wild type was observed.	RESULTS
96	101	acp3U	chemical	As expected, in a Δsnr35 deletion preventing pseudouridylation and N1-methylation (resulting in acp3U) as well as in a Δnep1 deletion strain where pseudouridine is not methylated (resulting in acp3Ψ) a primer extension stop signal of similar intensity as in the wild type was observed.	RESULTS
119	124	Δnep1	mutant	As expected, in a Δsnr35 deletion preventing pseudouridylation and N1-methylation (resulting in acp3U) as well as in a Δnep1 deletion strain where pseudouridine is not methylated (resulting in acp3Ψ) a primer extension stop signal of similar intensity as in the wild type was observed.	RESULTS
147	160	pseudouridine	chemical	As expected, in a Δsnr35 deletion preventing pseudouridylation and N1-methylation (resulting in acp3U) as well as in a Δnep1 deletion strain where pseudouridine is not methylated (resulting in acp3Ψ) a primer extension stop signal of similar intensity as in the wild type was observed.	RESULTS
164	178	not methylated	protein_state	As expected, in a Δsnr35 deletion preventing pseudouridylation and N1-methylation (resulting in acp3U) as well as in a Δnep1 deletion strain where pseudouridine is not methylated (resulting in acp3Ψ) a primer extension stop signal of similar intensity as in the wild type was observed.	RESULTS
193	198	acp3Ψ	chemical	As expected, in a Δsnr35 deletion preventing pseudouridylation and N1-methylation (resulting in acp3U) as well as in a Δnep1 deletion strain where pseudouridine is not methylated (resulting in acp3Ψ) a primer extension stop signal of similar intensity as in the wild type was observed.	RESULTS
202	230	primer extension stop signal	evidence	As expected, in a Δsnr35 deletion preventing pseudouridylation and N1-methylation (resulting in acp3U) as well as in a Δnep1 deletion strain where pseudouridine is not methylated (resulting in acp3Ψ) a primer extension stop signal of similar intensity as in the wild type was observed.	RESULTS
262	271	wild type	protein_state	As expected, in a Δsnr35 deletion preventing pseudouridylation and N1-methylation (resulting in acp3U) as well as in a Δnep1 deletion strain where pseudouridine is not methylated (resulting in acp3Ψ) a primer extension stop signal of similar intensity as in the wild type was observed.	RESULTS
5	17	Δtsr3 Δsnr35	mutant	In a Δtsr3 Δsnr35 double deletion strain the 18S rRNA contains an unmodified U and the primer extension stop signal was missing (Figure 1D).	RESULTS
45	53	18S rRNA	chemical	In a Δtsr3 Δsnr35 double deletion strain the 18S rRNA contains an unmodified U and the primer extension stop signal was missing (Figure 1D).	RESULTS
66	76	unmodified	protein_state	In a Δtsr3 Δsnr35 double deletion strain the 18S rRNA contains an unmodified U and the primer extension stop signal was missing (Figure 1D).	RESULTS
77	78	U	chemical	In a Δtsr3 Δsnr35 double deletion strain the 18S rRNA contains an unmodified U and the primer extension stop signal was missing (Figure 1D).	RESULTS
4	8	Tsr3	protein	The Tsr3 protein is highly conserved in yeast and humans (50% identity).	RESULTS
20	36	highly conserved	protein_state	The Tsr3 protein is highly conserved in yeast and humans (50% identity).	RESULTS
40	45	yeast	taxonomy_domain	The Tsr3 protein is highly conserved in yeast and humans (50% identity).	RESULTS
50	56	humans	species	The Tsr3 protein is highly conserved in yeast and humans (50% identity).	RESULTS
0	5	Human	species	Human 18S rRNA has also been shown to contain m1acp3Ψ in the 18S rRNA at position 1248.	RESULTS
6	14	18S rRNA	chemical	Human 18S rRNA has also been shown to contain m1acp3Ψ in the 18S rRNA at position 1248.	RESULTS
46	53	m1acp3Ψ	ptm	Human 18S rRNA has also been shown to contain m1acp3Ψ in the 18S rRNA at position 1248.	RESULTS
61	69	18S rRNA	chemical	Human 18S rRNA has also been shown to contain m1acp3Ψ in the 18S rRNA at position 1248.	RESULTS
82	86	1248	residue_number	Human 18S rRNA has also been shown to contain m1acp3Ψ in the 18S rRNA at position 1248.	RESULTS
6	30	siRNA-mediated depletion	experimental_method	After siRNA-mediated depletion of Tsr3 in human colon carcinoma HCT116(+/+) cells the acp primer extension arrest was reduced in comparison to cells transfected with a non-targeting scramble siRNA control (Figure 1E, compare lanes 544 and scramble).	RESULTS
34	38	Tsr3	protein	After siRNA-mediated depletion of Tsr3 in human colon carcinoma HCT116(+/+) cells the acp primer extension arrest was reduced in comparison to cells transfected with a non-targeting scramble siRNA control (Figure 1E, compare lanes 544 and scramble).	RESULTS
42	47	human	species	After siRNA-mediated depletion of Tsr3 in human colon carcinoma HCT116(+/+) cells the acp primer extension arrest was reduced in comparison to cells transfected with a non-targeting scramble siRNA control (Figure 1E, compare lanes 544 and scramble).	RESULTS
86	113	acp primer extension arrest	evidence	After siRNA-mediated depletion of Tsr3 in human colon carcinoma HCT116(+/+) cells the acp primer extension arrest was reduced in comparison to cells transfected with a non-targeting scramble siRNA control (Figure 1E, compare lanes 544 and scramble).	RESULTS
191	196	siRNA	chemical	After siRNA-mediated depletion of Tsr3 in human colon carcinoma HCT116(+/+) cells the acp primer extension arrest was reduced in comparison to cells transfected with a non-targeting scramble siRNA control (Figure 1E, compare lanes 544 and scramble).	RESULTS
18	23	siRNA	chemical	The efficiency of siRNA-mediated depletion was established by RT-qPCR and found to be very high with siRNA 544 (Supplementary Figure S2A, remaining TSR3 mRNA level of 2%).	RESULTS
62	69	RT-qPCR	experimental_method	The efficiency of siRNA-mediated depletion was established by RT-qPCR and found to be very high with siRNA 544 (Supplementary Figure S2A, remaining TSR3 mRNA level of 2%).	RESULTS
101	106	siRNA	chemical	The efficiency of siRNA-mediated depletion was established by RT-qPCR and found to be very high with siRNA 544 (Supplementary Figure S2A, remaining TSR3 mRNA level of 2%).	RESULTS
148	152	TSR3	protein	The efficiency of siRNA-mediated depletion was established by RT-qPCR and found to be very high with siRNA 544 (Supplementary Figure S2A, remaining TSR3 mRNA level of 2%).	RESULTS
35	40	siRNA	chemical	By comparison, treating cells with siRNA 545, which only reduced the TSR3 mRNA to 20%, did not markedly reduced the acp signal.	RESULTS
69	73	TSR3	protein	By comparison, treating cells with siRNA 545, which only reduced the TSR3 mRNA to 20%, did not markedly reduced the acp signal.	RESULTS
116	119	acp	chemical	By comparison, treating cells with siRNA 545, which only reduced the TSR3 mRNA to 20%, did not markedly reduced the acp signal.	RESULTS
42	48	HsTsr3	protein	This suggests that low residual levels of HsTsr3 are sufficient to modify the RNA.	RESULTS
78	81	RNA	chemical	This suggests that low residual levels of HsTsr3 are sufficient to modify the RNA.	RESULTS
6	12	HsTsr3	protein	Thus, HsTsr3 is also responsible for the acp modification of 18S rRNA nucleotide Ψ1248 in helix 31.	RESULTS
41	44	acp	chemical	Thus, HsTsr3 is also responsible for the acp modification of 18S rRNA nucleotide Ψ1248 in helix 31.	RESULTS
61	69	18S rRNA	chemical	Thus, HsTsr3 is also responsible for the acp modification of 18S rRNA nucleotide Ψ1248 in helix 31.	RESULTS
70	80	nucleotide	chemical	Thus, HsTsr3 is also responsible for the acp modification of 18S rRNA nucleotide Ψ1248 in helix 31.	RESULTS
81	86	Ψ1248	ptm	Thus, HsTsr3 is also responsible for the acp modification of 18S rRNA nucleotide Ψ1248 in helix 31.	RESULTS
90	98	helix 31	structure_element	Thus, HsTsr3 is also responsible for the acp modification of 18S rRNA nucleotide Ψ1248 in helix 31.	RESULTS
11	16	yeast	taxonomy_domain	Similar to yeast, siRNA-mediated depletion of the Ψ1248 N1-methyltransferase Nep1/Emg1 had no influence on the primer extension arrest (Figure 1E).	RESULTS
18	42	siRNA-mediated depletion	experimental_method	Similar to yeast, siRNA-mediated depletion of the Ψ1248 N1-methyltransferase Nep1/Emg1 had no influence on the primer extension arrest (Figure 1E).	RESULTS
50	76	Ψ1248 N1-methyltransferase	protein_type	Similar to yeast, siRNA-mediated depletion of the Ψ1248 N1-methyltransferase Nep1/Emg1 had no influence on the primer extension arrest (Figure 1E).	RESULTS
77	81	Nep1	protein	Similar to yeast, siRNA-mediated depletion of the Ψ1248 N1-methyltransferase Nep1/Emg1 had no influence on the primer extension arrest (Figure 1E).	RESULTS
82	86	Emg1	protein	Similar to yeast, siRNA-mediated depletion of the Ψ1248 N1-methyltransferase Nep1/Emg1 had no influence on the primer extension arrest (Figure 1E).	RESULTS
111	134	primer extension arrest	evidence	Similar to yeast, siRNA-mediated depletion of the Ψ1248 N1-methyltransferase Nep1/Emg1 had no influence on the primer extension arrest (Figure 1E).	RESULTS
31	36	Δtsr3	mutant	Phenotypic characterization of Δtsr3 mutants	RESULTS
13	16	acp	chemical	Although the acp modification of 18S rRNA is highly conserved in eukaryotes, yeast Δtsr3 mutants showed only a minor growth defect.	RESULTS
33	41	18S rRNA	chemical	Although the acp modification of 18S rRNA is highly conserved in eukaryotes, yeast Δtsr3 mutants showed only a minor growth defect.	RESULTS
45	61	highly conserved	protein_state	Although the acp modification of 18S rRNA is highly conserved in eukaryotes, yeast Δtsr3 mutants showed only a minor growth defect.	RESULTS
65	75	eukaryotes	taxonomy_domain	Although the acp modification of 18S rRNA is highly conserved in eukaryotes, yeast Δtsr3 mutants showed only a minor growth defect.	RESULTS
77	82	yeast	taxonomy_domain	Although the acp modification of 18S rRNA is highly conserved in eukaryotes, yeast Δtsr3 mutants showed only a minor growth defect.	RESULTS
83	88	Δtsr3	mutant	Although the acp modification of 18S rRNA is highly conserved in eukaryotes, yeast Δtsr3 mutants showed only a minor growth defect.	RESULTS
13	18	Δtsr3	mutant	However, the Δtsr3 deletion was synthetic sick with a Δsnr35 deletion preventing pseudouridylation and Nep1-catalyzed methylation of nucleotide 1191 (Figure 2A).	RESULTS
54	60	Δsnr35	mutant	However, the Δtsr3 deletion was synthetic sick with a Δsnr35 deletion preventing pseudouridylation and Nep1-catalyzed methylation of nucleotide 1191 (Figure 2A).	RESULTS
81	98	pseudouridylation	ptm	However, the Δtsr3 deletion was synthetic sick with a Δsnr35 deletion preventing pseudouridylation and Nep1-catalyzed methylation of nucleotide 1191 (Figure 2A).	RESULTS
103	107	Nep1	protein	However, the Δtsr3 deletion was synthetic sick with a Δsnr35 deletion preventing pseudouridylation and Nep1-catalyzed methylation of nucleotide 1191 (Figure 2A).	RESULTS
144	148	1191	residue_number	However, the Δtsr3 deletion was synthetic sick with a Δsnr35 deletion preventing pseudouridylation and Nep1-catalyzed methylation of nucleotide 1191 (Figure 2A).	RESULTS
64	75	Δtsr3 Δnep1	mutant	Interestingly, no increased growth defect could be observed for Δtsr3 Δnep1 recombinants containing the nep1 suppressor mutation Δnop6 as well as for Δtsr3 Δsnr35 Δnep1 recombinants with unmodified U1191 (Supplementary Figure S2D and E).	RESULTS
104	108	nep1	gene	Interestingly, no increased growth defect could be observed for Δtsr3 Δnep1 recombinants containing the nep1 suppressor mutation Δnop6 as well as for Δtsr3 Δsnr35 Δnep1 recombinants with unmodified U1191 (Supplementary Figure S2D and E).	RESULTS
129	134	Δnop6	mutant	Interestingly, no increased growth defect could be observed for Δtsr3 Δnep1 recombinants containing the nep1 suppressor mutation Δnop6 as well as for Δtsr3 Δsnr35 Δnep1 recombinants with unmodified U1191 (Supplementary Figure S2D and E).	RESULTS
150	168	Δtsr3 Δsnr35 Δnep1	mutant	Interestingly, no increased growth defect could be observed for Δtsr3 Δnep1 recombinants containing the nep1 suppressor mutation Δnop6 as well as for Δtsr3 Δsnr35 Δnep1 recombinants with unmodified U1191 (Supplementary Figure S2D and E).	RESULTS
187	197	unmodified	protein_state	Interestingly, no increased growth defect could be observed for Δtsr3 Δnep1 recombinants containing the nep1 suppressor mutation Δnop6 as well as for Δtsr3 Δsnr35 Δnep1 recombinants with unmodified U1191 (Supplementary Figure S2D and E).	RESULTS
198	203	U1191	residue_name_number	Interestingly, no increased growth defect could be observed for Δtsr3 Δnep1 recombinants containing the nep1 suppressor mutation Δnop6 as well as for Δtsr3 Δsnr35 Δnep1 recombinants with unmodified U1191 (Supplementary Figure S2D and E).	RESULTS
31	36	yeast	taxonomy_domain	Phenotypic characterization of yeast TSR3 deletion (Δtrs3) and human TSR3 depletion (siRNAs 544 and 545) and cellular localization of yeast Tsr3. (A) Growth of yeast wild type, Δtsr3, Δsnr35 and Δtsr3 Δsnr35 segregants after meiosis and tetrad dissection of Δtsr3/TSR3 Δsnr35/SNR35 heterozygous diploids.	FIG
37	41	TSR3	protein	Phenotypic characterization of yeast TSR3 deletion (Δtrs3) and human TSR3 depletion (siRNAs 544 and 545) and cellular localization of yeast Tsr3. (A) Growth of yeast wild type, Δtsr3, Δsnr35 and Δtsr3 Δsnr35 segregants after meiosis and tetrad dissection of Δtsr3/TSR3 Δsnr35/SNR35 heterozygous diploids.	FIG
52	57	Δtrs3	mutant	Phenotypic characterization of yeast TSR3 deletion (Δtrs3) and human TSR3 depletion (siRNAs 544 and 545) and cellular localization of yeast Tsr3. (A) Growth of yeast wild type, Δtsr3, Δsnr35 and Δtsr3 Δsnr35 segregants after meiosis and tetrad dissection of Δtsr3/TSR3 Δsnr35/SNR35 heterozygous diploids.	FIG
63	68	human	species	Phenotypic characterization of yeast TSR3 deletion (Δtrs3) and human TSR3 depletion (siRNAs 544 and 545) and cellular localization of yeast Tsr3. (A) Growth of yeast wild type, Δtsr3, Δsnr35 and Δtsr3 Δsnr35 segregants after meiosis and tetrad dissection of Δtsr3/TSR3 Δsnr35/SNR35 heterozygous diploids.	FIG
69	73	TSR3	protein	Phenotypic characterization of yeast TSR3 deletion (Δtrs3) and human TSR3 depletion (siRNAs 544 and 545) and cellular localization of yeast Tsr3. (A) Growth of yeast wild type, Δtsr3, Δsnr35 and Δtsr3 Δsnr35 segregants after meiosis and tetrad dissection of Δtsr3/TSR3 Δsnr35/SNR35 heterozygous diploids.	FIG
85	91	siRNAs	chemical	Phenotypic characterization of yeast TSR3 deletion (Δtrs3) and human TSR3 depletion (siRNAs 544 and 545) and cellular localization of yeast Tsr3. (A) Growth of yeast wild type, Δtsr3, Δsnr35 and Δtsr3 Δsnr35 segregants after meiosis and tetrad dissection of Δtsr3/TSR3 Δsnr35/SNR35 heterozygous diploids.	FIG
134	139	yeast	taxonomy_domain	Phenotypic characterization of yeast TSR3 deletion (Δtrs3) and human TSR3 depletion (siRNAs 544 and 545) and cellular localization of yeast Tsr3. (A) Growth of yeast wild type, Δtsr3, Δsnr35 and Δtsr3 Δsnr35 segregants after meiosis and tetrad dissection of Δtsr3/TSR3 Δsnr35/SNR35 heterozygous diploids.	FIG
140	144	Tsr3	protein	Phenotypic characterization of yeast TSR3 deletion (Δtrs3) and human TSR3 depletion (siRNAs 544 and 545) and cellular localization of yeast Tsr3. (A) Growth of yeast wild type, Δtsr3, Δsnr35 and Δtsr3 Δsnr35 segregants after meiosis and tetrad dissection of Δtsr3/TSR3 Δsnr35/SNR35 heterozygous diploids.	FIG
160	165	yeast	taxonomy_domain	Phenotypic characterization of yeast TSR3 deletion (Δtrs3) and human TSR3 depletion (siRNAs 544 and 545) and cellular localization of yeast Tsr3. (A) Growth of yeast wild type, Δtsr3, Δsnr35 and Δtsr3 Δsnr35 segregants after meiosis and tetrad dissection of Δtsr3/TSR3 Δsnr35/SNR35 heterozygous diploids.	FIG
166	175	wild type	protein_state	Phenotypic characterization of yeast TSR3 deletion (Δtrs3) and human TSR3 depletion (siRNAs 544 and 545) and cellular localization of yeast Tsr3. (A) Growth of yeast wild type, Δtsr3, Δsnr35 and Δtsr3 Δsnr35 segregants after meiosis and tetrad dissection of Δtsr3/TSR3 Δsnr35/SNR35 heterozygous diploids.	FIG
177	182	Δtsr3	mutant	Phenotypic characterization of yeast TSR3 deletion (Δtrs3) and human TSR3 depletion (siRNAs 544 and 545) and cellular localization of yeast Tsr3. (A) Growth of yeast wild type, Δtsr3, Δsnr35 and Δtsr3 Δsnr35 segregants after meiosis and tetrad dissection of Δtsr3/TSR3 Δsnr35/SNR35 heterozygous diploids.	FIG
184	190	Δsnr35	mutant	Phenotypic characterization of yeast TSR3 deletion (Δtrs3) and human TSR3 depletion (siRNAs 544 and 545) and cellular localization of yeast Tsr3. (A) Growth of yeast wild type, Δtsr3, Δsnr35 and Δtsr3 Δsnr35 segregants after meiosis and tetrad dissection of Δtsr3/TSR3 Δsnr35/SNR35 heterozygous diploids.	FIG
195	207	Δtsr3 Δsnr35	mutant	Phenotypic characterization of yeast TSR3 deletion (Δtrs3) and human TSR3 depletion (siRNAs 544 and 545) and cellular localization of yeast Tsr3. (A) Growth of yeast wild type, Δtsr3, Δsnr35 and Δtsr3 Δsnr35 segregants after meiosis and tetrad dissection of Δtsr3/TSR3 Δsnr35/SNR35 heterozygous diploids.	FIG
258	263	Δtsr3	mutant	Phenotypic characterization of yeast TSR3 deletion (Δtrs3) and human TSR3 depletion (siRNAs 544 and 545) and cellular localization of yeast Tsr3. (A) Growth of yeast wild type, Δtsr3, Δsnr35 and Δtsr3 Δsnr35 segregants after meiosis and tetrad dissection of Δtsr3/TSR3 Δsnr35/SNR35 heterozygous diploids.	FIG
264	268	TSR3	protein	Phenotypic characterization of yeast TSR3 deletion (Δtrs3) and human TSR3 depletion (siRNAs 544 and 545) and cellular localization of yeast Tsr3. (A) Growth of yeast wild type, Δtsr3, Δsnr35 and Δtsr3 Δsnr35 segregants after meiosis and tetrad dissection of Δtsr3/TSR3 Δsnr35/SNR35 heterozygous diploids.	FIG
269	275	Δsnr35	mutant	Phenotypic characterization of yeast TSR3 deletion (Δtrs3) and human TSR3 depletion (siRNAs 544 and 545) and cellular localization of yeast Tsr3. (A) Growth of yeast wild type, Δtsr3, Δsnr35 and Δtsr3 Δsnr35 segregants after meiosis and tetrad dissection of Δtsr3/TSR3 Δsnr35/SNR35 heterozygous diploids.	FIG
276	281	SNR35	protein	Phenotypic characterization of yeast TSR3 deletion (Δtrs3) and human TSR3 depletion (siRNAs 544 and 545) and cellular localization of yeast Tsr3. (A) Growth of yeast wild type, Δtsr3, Δsnr35 and Δtsr3 Δsnr35 segregants after meiosis and tetrad dissection of Δtsr3/TSR3 Δsnr35/SNR35 heterozygous diploids.	FIG
4	9	Δtsr3	mutant	The Δtsr3 deletion is synthetic sick with a Δsnr35 deletion preventing U1191 pseudouridylation.	FIG
44	50	Δsnr35	mutant	The Δtsr3 deletion is synthetic sick with a Δsnr35 deletion preventing U1191 pseudouridylation.	FIG
71	76	U1191	residue_name_number	The Δtsr3 deletion is synthetic sick with a Δsnr35 deletion preventing U1191 pseudouridylation.	FIG
7	28	agar diffusion assays	experimental_method	(B) In agar diffusion assays the yeast Δtsr3 deletion mutant shows a hypersensitivity against paromomycin and hygromycin B which is further increased by recombination with Δsnr35. (C) Northern blot analysis with an ITS1 hybridization probe after siRNA depletion of HsTSR3 (siRNAs 544 and 545) and a scrambled siRNA as control.	FIG
33	38	yeast	taxonomy_domain	(B) In agar diffusion assays the yeast Δtsr3 deletion mutant shows a hypersensitivity against paromomycin and hygromycin B which is further increased by recombination with Δsnr35. (C) Northern blot analysis with an ITS1 hybridization probe after siRNA depletion of HsTSR3 (siRNAs 544 and 545) and a scrambled siRNA as control.	FIG
39	44	Δtsr3	mutant	(B) In agar diffusion assays the yeast Δtsr3 deletion mutant shows a hypersensitivity against paromomycin and hygromycin B which is further increased by recombination with Δsnr35. (C) Northern blot analysis with an ITS1 hybridization probe after siRNA depletion of HsTSR3 (siRNAs 544 and 545) and a scrambled siRNA as control.	FIG
45	60	deletion mutant	protein_state	(B) In agar diffusion assays the yeast Δtsr3 deletion mutant shows a hypersensitivity against paromomycin and hygromycin B which is further increased by recombination with Δsnr35. (C) Northern blot analysis with an ITS1 hybridization probe after siRNA depletion of HsTSR3 (siRNAs 544 and 545) and a scrambled siRNA as control.	FIG
94	105	paromomycin	chemical	(B) In agar diffusion assays the yeast Δtsr3 deletion mutant shows a hypersensitivity against paromomycin and hygromycin B which is further increased by recombination with Δsnr35. (C) Northern blot analysis with an ITS1 hybridization probe after siRNA depletion of HsTSR3 (siRNAs 544 and 545) and a scrambled siRNA as control.	FIG
110	122	hygromycin B	chemical	(B) In agar diffusion assays the yeast Δtsr3 deletion mutant shows a hypersensitivity against paromomycin and hygromycin B which is further increased by recombination with Δsnr35. (C) Northern blot analysis with an ITS1 hybridization probe after siRNA depletion of HsTSR3 (siRNAs 544 and 545) and a scrambled siRNA as control.	FIG
172	178	Δsnr35	mutant	(B) In agar diffusion assays the yeast Δtsr3 deletion mutant shows a hypersensitivity against paromomycin and hygromycin B which is further increased by recombination with Δsnr35. (C) Northern blot analysis with an ITS1 hybridization probe after siRNA depletion of HsTSR3 (siRNAs 544 and 545) and a scrambled siRNA as control.	FIG
184	206	Northern blot analysis	experimental_method	(B) In agar diffusion assays the yeast Δtsr3 deletion mutant shows a hypersensitivity against paromomycin and hygromycin B which is further increased by recombination with Δsnr35. (C) Northern blot analysis with an ITS1 hybridization probe after siRNA depletion of HsTSR3 (siRNAs 544 and 545) and a scrambled siRNA as control.	FIG
246	261	siRNA depletion	experimental_method	(B) In agar diffusion assays the yeast Δtsr3 deletion mutant shows a hypersensitivity against paromomycin and hygromycin B which is further increased by recombination with Δsnr35. (C) Northern blot analysis with an ITS1 hybridization probe after siRNA depletion of HsTSR3 (siRNAs 544 and 545) and a scrambled siRNA as control.	FIG
265	271	HsTSR3	protein	(B) In agar diffusion assays the yeast Δtsr3 deletion mutant shows a hypersensitivity against paromomycin and hygromycin B which is further increased by recombination with Δsnr35. (C) Northern blot analysis with an ITS1 hybridization probe after siRNA depletion of HsTSR3 (siRNAs 544 and 545) and a scrambled siRNA as control.	FIG
273	279	siRNAs	chemical	(B) In agar diffusion assays the yeast Δtsr3 deletion mutant shows a hypersensitivity against paromomycin and hygromycin B which is further increased by recombination with Δsnr35. (C) Northern blot analysis with an ITS1 hybridization probe after siRNA depletion of HsTSR3 (siRNAs 544 and 545) and a scrambled siRNA as control.	FIG
309	314	siRNA	chemical	(B) In agar diffusion assays the yeast Δtsr3 deletion mutant shows a hypersensitivity against paromomycin and hygromycin B which is further increased by recombination with Δsnr35. (C) Northern blot analysis with an ITS1 hybridization probe after siRNA depletion of HsTSR3 (siRNAs 544 and 545) and a scrambled siRNA as control.	FIG
20	24	18SE	chemical	The accumulation of 18SE and 47S and/or 45S pre-RNAs is enforced upon HsTSR3 depletion.	FIG
29	32	47S	chemical	The accumulation of 18SE and 47S and/or 45S pre-RNAs is enforced upon HsTSR3 depletion.	FIG
40	52	45S pre-RNAs	chemical	The accumulation of 18SE and 47S and/or 45S pre-RNAs is enforced upon HsTSR3 depletion.	FIG
70	76	HsTSR3	protein	The accumulation of 18SE and 47S and/or 45S pre-RNAs is enforced upon HsTSR3 depletion.	FIG
45	48	18S	chemical	Right gel: Ethidium bromide staining showing 18S and 28S rRNAs.	FIG
53	62	28S rRNAs	chemical	Right gel: Ethidium bromide staining showing 18S and 28S rRNAs.	FIG
32	37	yeast	taxonomy_domain	(D) Cytoplasmic localization of yeast Tsr3 shown by fluorescence microscopy of GFP-fused Tsr3.	FIG
38	42	Tsr3	protein	(D) Cytoplasmic localization of yeast Tsr3 shown by fluorescence microscopy of GFP-fused Tsr3.	FIG
52	75	fluorescence microscopy	experimental_method	(D) Cytoplasmic localization of yeast Tsr3 shown by fluorescence microscopy of GFP-fused Tsr3.	FIG
79	93	GFP-fused Tsr3	mutant	(D) Cytoplasmic localization of yeast Tsr3 shown by fluorescence microscopy of GFP-fused Tsr3.	FIG
20	54	differential interference contrast	experimental_method	From left to right: differential interference contrast (DIC), green fluorescence of GFP-Tsr3, red fluorescence of Nop56-mRFP as nucleolar marker, and merge of GFP-Tsr3/Nop56-mRFP with DIC. (E) Elution profile (A254) after sucrose gradient separation of yeast ribosomal subunits and polysomes (upper part) and western blot analysis of 3xHA tagged Tsr3 (Tsr3-3xHA) after SDS-PAGE separation of polysome profile fractions taken every 20 s (lower part).	FIG
56	59	DIC	experimental_method	From left to right: differential interference contrast (DIC), green fluorescence of GFP-Tsr3, red fluorescence of Nop56-mRFP as nucleolar marker, and merge of GFP-Tsr3/Nop56-mRFP with DIC. (E) Elution profile (A254) after sucrose gradient separation of yeast ribosomal subunits and polysomes (upper part) and western blot analysis of 3xHA tagged Tsr3 (Tsr3-3xHA) after SDS-PAGE separation of polysome profile fractions taken every 20 s (lower part).	FIG
84	92	GFP-Tsr3	mutant	From left to right: differential interference contrast (DIC), green fluorescence of GFP-Tsr3, red fluorescence of Nop56-mRFP as nucleolar marker, and merge of GFP-Tsr3/Nop56-mRFP with DIC. (E) Elution profile (A254) after sucrose gradient separation of yeast ribosomal subunits and polysomes (upper part) and western blot analysis of 3xHA tagged Tsr3 (Tsr3-3xHA) after SDS-PAGE separation of polysome profile fractions taken every 20 s (lower part).	FIG
114	124	Nop56-mRFP	mutant	From left to right: differential interference contrast (DIC), green fluorescence of GFP-Tsr3, red fluorescence of Nop56-mRFP as nucleolar marker, and merge of GFP-Tsr3/Nop56-mRFP with DIC. (E) Elution profile (A254) after sucrose gradient separation of yeast ribosomal subunits and polysomes (upper part) and western blot analysis of 3xHA tagged Tsr3 (Tsr3-3xHA) after SDS-PAGE separation of polysome profile fractions taken every 20 s (lower part).	FIG
159	167	GFP-Tsr3	mutant	From left to right: differential interference contrast (DIC), green fluorescence of GFP-Tsr3, red fluorescence of Nop56-mRFP as nucleolar marker, and merge of GFP-Tsr3/Nop56-mRFP with DIC. (E) Elution profile (A254) after sucrose gradient separation of yeast ribosomal subunits and polysomes (upper part) and western blot analysis of 3xHA tagged Tsr3 (Tsr3-3xHA) after SDS-PAGE separation of polysome profile fractions taken every 20 s (lower part).	FIG
168	178	Nop56-mRFP	mutant	From left to right: differential interference contrast (DIC), green fluorescence of GFP-Tsr3, red fluorescence of Nop56-mRFP as nucleolar marker, and merge of GFP-Tsr3/Nop56-mRFP with DIC. (E) Elution profile (A254) after sucrose gradient separation of yeast ribosomal subunits and polysomes (upper part) and western blot analysis of 3xHA tagged Tsr3 (Tsr3-3xHA) after SDS-PAGE separation of polysome profile fractions taken every 20 s (lower part).	FIG
184	187	DIC	experimental_method	From left to right: differential interference contrast (DIC), green fluorescence of GFP-Tsr3, red fluorescence of Nop56-mRFP as nucleolar marker, and merge of GFP-Tsr3/Nop56-mRFP with DIC. (E) Elution profile (A254) after sucrose gradient separation of yeast ribosomal subunits and polysomes (upper part) and western blot analysis of 3xHA tagged Tsr3 (Tsr3-3xHA) after SDS-PAGE separation of polysome profile fractions taken every 20 s (lower part).	FIG
193	208	Elution profile	evidence	From left to right: differential interference contrast (DIC), green fluorescence of GFP-Tsr3, red fluorescence of Nop56-mRFP as nucleolar marker, and merge of GFP-Tsr3/Nop56-mRFP with DIC. (E) Elution profile (A254) after sucrose gradient separation of yeast ribosomal subunits and polysomes (upper part) and western blot analysis of 3xHA tagged Tsr3 (Tsr3-3xHA) after SDS-PAGE separation of polysome profile fractions taken every 20 s (lower part).	FIG
222	249	sucrose gradient separation	experimental_method	From left to right: differential interference contrast (DIC), green fluorescence of GFP-Tsr3, red fluorescence of Nop56-mRFP as nucleolar marker, and merge of GFP-Tsr3/Nop56-mRFP with DIC. (E) Elution profile (A254) after sucrose gradient separation of yeast ribosomal subunits and polysomes (upper part) and western blot analysis of 3xHA tagged Tsr3 (Tsr3-3xHA) after SDS-PAGE separation of polysome profile fractions taken every 20 s (lower part).	FIG
253	258	yeast	taxonomy_domain	From left to right: differential interference contrast (DIC), green fluorescence of GFP-Tsr3, red fluorescence of Nop56-mRFP as nucleolar marker, and merge of GFP-Tsr3/Nop56-mRFP with DIC. (E) Elution profile (A254) after sucrose gradient separation of yeast ribosomal subunits and polysomes (upper part) and western blot analysis of 3xHA tagged Tsr3 (Tsr3-3xHA) after SDS-PAGE separation of polysome profile fractions taken every 20 s (lower part).	FIG
259	277	ribosomal subunits	complex_assembly	From left to right: differential interference contrast (DIC), green fluorescence of GFP-Tsr3, red fluorescence of Nop56-mRFP as nucleolar marker, and merge of GFP-Tsr3/Nop56-mRFP with DIC. (E) Elution profile (A254) after sucrose gradient separation of yeast ribosomal subunits and polysomes (upper part) and western blot analysis of 3xHA tagged Tsr3 (Tsr3-3xHA) after SDS-PAGE separation of polysome profile fractions taken every 20 s (lower part).	FIG
282	291	polysomes	complex_assembly	From left to right: differential interference contrast (DIC), green fluorescence of GFP-Tsr3, red fluorescence of Nop56-mRFP as nucleolar marker, and merge of GFP-Tsr3/Nop56-mRFP with DIC. (E) Elution profile (A254) after sucrose gradient separation of yeast ribosomal subunits and polysomes (upper part) and western blot analysis of 3xHA tagged Tsr3 (Tsr3-3xHA) after SDS-PAGE separation of polysome profile fractions taken every 20 s (lower part).	FIG
309	321	western blot	experimental_method	From left to right: differential interference contrast (DIC), green fluorescence of GFP-Tsr3, red fluorescence of Nop56-mRFP as nucleolar marker, and merge of GFP-Tsr3/Nop56-mRFP with DIC. (E) Elution profile (A254) after sucrose gradient separation of yeast ribosomal subunits and polysomes (upper part) and western blot analysis of 3xHA tagged Tsr3 (Tsr3-3xHA) after SDS-PAGE separation of polysome profile fractions taken every 20 s (lower part).	FIG
334	338	3xHA	chemical	From left to right: differential interference contrast (DIC), green fluorescence of GFP-Tsr3, red fluorescence of Nop56-mRFP as nucleolar marker, and merge of GFP-Tsr3/Nop56-mRFP with DIC. (E) Elution profile (A254) after sucrose gradient separation of yeast ribosomal subunits and polysomes (upper part) and western blot analysis of 3xHA tagged Tsr3 (Tsr3-3xHA) after SDS-PAGE separation of polysome profile fractions taken every 20 s (lower part).	FIG
346	350	Tsr3	protein	From left to right: differential interference contrast (DIC), green fluorescence of GFP-Tsr3, red fluorescence of Nop56-mRFP as nucleolar marker, and merge of GFP-Tsr3/Nop56-mRFP with DIC. (E) Elution profile (A254) after sucrose gradient separation of yeast ribosomal subunits and polysomes (upper part) and western blot analysis of 3xHA tagged Tsr3 (Tsr3-3xHA) after SDS-PAGE separation of polysome profile fractions taken every 20 s (lower part).	FIG
352	361	Tsr3-3xHA	mutant	From left to right: differential interference contrast (DIC), green fluorescence of GFP-Tsr3, red fluorescence of Nop56-mRFP as nucleolar marker, and merge of GFP-Tsr3/Nop56-mRFP with DIC. (E) Elution profile (A254) after sucrose gradient separation of yeast ribosomal subunits and polysomes (upper part) and western blot analysis of 3xHA tagged Tsr3 (Tsr3-3xHA) after SDS-PAGE separation of polysome profile fractions taken every 20 s (lower part).	FIG
369	377	SDS-PAGE	experimental_method	From left to right: differential interference contrast (DIC), green fluorescence of GFP-Tsr3, red fluorescence of Nop56-mRFP as nucleolar marker, and merge of GFP-Tsr3/Nop56-mRFP with DIC. (E) Elution profile (A254) after sucrose gradient separation of yeast ribosomal subunits and polysomes (upper part) and western blot analysis of 3xHA tagged Tsr3 (Tsr3-3xHA) after SDS-PAGE separation of polysome profile fractions taken every 20 s (lower part).	FIG
4	8	TSR3	protein	The TSR3 gene was genetically modified at its native locus, resulting in a C-terminal fusion of Tsr3 with a 3xHA epitope expressed by the native promotor in yeast strain CEN.BM258-5B.	FIG
86	92	fusion	protein_state	The TSR3 gene was genetically modified at its native locus, resulting in a C-terminal fusion of Tsr3 with a 3xHA epitope expressed by the native promotor in yeast strain CEN.BM258-5B.	FIG
96	100	Tsr3	protein	The TSR3 gene was genetically modified at its native locus, resulting in a C-terminal fusion of Tsr3 with a 3xHA epitope expressed by the native promotor in yeast strain CEN.BM258-5B.	FIG
108	112	3xHA	chemical	The TSR3 gene was genetically modified at its native locus, resulting in a C-terminal fusion of Tsr3 with a 3xHA epitope expressed by the native promotor in yeast strain CEN.BM258-5B.	FIG
157	162	yeast	taxonomy_domain	The TSR3 gene was genetically modified at its native locus, resulting in a C-terminal fusion of Tsr3 with a 3xHA epitope expressed by the native promotor in yeast strain CEN.BM258-5B.	FIG
21	24	acp	chemical	The influence of the acp modification of nucleotide 1191 on ribosome function was analyzed by treating Δtsr3 mutants with protein synthesis inhibitors.	RESULTS
41	51	nucleotide	chemical	The influence of the acp modification of nucleotide 1191 on ribosome function was analyzed by treating Δtsr3 mutants with protein synthesis inhibitors.	RESULTS
52	56	1191	residue_number	The influence of the acp modification of nucleotide 1191 on ribosome function was analyzed by treating Δtsr3 mutants with protein synthesis inhibitors.	RESULTS
103	108	Δtsr3	mutant	The influence of the acp modification of nucleotide 1191 on ribosome function was analyzed by treating Δtsr3 mutants with protein synthesis inhibitors.	RESULTS
35	39	nep1	gene	Similar to a temperature-sensitive nep1 mutant, the Δtsr3 deletion caused hypersensitivity to paromomycin and, to a lesser extent, to hygromycin B (Figure 2B), but not to G418 or cycloheximide (data not shown).	RESULTS
40	46	mutant	protein_state	Similar to a temperature-sensitive nep1 mutant, the Δtsr3 deletion caused hypersensitivity to paromomycin and, to a lesser extent, to hygromycin B (Figure 2B), but not to G418 or cycloheximide (data not shown).	RESULTS
52	57	Δtsr3	mutant	Similar to a temperature-sensitive nep1 mutant, the Δtsr3 deletion caused hypersensitivity to paromomycin and, to a lesser extent, to hygromycin B (Figure 2B), but not to G418 or cycloheximide (data not shown).	RESULTS
94	105	paromomycin	chemical	Similar to a temperature-sensitive nep1 mutant, the Δtsr3 deletion caused hypersensitivity to paromomycin and, to a lesser extent, to hygromycin B (Figure 2B), but not to G418 or cycloheximide (data not shown).	RESULTS
134	146	hygromycin B	chemical	Similar to a temperature-sensitive nep1 mutant, the Δtsr3 deletion caused hypersensitivity to paromomycin and, to a lesser extent, to hygromycin B (Figure 2B), but not to G418 or cycloheximide (data not shown).	RESULTS
171	175	G418	chemical	Similar to a temperature-sensitive nep1 mutant, the Δtsr3 deletion caused hypersensitivity to paromomycin and, to a lesser extent, to hygromycin B (Figure 2B), but not to G418 or cycloheximide (data not shown).	RESULTS
179	192	cycloheximide	chemical	Similar to a temperature-sensitive nep1 mutant, the Δtsr3 deletion caused hypersensitivity to paromomycin and, to a lesser extent, to hygromycin B (Figure 2B), but not to G418 or cycloheximide (data not shown).	RESULTS
59	70	paromomycin	chemical	In accordance with the synthetic sick growth phenotype the paromomycin and hygromycin B hypersensitivity further increased in a Δtsr3 Δsnr35 recombination strain (Figure 2B).	RESULTS
75	87	hygromycin B	chemical	In accordance with the synthetic sick growth phenotype the paromomycin and hygromycin B hypersensitivity further increased in a Δtsr3 Δsnr35 recombination strain (Figure 2B).	RESULTS
128	140	Δtsr3 Δsnr35	mutant	In accordance with the synthetic sick growth phenotype the paromomycin and hygromycin B hypersensitivity further increased in a Δtsr3 Δsnr35 recombination strain (Figure 2B).	RESULTS
5	10	yeast	taxonomy_domain	In a yeast Δtsr3 strain as well as in the Δtsr3 Δsnr35 recombinant 20S pre-rRNA accumulated significantly and the level of mature 18S rRNA was reduced (Supplementary Figures S2C and S3D), as reported previously.	RESULTS
11	16	Δtsr3	mutant	In a yeast Δtsr3 strain as well as in the Δtsr3 Δsnr35 recombinant 20S pre-rRNA accumulated significantly and the level of mature 18S rRNA was reduced (Supplementary Figures S2C and S3D), as reported previously.	RESULTS
42	54	Δtsr3 Δsnr35	mutant	In a yeast Δtsr3 strain as well as in the Δtsr3 Δsnr35 recombinant 20S pre-rRNA accumulated significantly and the level of mature 18S rRNA was reduced (Supplementary Figures S2C and S3D), as reported previously.	RESULTS
67	79	20S pre-rRNA	chemical	In a yeast Δtsr3 strain as well as in the Δtsr3 Δsnr35 recombinant 20S pre-rRNA accumulated significantly and the level of mature 18S rRNA was reduced (Supplementary Figures S2C and S3D), as reported previously.	RESULTS
130	138	18S rRNA	chemical	In a yeast Δtsr3 strain as well as in the Δtsr3 Δsnr35 recombinant 20S pre-rRNA accumulated significantly and the level of mature 18S rRNA was reduced (Supplementary Figures S2C and S3D), as reported previously.	RESULTS
18	26	20S rRNA	chemical	A minor effect on 20S rRNA accumulation was also observed for Δsnr35, but - probably due to different strain backgrounds – to a weaker extent than described earlier.	RESULTS
62	68	Δsnr35	mutant	A minor effect on 20S rRNA accumulation was also observed for Δsnr35, but - probably due to different strain backgrounds – to a weaker extent than described earlier.	RESULTS
3	8	human	species	In human cells, the depletion of HsTsr3 in HCT116(+/+) cells caused an accumulation of the human 20S pre-rRNA equivalent 18S-E suggesting an evolutionary conserved role of Tsr3 in the late steps of 18S rRNA processing (Figure 2C and Supplementary Figure S2B).	RESULTS
20	32	depletion of	experimental_method	In human cells, the depletion of HsTsr3 in HCT116(+/+) cells caused an accumulation of the human 20S pre-rRNA equivalent 18S-E suggesting an evolutionary conserved role of Tsr3 in the late steps of 18S rRNA processing (Figure 2C and Supplementary Figure S2B).	RESULTS
33	39	HsTsr3	protein	In human cells, the depletion of HsTsr3 in HCT116(+/+) cells caused an accumulation of the human 20S pre-rRNA equivalent 18S-E suggesting an evolutionary conserved role of Tsr3 in the late steps of 18S rRNA processing (Figure 2C and Supplementary Figure S2B).	RESULTS
91	96	human	species	In human cells, the depletion of HsTsr3 in HCT116(+/+) cells caused an accumulation of the human 20S pre-rRNA equivalent 18S-E suggesting an evolutionary conserved role of Tsr3 in the late steps of 18S rRNA processing (Figure 2C and Supplementary Figure S2B).	RESULTS
97	109	20S pre-rRNA	chemical	In human cells, the depletion of HsTsr3 in HCT116(+/+) cells caused an accumulation of the human 20S pre-rRNA equivalent 18S-E suggesting an evolutionary conserved role of Tsr3 in the late steps of 18S rRNA processing (Figure 2C and Supplementary Figure S2B).	RESULTS
121	126	18S-E	chemical	In human cells, the depletion of HsTsr3 in HCT116(+/+) cells caused an accumulation of the human 20S pre-rRNA equivalent 18S-E suggesting an evolutionary conserved role of Tsr3 in the late steps of 18S rRNA processing (Figure 2C and Supplementary Figure S2B).	RESULTS
172	176	Tsr3	protein	In human cells, the depletion of HsTsr3 in HCT116(+/+) cells caused an accumulation of the human 20S pre-rRNA equivalent 18S-E suggesting an evolutionary conserved role of Tsr3 in the late steps of 18S rRNA processing (Figure 2C and Supplementary Figure S2B).	RESULTS
198	206	18S rRNA	chemical	In human cells, the depletion of HsTsr3 in HCT116(+/+) cells caused an accumulation of the human 20S pre-rRNA equivalent 18S-E suggesting an evolutionary conserved role of Tsr3 in the late steps of 18S rRNA processing (Figure 2C and Supplementary Figure S2B).	RESULTS
102	107	yeast	taxonomy_domain	Surprisingly, early nucleolar processing reactions were also inhibited, and this was observed in both yeast Δtsr3 cells (see accumulation of 35S in Supplementary Figure S2C) and Tsr3 depleted human cells (see 47S/45S accumulation in Figure 2C and Northern blot quantification in Supplementary Figure S2B).	RESULTS
108	113	Δtsr3	mutant	Surprisingly, early nucleolar processing reactions were also inhibited, and this was observed in both yeast Δtsr3 cells (see accumulation of 35S in Supplementary Figure S2C) and Tsr3 depleted human cells (see 47S/45S accumulation in Figure 2C and Northern blot quantification in Supplementary Figure S2B).	RESULTS
141	144	35S	complex_assembly	Surprisingly, early nucleolar processing reactions were also inhibited, and this was observed in both yeast Δtsr3 cells (see accumulation of 35S in Supplementary Figure S2C) and Tsr3 depleted human cells (see 47S/45S accumulation in Figure 2C and Northern blot quantification in Supplementary Figure S2B).	RESULTS
178	182	Tsr3	protein	Surprisingly, early nucleolar processing reactions were also inhibited, and this was observed in both yeast Δtsr3 cells (see accumulation of 35S in Supplementary Figure S2C) and Tsr3 depleted human cells (see 47S/45S accumulation in Figure 2C and Northern blot quantification in Supplementary Figure S2B).	RESULTS
192	197	human	species	Surprisingly, early nucleolar processing reactions were also inhibited, and this was observed in both yeast Δtsr3 cells (see accumulation of 35S in Supplementary Figure S2C) and Tsr3 depleted human cells (see 47S/45S accumulation in Figure 2C and Northern blot quantification in Supplementary Figure S2B).	RESULTS
209	212	47S	complex_assembly	Surprisingly, early nucleolar processing reactions were also inhibited, and this was observed in both yeast Δtsr3 cells (see accumulation of 35S in Supplementary Figure S2C) and Tsr3 depleted human cells (see 47S/45S accumulation in Figure 2C and Northern blot quantification in Supplementary Figure S2B).	RESULTS
213	216	45S	complex_assembly	Surprisingly, early nucleolar processing reactions were also inhibited, and this was observed in both yeast Δtsr3 cells (see accumulation of 35S in Supplementary Figure S2C) and Tsr3 depleted human cells (see 47S/45S accumulation in Figure 2C and Northern blot quantification in Supplementary Figure S2B).	RESULTS
247	260	Northern blot	experimental_method	Surprisingly, early nucleolar processing reactions were also inhibited, and this was observed in both yeast Δtsr3 cells (see accumulation of 35S in Supplementary Figure S2C) and Tsr3 depleted human cells (see 47S/45S accumulation in Figure 2C and Northern blot quantification in Supplementary Figure S2B).	RESULTS
33	41	18S rRNA	chemical	Consistent with its role in late 18S rRNA processing, TSR3 deletion leads to a ribosomal subunit imbalance with a reduced 40S to 60S ratio of 0.81 (σ = 0.024) which was further increased in a Δtsr3 Δsnr35 recombinant to 0.73 (σ = 0.023) (Supplementary Figure S2F).	RESULTS
54	58	TSR3	protein	Consistent with its role in late 18S rRNA processing, TSR3 deletion leads to a ribosomal subunit imbalance with a reduced 40S to 60S ratio of 0.81 (σ = 0.024) which was further increased in a Δtsr3 Δsnr35 recombinant to 0.73 (σ = 0.023) (Supplementary Figure S2F).	RESULTS
122	125	40S	complex_assembly	Consistent with its role in late 18S rRNA processing, TSR3 deletion leads to a ribosomal subunit imbalance with a reduced 40S to 60S ratio of 0.81 (σ = 0.024) which was further increased in a Δtsr3 Δsnr35 recombinant to 0.73 (σ = 0.023) (Supplementary Figure S2F).	RESULTS
129	132	60S	complex_assembly	Consistent with its role in late 18S rRNA processing, TSR3 deletion leads to a ribosomal subunit imbalance with a reduced 40S to 60S ratio of 0.81 (σ = 0.024) which was further increased in a Δtsr3 Δsnr35 recombinant to 0.73 (σ = 0.023) (Supplementary Figure S2F).	RESULTS
192	204	Δtsr3 Δsnr35	mutant	Consistent with its role in late 18S rRNA processing, TSR3 deletion leads to a ribosomal subunit imbalance with a reduced 40S to 60S ratio of 0.81 (σ = 0.024) which was further increased in a Δtsr3 Δsnr35 recombinant to 0.73 (σ = 0.023) (Supplementary Figure S2F).	RESULTS
3	20	polysome profiles	evidence	In polysome profiles, a reduced level of 80S ribosomes and a strong signal for free 60S subunits was observed in line with the 40S subunit deficiency (Supplementary Figure S2G).	RESULTS
41	54	80S ribosomes	complex_assembly	In polysome profiles, a reduced level of 80S ribosomes and a strong signal for free 60S subunits was observed in line with the 40S subunit deficiency (Supplementary Figure S2G).	RESULTS
84	87	60S	complex_assembly	In polysome profiles, a reduced level of 80S ribosomes and a strong signal for free 60S subunits was observed in line with the 40S subunit deficiency (Supplementary Figure S2G).	RESULTS
127	130	40S	complex_assembly	In polysome profiles, a reduced level of 80S ribosomes and a strong signal for free 60S subunits was observed in line with the 40S subunit deficiency (Supplementary Figure S2G).	RESULTS
25	29	Tsr3	protein	Cellular localization of Tsr3 in S. cerevisiae	RESULTS
33	46	S. cerevisiae	species	Cellular localization of Tsr3 in S. cerevisiae	RESULTS
0	23	Fluorescence microscopy	experimental_method	Fluorescence microscopy of GFP-tagged Tsr3 localized the fusion protein in the cytoplasm of yeast cells and no co-localization with the nucleolar marker protein Nop56 could be observed (Figure 2D).	RESULTS
27	37	GFP-tagged	protein_state	Fluorescence microscopy of GFP-tagged Tsr3 localized the fusion protein in the cytoplasm of yeast cells and no co-localization with the nucleolar marker protein Nop56 could be observed (Figure 2D).	RESULTS
38	42	Tsr3	protein	Fluorescence microscopy of GFP-tagged Tsr3 localized the fusion protein in the cytoplasm of yeast cells and no co-localization with the nucleolar marker protein Nop56 could be observed (Figure 2D).	RESULTS
92	97	yeast	taxonomy_domain	Fluorescence microscopy of GFP-tagged Tsr3 localized the fusion protein in the cytoplasm of yeast cells and no co-localization with the nucleolar marker protein Nop56 could be observed (Figure 2D).	RESULTS
161	166	Nop56	protein	Fluorescence microscopy of GFP-tagged Tsr3 localized the fusion protein in the cytoplasm of yeast cells and no co-localization with the nucleolar marker protein Nop56 could be observed (Figure 2D).	RESULTS
63	66	acp	chemical	This agrees with previous biochemical data suggesting that the acp modification of 18S rRNA occurs late during 40S subunit biogenesis in the cytoplasm, and makes an additional nuclear localization as reported in a previous large-scale analysis unlikely.	RESULTS
83	91	18S rRNA	chemical	This agrees with previous biochemical data suggesting that the acp modification of 18S rRNA occurs late during 40S subunit biogenesis in the cytoplasm, and makes an additional nuclear localization as reported in a previous large-scale analysis unlikely.	RESULTS
111	114	40S	complex_assembly	This agrees with previous biochemical data suggesting that the acp modification of 18S rRNA occurs late during 40S subunit biogenesis in the cytoplasm, and makes an additional nuclear localization as reported in a previous large-scale analysis unlikely.	RESULTS
6	34	polysome gradient separation	experimental_method	After polysome gradient separation C-terminally epitope-labeled Tsr3-3xHA was exclusively detectable in the low-density fraction (Figure 2E).	RESULTS
64	73	Tsr3-3xHA	mutant	After polysome gradient separation C-terminally epitope-labeled Tsr3-3xHA was exclusively detectable in the low-density fraction (Figure 2E).	RESULTS
5	39	distribution on a density gradient	evidence	Such distribution on a density gradient suggests that Tsr3 only interacts transiently with pre-40S subunits, which presumably explains why it was not characterized in pre-ribosome affinity purifications.	RESULTS
54	58	Tsr3	protein	Such distribution on a density gradient suggests that Tsr3 only interacts transiently with pre-40S subunits, which presumably explains why it was not characterized in pre-ribosome affinity purifications.	RESULTS
91	107	pre-40S subunits	complex_assembly	Such distribution on a density gradient suggests that Tsr3 only interacts transiently with pre-40S subunits, which presumably explains why it was not characterized in pre-ribosome affinity purifications.	RESULTS
167	202	pre-ribosome affinity purifications	experimental_method	Such distribution on a density gradient suggests that Tsr3 only interacts transiently with pre-40S subunits, which presumably explains why it was not characterized in pre-ribosome affinity purifications.	RESULTS
0	9	Structure	evidence	Structure of Tsr3	RESULTS
13	17	Tsr3	protein	Structure of Tsr3	RESULTS
34	47	S. cerevisiae	species	Searches for sequence homologs of S. cerevisiae Tsr3 (ScTsr3) by us and others revealed that the genomes of many archaea contain genes encoding Tsr3-like proteins.	RESULTS
48	52	Tsr3	protein	Searches for sequence homologs of S. cerevisiae Tsr3 (ScTsr3) by us and others revealed that the genomes of many archaea contain genes encoding Tsr3-like proteins.	RESULTS
54	60	ScTsr3	protein	Searches for sequence homologs of S. cerevisiae Tsr3 (ScTsr3) by us and others revealed that the genomes of many archaea contain genes encoding Tsr3-like proteins.	RESULTS
113	120	archaea	taxonomy_domain	Searches for sequence homologs of S. cerevisiae Tsr3 (ScTsr3) by us and others revealed that the genomes of many archaea contain genes encoding Tsr3-like proteins.	RESULTS
144	162	Tsr3-like proteins	protein_type	Searches for sequence homologs of S. cerevisiae Tsr3 (ScTsr3) by us and others revealed that the genomes of many archaea contain genes encoding Tsr3-like proteins.	RESULTS
15	23	archaeal	taxonomy_domain	However, these archaeal homologs are significantly smaller than ScTsr3 (∼190 aa in archaea vs. 313 aa in yeast) due to shortened N- and C-termini (Supplementary Figure S1A).	RESULTS
64	70	ScTsr3	protein	However, these archaeal homologs are significantly smaller than ScTsr3 (∼190 aa in archaea vs. 313 aa in yeast) due to shortened N- and C-termini (Supplementary Figure S1A).	RESULTS
83	90	archaea	taxonomy_domain	However, these archaeal homologs are significantly smaller than ScTsr3 (∼190 aa in archaea vs. 313 aa in yeast) due to shortened N- and C-termini (Supplementary Figure S1A).	RESULTS
105	110	yeast	taxonomy_domain	However, these archaeal homologs are significantly smaller than ScTsr3 (∼190 aa in archaea vs. 313 aa in yeast) due to shortened N- and C-termini (Supplementary Figure S1A).	RESULTS
41	45	Tsr3	protein	To locate the domains most important for Tsr3 activity, ScTsr3 fragments of different lengths containing the highly conserved central part were expressed in a Δtsr3 mutant (Figure 3A) and analyzed by primer extension (Figure 3B) and Northern blotting (Figure 3C).	RESULTS
56	62	ScTsr3	protein	To locate the domains most important for Tsr3 activity, ScTsr3 fragments of different lengths containing the highly conserved central part were expressed in a Δtsr3 mutant (Figure 3A) and analyzed by primer extension (Figure 3B) and Northern blotting (Figure 3C).	RESULTS
109	125	highly conserved	protein_state	To locate the domains most important for Tsr3 activity, ScTsr3 fragments of different lengths containing the highly conserved central part were expressed in a Δtsr3 mutant (Figure 3A) and analyzed by primer extension (Figure 3B) and Northern blotting (Figure 3C).	RESULTS
144	153	expressed	experimental_method	To locate the domains most important for Tsr3 activity, ScTsr3 fragments of different lengths containing the highly conserved central part were expressed in a Δtsr3 mutant (Figure 3A) and analyzed by primer extension (Figure 3B) and Northern blotting (Figure 3C).	RESULTS
159	164	Δtsr3	mutant	To locate the domains most important for Tsr3 activity, ScTsr3 fragments of different lengths containing the highly conserved central part were expressed in a Δtsr3 mutant (Figure 3A) and analyzed by primer extension (Figure 3B) and Northern blotting (Figure 3C).	RESULTS
165	171	mutant	protein_state	To locate the domains most important for Tsr3 activity, ScTsr3 fragments of different lengths containing the highly conserved central part were expressed in a Δtsr3 mutant (Figure 3A) and analyzed by primer extension (Figure 3B) and Northern blotting (Figure 3C).	RESULTS
200	216	primer extension	experimental_method	To locate the domains most important for Tsr3 activity, ScTsr3 fragments of different lengths containing the highly conserved central part were expressed in a Δtsr3 mutant (Figure 3A) and analyzed by primer extension (Figure 3B) and Northern blotting (Figure 3C).	RESULTS
233	250	Northern blotting	experimental_method	To locate the domains most important for Tsr3 activity, ScTsr3 fragments of different lengths containing the highly conserved central part were expressed in a Δtsr3 mutant (Figure 3A) and analyzed by primer extension (Figure 3B) and Northern blotting (Figure 3C).	RESULTS
11	22	truncations	experimental_method	N-terminal truncations of up to 45 aa and C-terminal truncations of up to 76 aa mediated acp modification as efficiently as the full-length protein and no significant increased levels of 20S pre-RNA were detected.	RESULTS
32	37	45 aa	residue_range	N-terminal truncations of up to 45 aa and C-terminal truncations of up to 76 aa mediated acp modification as efficiently as the full-length protein and no significant increased levels of 20S pre-RNA were detected.	RESULTS
53	64	truncations	experimental_method	N-terminal truncations of up to 45 aa and C-terminal truncations of up to 76 aa mediated acp modification as efficiently as the full-length protein and no significant increased levels of 20S pre-RNA were detected.	RESULTS
74	79	76 aa	residue_range	N-terminal truncations of up to 45 aa and C-terminal truncations of up to 76 aa mediated acp modification as efficiently as the full-length protein and no significant increased levels of 20S pre-RNA were detected.	RESULTS
89	92	acp	chemical	N-terminal truncations of up to 45 aa and C-terminal truncations of up to 76 aa mediated acp modification as efficiently as the full-length protein and no significant increased levels of 20S pre-RNA were detected.	RESULTS
128	139	full-length	protein_state	N-terminal truncations of up to 45 aa and C-terminal truncations of up to 76 aa mediated acp modification as efficiently as the full-length protein and no significant increased levels of 20S pre-RNA were detected.	RESULTS
187	198	20S pre-RNA	chemical	N-terminal truncations of up to 45 aa and C-terminal truncations of up to 76 aa mediated acp modification as efficiently as the full-length protein and no significant increased levels of 20S pre-RNA were detected.	RESULTS
7	11	Tsr3	protein	Even a Tsr3 fragment with a 90 aa C-terminal truncation showed a residual primer extension stop, whereas N-terminal truncations exceeding 46 aa almost completely abolished the primer extension arrest (Figure 3B).	RESULTS
28	33	90 aa	residue_range	Even a Tsr3 fragment with a 90 aa C-terminal truncation showed a residual primer extension stop, whereas N-terminal truncations exceeding 46 aa almost completely abolished the primer extension arrest (Figure 3B).	RESULTS
138	143	46 aa	residue_range	Even a Tsr3 fragment with a 90 aa C-terminal truncation showed a residual primer extension stop, whereas N-terminal truncations exceeding 46 aa almost completely abolished the primer extension arrest (Figure 3B).	RESULTS
27	32	yeast	taxonomy_domain	Domain characterization of yeast Tsr3 and correlation of acp modification with late 18S rRNA processing steps. (A) Scheme of the TSR3 gene with truncation positions in the open reading frame.	FIG
33	37	Tsr3	protein	Domain characterization of yeast Tsr3 and correlation of acp modification with late 18S rRNA processing steps. (A) Scheme of the TSR3 gene with truncation positions in the open reading frame.	FIG
57	60	acp	chemical	Domain characterization of yeast Tsr3 and correlation of acp modification with late 18S rRNA processing steps. (A) Scheme of the TSR3 gene with truncation positions in the open reading frame.	FIG
84	92	18S rRNA	chemical	Domain characterization of yeast Tsr3 and correlation of acp modification with late 18S rRNA processing steps. (A) Scheme of the TSR3 gene with truncation positions in the open reading frame.	FIG
129	133	TSR3	protein	Domain characterization of yeast Tsr3 and correlation of acp modification with late 18S rRNA processing steps. (A) Scheme of the TSR3 gene with truncation positions in the open reading frame.	FIG
0	4	TSR3	protein	TSR3 fragments of different length were expressed under the native promotor from multicopy plasmids in a Δtsr3 deletion strain.	FIG
105	110	Δtsr3	mutant	TSR3 fragments of different length were expressed under the native promotor from multicopy plasmids in a Δtsr3 deletion strain.	FIG
4	29	Primer extension analysis	experimental_method	(B) Primer extension analysis of 18S rRNA acp modification in yeast cells expressing the indicated TSR3 fragments.	FIG
33	41	18S rRNA	chemical	(B) Primer extension analysis of 18S rRNA acp modification in yeast cells expressing the indicated TSR3 fragments.	FIG
42	45	acp	chemical	(B) Primer extension analysis of 18S rRNA acp modification in yeast cells expressing the indicated TSR3 fragments.	FIG
62	67	yeast	taxonomy_domain	(B) Primer extension analysis of 18S rRNA acp modification in yeast cells expressing the indicated TSR3 fragments.	FIG
99	103	TSR3	protein	(B) Primer extension analysis of 18S rRNA acp modification in yeast cells expressing the indicated TSR3 fragments.	FIG
11	20	deletions	experimental_method	N-terminal deletions of 36 or 45 amino acids and C-terminal deletions of 43 or 76 residues show a primer extension stop comparable to the wild type.	FIG
24	26	36	residue_range	N-terminal deletions of 36 or 45 amino acids and C-terminal deletions of 43 or 76 residues show a primer extension stop comparable to the wild type.	FIG
30	32	45	residue_range	N-terminal deletions of 36 or 45 amino acids and C-terminal deletions of 43 or 76 residues show a primer extension stop comparable to the wild type.	FIG
60	69	deletions	experimental_method	N-terminal deletions of 36 or 45 amino acids and C-terminal deletions of 43 or 76 residues show a primer extension stop comparable to the wild type.	FIG
73	75	43	residue_range	N-terminal deletions of 36 or 45 amino acids and C-terminal deletions of 43 or 76 residues show a primer extension stop comparable to the wild type.	FIG
79	81	76	residue_range	N-terminal deletions of 36 or 45 amino acids and C-terminal deletions of 43 or 76 residues show a primer extension stop comparable to the wild type.	FIG
98	119	primer extension stop	evidence	N-terminal deletions of 36 or 45 amino acids and C-terminal deletions of 43 or 76 residues show a primer extension stop comparable to the wild type.	FIG
138	147	wild type	protein_state	N-terminal deletions of 36 or 45 amino acids and C-terminal deletions of 43 or 76 residues show a primer extension stop comparable to the wild type.	FIG
0	4	Tsr3	protein	Tsr3 fragments 37–223 or 46–223 cause a nearly complete loss of the arrest signal.	FIG
15	21	37–223	residue_range	Tsr3 fragments 37–223 or 46–223 cause a nearly complete loss of the arrest signal.	FIG
25	31	46–223	residue_range	Tsr3 fragments 37–223 or 46–223 cause a nearly complete loss of the arrest signal.	FIG
32	36	Tsr3	protein	The box highlights the shortest Tsr3 fragment (aa 46–270) with wild type activity (strong primer extension block). (C) Northern blot analysis of 20S pre-rRNA accumulation.	FIG
50	56	46–270	residue_range	The box highlights the shortest Tsr3 fragment (aa 46–270) with wild type activity (strong primer extension block). (C) Northern blot analysis of 20S pre-rRNA accumulation.	FIG
63	72	wild type	protein_state	The box highlights the shortest Tsr3 fragment (aa 46–270) with wild type activity (strong primer extension block). (C) Northern blot analysis of 20S pre-rRNA accumulation.	FIG
90	112	primer extension block	evidence	The box highlights the shortest Tsr3 fragment (aa 46–270) with wild type activity (strong primer extension block). (C) Northern blot analysis of 20S pre-rRNA accumulation.	FIG
119	132	Northern blot	experimental_method	The box highlights the shortest Tsr3 fragment (aa 46–270) with wild type activity (strong primer extension block). (C) Northern blot analysis of 20S pre-rRNA accumulation.	FIG
145	157	20S pre-rRNA	chemical	The box highlights the shortest Tsr3 fragment (aa 46–270) with wild type activity (strong primer extension block). (C) Northern blot analysis of 20S pre-rRNA accumulation.	FIG
7	15	20S rRNA	chemical	A weak 20S rRNA signal, indicating normal processing, is observed for Tsr3 fragment 46–270 (highlighted in a box) showing its functionality.	FIG
70	74	Tsr3	protein	A weak 20S rRNA signal, indicating normal processing, is observed for Tsr3 fragment 46–270 (highlighted in a box) showing its functionality.	FIG
84	90	46–270	residue_range	A weak 20S rRNA signal, indicating normal processing, is observed for Tsr3 fragment 46–270 (highlighted in a box) showing its functionality.	FIG
52	57	Δtsr3	mutant	Strong 20S rRNA accumulation similar to that of the Δtsr3 deletion is observed for Tsr3 fragments 37–223 or 46–223.	FIG
58	66	deletion	experimental_method	Strong 20S rRNA accumulation similar to that of the Δtsr3 deletion is observed for Tsr3 fragments 37–223 or 46–223.	FIG
83	87	Tsr3	protein	Strong 20S rRNA accumulation similar to that of the Δtsr3 deletion is observed for Tsr3 fragments 37–223 or 46–223.	FIG
98	104	37–223	residue_range	Strong 20S rRNA accumulation similar to that of the Δtsr3 deletion is observed for Tsr3 fragments 37–223 or 46–223.	FIG
108	114	46–223	residue_range	Strong 20S rRNA accumulation similar to that of the Δtsr3 deletion is observed for Tsr3 fragments 37–223 or 46–223.	FIG
10	18	archaeal	taxonomy_domain	Thus, the archaeal homologs correspond to the functional core of Tsr3.	RESULTS
65	69	Tsr3	protein	Thus, the archaeal homologs correspond to the functional core of Tsr3.	RESULTS
44	48	Tsr3	protein	In order to define the structural basis for Tsr3 function, homologs from thermophilic archaea were screened for crystallization.	RESULTS
73	93	thermophilic archaea	taxonomy_domain	In order to define the structural basis for Tsr3 function, homologs from thermophilic archaea were screened for crystallization.	RESULTS
112	127	crystallization	experimental_method	In order to define the structural basis for Tsr3 function, homologs from thermophilic archaea were screened for crystallization.	RESULTS
14	22	archaeal	taxonomy_domain	We focused on archaeal species containing a putative Nep1 homolog suggesting that these species are in principle capable of synthesizing N1-methyl-N3-acp-pseudouridine.	RESULTS
53	57	Nep1	protein	We focused on archaeal species containing a putative Nep1 homolog suggesting that these species are in principle capable of synthesizing N1-methyl-N3-acp-pseudouridine.	RESULTS
137	167	N1-methyl-N3-acp-pseudouridine	chemical	We focused on archaeal species containing a putative Nep1 homolog suggesting that these species are in principle capable of synthesizing N1-methyl-N3-acp-pseudouridine.	RESULTS
17	25	crystals	evidence	Well diffracting crystals were obtained for Tsr3 homologs from the two crenarchaeal species Vulcanisaeta distributa (VdTsr3) and Sulfolobus solfataricus (SsTsr3) which share 36% (VdTsr3) and 38% (SsTsr3) identity with the ScTsr3 core region (ScTsr3 aa 46–223).	RESULTS
44	48	Tsr3	protein	Well diffracting crystals were obtained for Tsr3 homologs from the two crenarchaeal species Vulcanisaeta distributa (VdTsr3) and Sulfolobus solfataricus (SsTsr3) which share 36% (VdTsr3) and 38% (SsTsr3) identity with the ScTsr3 core region (ScTsr3 aa 46–223).	RESULTS
71	83	crenarchaeal	taxonomy_domain	Well diffracting crystals were obtained for Tsr3 homologs from the two crenarchaeal species Vulcanisaeta distributa (VdTsr3) and Sulfolobus solfataricus (SsTsr3) which share 36% (VdTsr3) and 38% (SsTsr3) identity with the ScTsr3 core region (ScTsr3 aa 46–223).	RESULTS
92	115	Vulcanisaeta distributa	species	Well diffracting crystals were obtained for Tsr3 homologs from the two crenarchaeal species Vulcanisaeta distributa (VdTsr3) and Sulfolobus solfataricus (SsTsr3) which share 36% (VdTsr3) and 38% (SsTsr3) identity with the ScTsr3 core region (ScTsr3 aa 46–223).	RESULTS
117	123	VdTsr3	protein	Well diffracting crystals were obtained for Tsr3 homologs from the two crenarchaeal species Vulcanisaeta distributa (VdTsr3) and Sulfolobus solfataricus (SsTsr3) which share 36% (VdTsr3) and 38% (SsTsr3) identity with the ScTsr3 core region (ScTsr3 aa 46–223).	RESULTS
129	152	Sulfolobus solfataricus	species	Well diffracting crystals were obtained for Tsr3 homologs from the two crenarchaeal species Vulcanisaeta distributa (VdTsr3) and Sulfolobus solfataricus (SsTsr3) which share 36% (VdTsr3) and 38% (SsTsr3) identity with the ScTsr3 core region (ScTsr3 aa 46–223).	RESULTS
154	160	SsTsr3	protein	Well diffracting crystals were obtained for Tsr3 homologs from the two crenarchaeal species Vulcanisaeta distributa (VdTsr3) and Sulfolobus solfataricus (SsTsr3) which share 36% (VdTsr3) and 38% (SsTsr3) identity with the ScTsr3 core region (ScTsr3 aa 46–223).	RESULTS
179	185	VdTsr3	protein	Well diffracting crystals were obtained for Tsr3 homologs from the two crenarchaeal species Vulcanisaeta distributa (VdTsr3) and Sulfolobus solfataricus (SsTsr3) which share 36% (VdTsr3) and 38% (SsTsr3) identity with the ScTsr3 core region (ScTsr3 aa 46–223).	RESULTS
196	202	SsTsr3	protein	Well diffracting crystals were obtained for Tsr3 homologs from the two crenarchaeal species Vulcanisaeta distributa (VdTsr3) and Sulfolobus solfataricus (SsTsr3) which share 36% (VdTsr3) and 38% (SsTsr3) identity with the ScTsr3 core region (ScTsr3 aa 46–223).	RESULTS
222	228	ScTsr3	protein	Well diffracting crystals were obtained for Tsr3 homologs from the two crenarchaeal species Vulcanisaeta distributa (VdTsr3) and Sulfolobus solfataricus (SsTsr3) which share 36% (VdTsr3) and 38% (SsTsr3) identity with the ScTsr3 core region (ScTsr3 aa 46–223).	RESULTS
229	240	core region	structure_element	Well diffracting crystals were obtained for Tsr3 homologs from the two crenarchaeal species Vulcanisaeta distributa (VdTsr3) and Sulfolobus solfataricus (SsTsr3) which share 36% (VdTsr3) and 38% (SsTsr3) identity with the ScTsr3 core region (ScTsr3 aa 46–223).	RESULTS
242	248	ScTsr3	protein	Well diffracting crystals were obtained for Tsr3 homologs from the two crenarchaeal species Vulcanisaeta distributa (VdTsr3) and Sulfolobus solfataricus (SsTsr3) which share 36% (VdTsr3) and 38% (SsTsr3) identity with the ScTsr3 core region (ScTsr3 aa 46–223).	RESULTS
252	258	46–223	residue_range	Well diffracting crystals were obtained for Tsr3 homologs from the two crenarchaeal species Vulcanisaeta distributa (VdTsr3) and Sulfolobus solfataricus (SsTsr3) which share 36% (VdTsr3) and 38% (SsTsr3) identity with the ScTsr3 core region (ScTsr3 aa 46–223).	RESULTS
10	25	S. solfataricus	species	While for S. solfataricus the existence of a modified nucleotide of unknown chemical composition in the loop capping helix 31 of its 16S rRNA has been demonstrated, no information regarding rRNA modifications is yet available for V. distributa.	RESULTS
54	64	nucleotide	chemical	While for S. solfataricus the existence of a modified nucleotide of unknown chemical composition in the loop capping helix 31 of its 16S rRNA has been demonstrated, no information regarding rRNA modifications is yet available for V. distributa.	RESULTS
104	125	loop capping helix 31	structure_element	While for S. solfataricus the existence of a modified nucleotide of unknown chemical composition in the loop capping helix 31 of its 16S rRNA has been demonstrated, no information regarding rRNA modifications is yet available for V. distributa.	RESULTS
133	141	16S rRNA	chemical	While for S. solfataricus the existence of a modified nucleotide of unknown chemical composition in the loop capping helix 31 of its 16S rRNA has been demonstrated, no information regarding rRNA modifications is yet available for V. distributa.	RESULTS
230	243	V. distributa	species	While for S. solfataricus the existence of a modified nucleotide of unknown chemical composition in the loop capping helix 31 of its 16S rRNA has been demonstrated, no information regarding rRNA modifications is yet available for V. distributa.	RESULTS
0	8	Crystals	evidence	Crystals of VdTsr3 diffracted to a resolution of 1.6 Å whereas crystals of SsTsr3 diffracted to 2.25 Å. Serendipitously, VdTsr3 was purified and crystallized in complex with endogenous (E. coli) SAM (Supplementary Figure S4) while SsTsr3 crystals contained the protein in the apo state.	RESULTS
12	18	VdTsr3	protein	Crystals of VdTsr3 diffracted to a resolution of 1.6 Å whereas crystals of SsTsr3 diffracted to 2.25 Å. Serendipitously, VdTsr3 was purified and crystallized in complex with endogenous (E. coli) SAM (Supplementary Figure S4) while SsTsr3 crystals contained the protein in the apo state.	RESULTS
63	71	crystals	evidence	Crystals of VdTsr3 diffracted to a resolution of 1.6 Å whereas crystals of SsTsr3 diffracted to 2.25 Å. Serendipitously, VdTsr3 was purified and crystallized in complex with endogenous (E. coli) SAM (Supplementary Figure S4) while SsTsr3 crystals contained the protein in the apo state.	RESULTS
75	81	SsTsr3	protein	Crystals of VdTsr3 diffracted to a resolution of 1.6 Å whereas crystals of SsTsr3 diffracted to 2.25 Å. Serendipitously, VdTsr3 was purified and crystallized in complex with endogenous (E. coli) SAM (Supplementary Figure S4) while SsTsr3 crystals contained the protein in the apo state.	RESULTS
121	127	VdTsr3	protein	Crystals of VdTsr3 diffracted to a resolution of 1.6 Å whereas crystals of SsTsr3 diffracted to 2.25 Å. Serendipitously, VdTsr3 was purified and crystallized in complex with endogenous (E. coli) SAM (Supplementary Figure S4) while SsTsr3 crystals contained the protein in the apo state.	RESULTS
145	157	crystallized	experimental_method	Crystals of VdTsr3 diffracted to a resolution of 1.6 Å whereas crystals of SsTsr3 diffracted to 2.25 Å. Serendipitously, VdTsr3 was purified and crystallized in complex with endogenous (E. coli) SAM (Supplementary Figure S4) while SsTsr3 crystals contained the protein in the apo state.	RESULTS
158	173	in complex with	protein_state	Crystals of VdTsr3 diffracted to a resolution of 1.6 Å whereas crystals of SsTsr3 diffracted to 2.25 Å. Serendipitously, VdTsr3 was purified and crystallized in complex with endogenous (E. coli) SAM (Supplementary Figure S4) while SsTsr3 crystals contained the protein in the apo state.	RESULTS
174	184	endogenous	protein_state	Crystals of VdTsr3 diffracted to a resolution of 1.6 Å whereas crystals of SsTsr3 diffracted to 2.25 Å. Serendipitously, VdTsr3 was purified and crystallized in complex with endogenous (E. coli) SAM (Supplementary Figure S4) while SsTsr3 crystals contained the protein in the apo state.	RESULTS
186	193	E. coli	species	Crystals of VdTsr3 diffracted to a resolution of 1.6 Å whereas crystals of SsTsr3 diffracted to 2.25 Å. Serendipitously, VdTsr3 was purified and crystallized in complex with endogenous (E. coli) SAM (Supplementary Figure S4) while SsTsr3 crystals contained the protein in the apo state.	RESULTS
195	198	SAM	chemical	Crystals of VdTsr3 diffracted to a resolution of 1.6 Å whereas crystals of SsTsr3 diffracted to 2.25 Å. Serendipitously, VdTsr3 was purified and crystallized in complex with endogenous (E. coli) SAM (Supplementary Figure S4) while SsTsr3 crystals contained the protein in the apo state.	RESULTS
231	237	SsTsr3	protein	Crystals of VdTsr3 diffracted to a resolution of 1.6 Å whereas crystals of SsTsr3 diffracted to 2.25 Å. Serendipitously, VdTsr3 was purified and crystallized in complex with endogenous (E. coli) SAM (Supplementary Figure S4) while SsTsr3 crystals contained the protein in the apo state.	RESULTS
238	246	crystals	evidence	Crystals of VdTsr3 diffracted to a resolution of 1.6 Å whereas crystals of SsTsr3 diffracted to 2.25 Å. Serendipitously, VdTsr3 was purified and crystallized in complex with endogenous (E. coli) SAM (Supplementary Figure S4) while SsTsr3 crystals contained the protein in the apo state.	RESULTS
276	279	apo	protein_state	Crystals of VdTsr3 diffracted to a resolution of 1.6 Å whereas crystals of SsTsr3 diffracted to 2.25 Å. Serendipitously, VdTsr3 was purified and crystallized in complex with endogenous (E. coli) SAM (Supplementary Figure S4) while SsTsr3 crystals contained the protein in the apo state.	RESULTS
4	13	structure	evidence	The structure of VdTsr3 was solved ab initio, by single-wavelength anomalous diffraction phasing (Se-SAD) with Se containing derivatives (selenomethionine and seleno-substituted SAM).	RESULTS
17	23	VdTsr3	protein	The structure of VdTsr3 was solved ab initio, by single-wavelength anomalous diffraction phasing (Se-SAD) with Se containing derivatives (selenomethionine and seleno-substituted SAM).	RESULTS
49	96	single-wavelength anomalous diffraction phasing	experimental_method	The structure of VdTsr3 was solved ab initio, by single-wavelength anomalous diffraction phasing (Se-SAD) with Se containing derivatives (selenomethionine and seleno-substituted SAM).	RESULTS
98	104	Se-SAD	experimental_method	The structure of VdTsr3 was solved ab initio, by single-wavelength anomalous diffraction phasing (Se-SAD) with Se containing derivatives (selenomethionine and seleno-substituted SAM).	RESULTS
111	113	Se	chemical	The structure of VdTsr3 was solved ab initio, by single-wavelength anomalous diffraction phasing (Se-SAD) with Se containing derivatives (selenomethionine and seleno-substituted SAM).	RESULTS
138	154	selenomethionine	chemical	The structure of VdTsr3 was solved ab initio, by single-wavelength anomalous diffraction phasing (Se-SAD) with Se containing derivatives (selenomethionine and seleno-substituted SAM).	RESULTS
159	181	seleno-substituted SAM	chemical	The structure of VdTsr3 was solved ab initio, by single-wavelength anomalous diffraction phasing (Se-SAD) with Se containing derivatives (selenomethionine and seleno-substituted SAM).	RESULTS
4	13	structure	evidence	The structure of SsTsr3 was solved by molecular replacement using VdTsr3 as a search model (see Supplementary Table S1 for data collection and refinement statistics).	RESULTS
17	23	SsTsr3	protein	The structure of SsTsr3 was solved by molecular replacement using VdTsr3 as a search model (see Supplementary Table S1 for data collection and refinement statistics).	RESULTS
38	59	molecular replacement	experimental_method	The structure of SsTsr3 was solved by molecular replacement using VdTsr3 as a search model (see Supplementary Table S1 for data collection and refinement statistics).	RESULTS
66	72	VdTsr3	protein	The structure of SsTsr3 was solved by molecular replacement using VdTsr3 as a search model (see Supplementary Table S1 for data collection and refinement statistics).	RESULTS
4	13	structure	evidence	The structure of VdTsr3 can be divided into two domains (Figure 4A).	RESULTS
17	23	VdTsr3	protein	The structure of VdTsr3 can be divided into two domains (Figure 4A).	RESULTS
4	21	N-terminal domain	structure_element	The N-terminal domain (aa 1–92) has a mixed α/β-structure centered around a five-stranded all-parallel β-sheet (Figure 4B) with the strand order β5↑-β3↑-β4↑-β1↑-β2↑. The loops connecting β1 and β2, β3 and β4 and β4 and β5 include α-helices α1, α2 and α3, respectively.	RESULTS
26	30	1–92	residue_range	The N-terminal domain (aa 1–92) has a mixed α/β-structure centered around a five-stranded all-parallel β-sheet (Figure 4B) with the strand order β5↑-β3↑-β4↑-β1↑-β2↑. The loops connecting β1 and β2, β3 and β4 and β4 and β5 include α-helices α1, α2 and α3, respectively.	RESULTS
44	57	α/β-structure	structure_element	The N-terminal domain (aa 1–92) has a mixed α/β-structure centered around a five-stranded all-parallel β-sheet (Figure 4B) with the strand order β5↑-β3↑-β4↑-β1↑-β2↑. The loops connecting β1 and β2, β3 and β4 and β4 and β5 include α-helices α1, α2 and α3, respectively.	RESULTS
76	110	five-stranded all-parallel β-sheet	structure_element	The N-terminal domain (aa 1–92) has a mixed α/β-structure centered around a five-stranded all-parallel β-sheet (Figure 4B) with the strand order β5↑-β3↑-β4↑-β1↑-β2↑. The loops connecting β1 and β2, β3 and β4 and β4 and β5 include α-helices α1, α2 and α3, respectively.	RESULTS
145	148	β5↑	structure_element	The N-terminal domain (aa 1–92) has a mixed α/β-structure centered around a five-stranded all-parallel β-sheet (Figure 4B) with the strand order β5↑-β3↑-β4↑-β1↑-β2↑. The loops connecting β1 and β2, β3 and β4 and β4 and β5 include α-helices α1, α2 and α3, respectively.	RESULTS
149	152	β3↑	structure_element	The N-terminal domain (aa 1–92) has a mixed α/β-structure centered around a five-stranded all-parallel β-sheet (Figure 4B) with the strand order β5↑-β3↑-β4↑-β1↑-β2↑. The loops connecting β1 and β2, β3 and β4 and β4 and β5 include α-helices α1, α2 and α3, respectively.	RESULTS
153	156	β4↑	structure_element	The N-terminal domain (aa 1–92) has a mixed α/β-structure centered around a five-stranded all-parallel β-sheet (Figure 4B) with the strand order β5↑-β3↑-β4↑-β1↑-β2↑. The loops connecting β1 and β2, β3 and β4 and β4 and β5 include α-helices α1, α2 and α3, respectively.	RESULTS
157	160	β1↑	structure_element	The N-terminal domain (aa 1–92) has a mixed α/β-structure centered around a five-stranded all-parallel β-sheet (Figure 4B) with the strand order β5↑-β3↑-β4↑-β1↑-β2↑. The loops connecting β1 and β2, β3 and β4 and β4 and β5 include α-helices α1, α2 and α3, respectively.	RESULTS
161	164	β2↑	structure_element	The N-terminal domain (aa 1–92) has a mixed α/β-structure centered around a five-stranded all-parallel β-sheet (Figure 4B) with the strand order β5↑-β3↑-β4↑-β1↑-β2↑. The loops connecting β1 and β2, β3 and β4 and β4 and β5 include α-helices α1, α2 and α3, respectively.	RESULTS
170	175	loops	structure_element	The N-terminal domain (aa 1–92) has a mixed α/β-structure centered around a five-stranded all-parallel β-sheet (Figure 4B) with the strand order β5↑-β3↑-β4↑-β1↑-β2↑. The loops connecting β1 and β2, β3 and β4 and β4 and β5 include α-helices α1, α2 and α3, respectively.	RESULTS
187	189	β1	structure_element	The N-terminal domain (aa 1–92) has a mixed α/β-structure centered around a five-stranded all-parallel β-sheet (Figure 4B) with the strand order β5↑-β3↑-β4↑-β1↑-β2↑. The loops connecting β1 and β2, β3 and β4 and β4 and β5 include α-helices α1, α2 and α3, respectively.	RESULTS
194	196	β2	structure_element	The N-terminal domain (aa 1–92) has a mixed α/β-structure centered around a five-stranded all-parallel β-sheet (Figure 4B) with the strand order β5↑-β3↑-β4↑-β1↑-β2↑. The loops connecting β1 and β2, β3 and β4 and β4 and β5 include α-helices α1, α2 and α3, respectively.	RESULTS
198	200	β3	structure_element	The N-terminal domain (aa 1–92) has a mixed α/β-structure centered around a five-stranded all-parallel β-sheet (Figure 4B) with the strand order β5↑-β3↑-β4↑-β1↑-β2↑. The loops connecting β1 and β2, β3 and β4 and β4 and β5 include α-helices α1, α2 and α3, respectively.	RESULTS
205	207	β4	structure_element	The N-terminal domain (aa 1–92) has a mixed α/β-structure centered around a five-stranded all-parallel β-sheet (Figure 4B) with the strand order β5↑-β3↑-β4↑-β1↑-β2↑. The loops connecting β1 and β2, β3 and β4 and β4 and β5 include α-helices α1, α2 and α3, respectively.	RESULTS
212	214	β4	structure_element	The N-terminal domain (aa 1–92) has a mixed α/β-structure centered around a five-stranded all-parallel β-sheet (Figure 4B) with the strand order β5↑-β3↑-β4↑-β1↑-β2↑. The loops connecting β1 and β2, β3 and β4 and β4 and β5 include α-helices α1, α2 and α3, respectively.	RESULTS
219	221	β5	structure_element	The N-terminal domain (aa 1–92) has a mixed α/β-structure centered around a five-stranded all-parallel β-sheet (Figure 4B) with the strand order β5↑-β3↑-β4↑-β1↑-β2↑. The loops connecting β1 and β2, β3 and β4 and β4 and β5 include α-helices α1, α2 and α3, respectively.	RESULTS
230	239	α-helices	structure_element	The N-terminal domain (aa 1–92) has a mixed α/β-structure centered around a five-stranded all-parallel β-sheet (Figure 4B) with the strand order β5↑-β3↑-β4↑-β1↑-β2↑. The loops connecting β1 and β2, β3 and β4 and β4 and β5 include α-helices α1, α2 and α3, respectively.	RESULTS
240	242	α1	structure_element	The N-terminal domain (aa 1–92) has a mixed α/β-structure centered around a five-stranded all-parallel β-sheet (Figure 4B) with the strand order β5↑-β3↑-β4↑-β1↑-β2↑. The loops connecting β1 and β2, β3 and β4 and β4 and β5 include α-helices α1, α2 and α3, respectively.	RESULTS
244	246	α2	structure_element	The N-terminal domain (aa 1–92) has a mixed α/β-structure centered around a five-stranded all-parallel β-sheet (Figure 4B) with the strand order β5↑-β3↑-β4↑-β1↑-β2↑. The loops connecting β1 and β2, β3 and β4 and β4 and β5 include α-helices α1, α2 and α3, respectively.	RESULTS
251	253	α3	structure_element	The N-terminal domain (aa 1–92) has a mixed α/β-structure centered around a five-stranded all-parallel β-sheet (Figure 4B) with the strand order β5↑-β3↑-β4↑-β1↑-β2↑. The loops connecting β1 and β2, β3 and β4 and β4 and β5 include α-helices α1, α2 and α3, respectively.	RESULTS
4	8	loop	structure_element	The loop connecting β2 and β3 contains a single turn of a 310-helix. Helices α1 and α2 are located on one side of the five-stranded β-sheet while α3 packs against the opposite β-sheet surface.	RESULTS
20	22	β2	structure_element	The loop connecting β2 and β3 contains a single turn of a 310-helix. Helices α1 and α2 are located on one side of the five-stranded β-sheet while α3 packs against the opposite β-sheet surface.	RESULTS
27	29	β3	structure_element	The loop connecting β2 and β3 contains a single turn of a 310-helix. Helices α1 and α2 are located on one side of the five-stranded β-sheet while α3 packs against the opposite β-sheet surface.	RESULTS
58	67	310-helix	structure_element	The loop connecting β2 and β3 contains a single turn of a 310-helix. Helices α1 and α2 are located on one side of the five-stranded β-sheet while α3 packs against the opposite β-sheet surface.	RESULTS
69	76	Helices	structure_element	The loop connecting β2 and β3 contains a single turn of a 310-helix. Helices α1 and α2 are located on one side of the five-stranded β-sheet while α3 packs against the opposite β-sheet surface.	RESULTS
77	79	α1	structure_element	The loop connecting β2 and β3 contains a single turn of a 310-helix. Helices α1 and α2 are located on one side of the five-stranded β-sheet while α3 packs against the opposite β-sheet surface.	RESULTS
84	86	α2	structure_element	The loop connecting β2 and β3 contains a single turn of a 310-helix. Helices α1 and α2 are located on one side of the five-stranded β-sheet while α3 packs against the opposite β-sheet surface.	RESULTS
118	139	five-stranded β-sheet	structure_element	The loop connecting β2 and β3 contains a single turn of a 310-helix. Helices α1 and α2 are located on one side of the five-stranded β-sheet while α3 packs against the opposite β-sheet surface.	RESULTS
146	148	α3	structure_element	The loop connecting β2 and β3 contains a single turn of a 310-helix. Helices α1 and α2 are located on one side of the five-stranded β-sheet while α3 packs against the opposite β-sheet surface.	RESULTS
176	183	β-sheet	structure_element	The loop connecting β2 and β3 contains a single turn of a 310-helix. Helices α1 and α2 are located on one side of the five-stranded β-sheet while α3 packs against the opposite β-sheet surface.	RESULTS
4	21	C-terminal domain	structure_element	The C-terminal domain (aa 93–184) has a globular all α-helical structure comprising α-helices α4 to α9.	RESULTS
26	32	93–184	residue_range	The C-terminal domain (aa 93–184) has a globular all α-helical structure comprising α-helices α4 to α9.	RESULTS
40	72	globular all α-helical structure	structure_element	The C-terminal domain (aa 93–184) has a globular all α-helical structure comprising α-helices α4 to α9.	RESULTS
84	93	α-helices	structure_element	The C-terminal domain (aa 93–184) has a globular all α-helical structure comprising α-helices α4 to α9.	RESULTS
94	102	α4 to α9	structure_element	The C-terminal domain (aa 93–184) has a globular all α-helical structure comprising α-helices α4 to α9.	RESULTS
23	40	C-terminal domain	structure_element	Remarkably, the entire C-terminal domain (92 aa) of the protein is threaded through the loop which connects β-strand β3 and α-helix α2 of the N-terminal domain.	RESULTS
42	47	92 aa	residue_range	Remarkably, the entire C-terminal domain (92 aa) of the protein is threaded through the loop which connects β-strand β3 and α-helix α2 of the N-terminal domain.	RESULTS
88	92	loop	structure_element	Remarkably, the entire C-terminal domain (92 aa) of the protein is threaded through the loop which connects β-strand β3 and α-helix α2 of the N-terminal domain.	RESULTS
108	116	β-strand	structure_element	Remarkably, the entire C-terminal domain (92 aa) of the protein is threaded through the loop which connects β-strand β3 and α-helix α2 of the N-terminal domain.	RESULTS
117	119	β3	structure_element	Remarkably, the entire C-terminal domain (92 aa) of the protein is threaded through the loop which connects β-strand β3 and α-helix α2 of the N-terminal domain.	RESULTS
124	131	α-helix	structure_element	Remarkably, the entire C-terminal domain (92 aa) of the protein is threaded through the loop which connects β-strand β3 and α-helix α2 of the N-terminal domain.	RESULTS
132	134	α2	structure_element	Remarkably, the entire C-terminal domain (92 aa) of the protein is threaded through the loop which connects β-strand β3 and α-helix α2 of the N-terminal domain.	RESULTS
142	159	N-terminal domain	structure_element	Remarkably, the entire C-terminal domain (92 aa) of the protein is threaded through the loop which connects β-strand β3 and α-helix α2 of the N-terminal domain.	RESULTS
10	16	VdTsr3	protein	Thus, the VdTsr3 structure contains a deep trefoil knot.	RESULTS
17	26	structure	evidence	Thus, the VdTsr3 structure contains a deep trefoil knot.	RESULTS
38	55	deep trefoil knot	structure_element	Thus, the VdTsr3 structure contains a deep trefoil knot.	RESULTS
4	13	structure	evidence	The structure of SsTsr3 in the apo state is very similar to that of VdTsr3 (Figure 4C) with an RMSD for equivalent Cα atoms of 1.1 Å. The only significant difference in the global structure of the two proteins is the presence of an extended α-helix α8 and the absence of α-helix α9 in SsTsr3.	RESULTS
17	23	SsTsr3	protein	The structure of SsTsr3 in the apo state is very similar to that of VdTsr3 (Figure 4C) with an RMSD for equivalent Cα atoms of 1.1 Å. The only significant difference in the global structure of the two proteins is the presence of an extended α-helix α8 and the absence of α-helix α9 in SsTsr3.	RESULTS
31	34	apo	protein_state	The structure of SsTsr3 in the apo state is very similar to that of VdTsr3 (Figure 4C) with an RMSD for equivalent Cα atoms of 1.1 Å. The only significant difference in the global structure of the two proteins is the presence of an extended α-helix α8 and the absence of α-helix α9 in SsTsr3.	RESULTS
68	74	VdTsr3	protein	The structure of SsTsr3 in the apo state is very similar to that of VdTsr3 (Figure 4C) with an RMSD for equivalent Cα atoms of 1.1 Å. The only significant difference in the global structure of the two proteins is the presence of an extended α-helix α8 and the absence of α-helix α9 in SsTsr3.	RESULTS
95	99	RMSD	evidence	The structure of SsTsr3 in the apo state is very similar to that of VdTsr3 (Figure 4C) with an RMSD for equivalent Cα atoms of 1.1 Å. The only significant difference in the global structure of the two proteins is the presence of an extended α-helix α8 and the absence of α-helix α9 in SsTsr3.	RESULTS
180	189	structure	evidence	The structure of SsTsr3 in the apo state is very similar to that of VdTsr3 (Figure 4C) with an RMSD for equivalent Cα atoms of 1.1 Å. The only significant difference in the global structure of the two proteins is the presence of an extended α-helix α8 and the absence of α-helix α9 in SsTsr3.	RESULTS
241	248	α-helix	structure_element	The structure of SsTsr3 in the apo state is very similar to that of VdTsr3 (Figure 4C) with an RMSD for equivalent Cα atoms of 1.1 Å. The only significant difference in the global structure of the two proteins is the presence of an extended α-helix α8 and the absence of α-helix α9 in SsTsr3.	RESULTS
249	251	α8	structure_element	The structure of SsTsr3 in the apo state is very similar to that of VdTsr3 (Figure 4C) with an RMSD for equivalent Cα atoms of 1.1 Å. The only significant difference in the global structure of the two proteins is the presence of an extended α-helix α8 and the absence of α-helix α9 in SsTsr3.	RESULTS
260	270	absence of	protein_state	The structure of SsTsr3 in the apo state is very similar to that of VdTsr3 (Figure 4C) with an RMSD for equivalent Cα atoms of 1.1 Å. The only significant difference in the global structure of the two proteins is the presence of an extended α-helix α8 and the absence of α-helix α9 in SsTsr3.	RESULTS
271	278	α-helix	structure_element	The structure of SsTsr3 in the apo state is very similar to that of VdTsr3 (Figure 4C) with an RMSD for equivalent Cα atoms of 1.1 Å. The only significant difference in the global structure of the two proteins is the presence of an extended α-helix α8 and the absence of α-helix α9 in SsTsr3.	RESULTS
279	281	α9	structure_element	The structure of SsTsr3 in the apo state is very similar to that of VdTsr3 (Figure 4C) with an RMSD for equivalent Cα atoms of 1.1 Å. The only significant difference in the global structure of the two proteins is the presence of an extended α-helix α8 and the absence of α-helix α9 in SsTsr3.	RESULTS
285	291	SsTsr3	protein	The structure of SsTsr3 in the apo state is very similar to that of VdTsr3 (Figure 4C) with an RMSD for equivalent Cα atoms of 1.1 Å. The only significant difference in the global structure of the two proteins is the presence of an extended α-helix α8 and the absence of α-helix α9 in SsTsr3.	RESULTS
0	4	Tsr3	protein	Tsr3 has a fold similar to SPOUT-class RNA methyltransferases. (A) Cartoon representation of the X-ray structure of VdTsr3 in two orientations.	FIG
27	61	SPOUT-class RNA methyltransferases	protein_type	Tsr3 has a fold similar to SPOUT-class RNA methyltransferases. (A) Cartoon representation of the X-ray structure of VdTsr3 in two orientations.	FIG
97	112	X-ray structure	evidence	Tsr3 has a fold similar to SPOUT-class RNA methyltransferases. (A) Cartoon representation of the X-ray structure of VdTsr3 in two orientations.	FIG
116	122	VdTsr3	protein	Tsr3 has a fold similar to SPOUT-class RNA methyltransferases. (A) Cartoon representation of the X-ray structure of VdTsr3 in two orientations.	FIG
0	9	β-strands	structure_element	β-strands are colored in crimson whereas α-helices in the N-terminal domain are colored light blue and α-helices in the C-terminal domain are colored dark blue.	FIG
41	50	α-helices	structure_element	β-strands are colored in crimson whereas α-helices in the N-terminal domain are colored light blue and α-helices in the C-terminal domain are colored dark blue.	FIG
58	75	N-terminal domain	structure_element	β-strands are colored in crimson whereas α-helices in the N-terminal domain are colored light blue and α-helices in the C-terminal domain are colored dark blue.	FIG
103	112	α-helices	structure_element	β-strands are colored in crimson whereas α-helices in the N-terminal domain are colored light blue and α-helices in the C-terminal domain are colored dark blue.	FIG
120	137	C-terminal domain	structure_element	β-strands are colored in crimson whereas α-helices in the N-terminal domain are colored light blue and α-helices in the C-terminal domain are colored dark blue.	FIG
10	30	S-adenosylmethionine	chemical	The bound S-adenosylmethionine is shown in a stick representation and colored by atom type.	FIG
38	54	topological knot	structure_element	A red arrow marks the location of the topological knot in the structure. (B) Secondary structure representation of the VdTsr3 structure.	FIG
62	71	structure	evidence	A red arrow marks the location of the topological knot in the structure. (B) Secondary structure representation of the VdTsr3 structure.	FIG
119	125	VdTsr3	protein	A red arrow marks the location of the topological knot in the structure. (B) Secondary structure representation of the VdTsr3 structure.	FIG
126	135	structure	evidence	A red arrow marks the location of the topological knot in the structure. (B) Secondary structure representation of the VdTsr3 structure.	FIG
44	68	Structural superposition	experimental_method	The color coding is the same as in (A). (C) Structural superposition of the X-ray structures of VdTsr3 in the SAM-bound state (red) and SsTsr3 (blue) in the apo state.	FIG
76	92	X-ray structures	evidence	The color coding is the same as in (A). (C) Structural superposition of the X-ray structures of VdTsr3 in the SAM-bound state (red) and SsTsr3 (blue) in the apo state.	FIG
96	102	VdTsr3	protein	The color coding is the same as in (A). (C) Structural superposition of the X-ray structures of VdTsr3 in the SAM-bound state (red) and SsTsr3 (blue) in the apo state.	FIG
110	119	SAM-bound	protein_state	The color coding is the same as in (A). (C) Structural superposition of the X-ray structures of VdTsr3 in the SAM-bound state (red) and SsTsr3 (blue) in the apo state.	FIG
136	142	SsTsr3	protein	The color coding is the same as in (A). (C) Structural superposition of the X-ray structures of VdTsr3 in the SAM-bound state (red) and SsTsr3 (blue) in the apo state.	FIG
157	160	apo	protein_state	The color coding is the same as in (A). (C) Structural superposition of the X-ray structures of VdTsr3 in the SAM-bound state (red) and SsTsr3 (blue) in the apo state.	FIG
21	28	α-helix	structure_element	The locations of the α-helix α8 which is longer in SsTsr3 and of α-helix α9 which is only present in VdTsr3 are indicated. (D) Secondary structure cartoon (left) of S. pombe Trm10 (pdb4jwf)—the SPOUT-class RNA methyltransferase structurally most similar to Tsr3 and superposition of the VdTsr3 and Trm10 X-ray structures (right). (E) Analytical gel filtration profiles for VdTsr3 (red) and SsTsr3 (blue) show that both proteins are monomeric in solution.	FIG
29	31	α8	structure_element	The locations of the α-helix α8 which is longer in SsTsr3 and of α-helix α9 which is only present in VdTsr3 are indicated. (D) Secondary structure cartoon (left) of S. pombe Trm10 (pdb4jwf)—the SPOUT-class RNA methyltransferase structurally most similar to Tsr3 and superposition of the VdTsr3 and Trm10 X-ray structures (right). (E) Analytical gel filtration profiles for VdTsr3 (red) and SsTsr3 (blue) show that both proteins are monomeric in solution.	FIG
51	57	SsTsr3	protein	The locations of the α-helix α8 which is longer in SsTsr3 and of α-helix α9 which is only present in VdTsr3 are indicated. (D) Secondary structure cartoon (left) of S. pombe Trm10 (pdb4jwf)—the SPOUT-class RNA methyltransferase structurally most similar to Tsr3 and superposition of the VdTsr3 and Trm10 X-ray structures (right). (E) Analytical gel filtration profiles for VdTsr3 (red) and SsTsr3 (blue) show that both proteins are monomeric in solution.	FIG
65	72	α-helix	structure_element	The locations of the α-helix α8 which is longer in SsTsr3 and of α-helix α9 which is only present in VdTsr3 are indicated. (D) Secondary structure cartoon (left) of S. pombe Trm10 (pdb4jwf)—the SPOUT-class RNA methyltransferase structurally most similar to Tsr3 and superposition of the VdTsr3 and Trm10 X-ray structures (right). (E) Analytical gel filtration profiles for VdTsr3 (red) and SsTsr3 (blue) show that both proteins are monomeric in solution.	FIG
73	75	α9	structure_element	The locations of the α-helix α8 which is longer in SsTsr3 and of α-helix α9 which is only present in VdTsr3 are indicated. (D) Secondary structure cartoon (left) of S. pombe Trm10 (pdb4jwf)—the SPOUT-class RNA methyltransferase structurally most similar to Tsr3 and superposition of the VdTsr3 and Trm10 X-ray structures (right). (E) Analytical gel filtration profiles for VdTsr3 (red) and SsTsr3 (blue) show that both proteins are monomeric in solution.	FIG
101	107	VdTsr3	protein	The locations of the α-helix α8 which is longer in SsTsr3 and of α-helix α9 which is only present in VdTsr3 are indicated. (D) Secondary structure cartoon (left) of S. pombe Trm10 (pdb4jwf)—the SPOUT-class RNA methyltransferase structurally most similar to Tsr3 and superposition of the VdTsr3 and Trm10 X-ray structures (right). (E) Analytical gel filtration profiles for VdTsr3 (red) and SsTsr3 (blue) show that both proteins are monomeric in solution.	FIG
165	173	S. pombe	species	The locations of the α-helix α8 which is longer in SsTsr3 and of α-helix α9 which is only present in VdTsr3 are indicated. (D) Secondary structure cartoon (left) of S. pombe Trm10 (pdb4jwf)—the SPOUT-class RNA methyltransferase structurally most similar to Tsr3 and superposition of the VdTsr3 and Trm10 X-ray structures (right). (E) Analytical gel filtration profiles for VdTsr3 (red) and SsTsr3 (blue) show that both proteins are monomeric in solution.	FIG
174	179	Trm10	protein	The locations of the α-helix α8 which is longer in SsTsr3 and of α-helix α9 which is only present in VdTsr3 are indicated. (D) Secondary structure cartoon (left) of S. pombe Trm10 (pdb4jwf)—the SPOUT-class RNA methyltransferase structurally most similar to Tsr3 and superposition of the VdTsr3 and Trm10 X-ray structures (right). (E) Analytical gel filtration profiles for VdTsr3 (red) and SsTsr3 (blue) show that both proteins are monomeric in solution.	FIG
194	227	SPOUT-class RNA methyltransferase	protein_type	The locations of the α-helix α8 which is longer in SsTsr3 and of α-helix α9 which is only present in VdTsr3 are indicated. (D) Secondary structure cartoon (left) of S. pombe Trm10 (pdb4jwf)—the SPOUT-class RNA methyltransferase structurally most similar to Tsr3 and superposition of the VdTsr3 and Trm10 X-ray structures (right). (E) Analytical gel filtration profiles for VdTsr3 (red) and SsTsr3 (blue) show that both proteins are monomeric in solution.	FIG
257	261	Tsr3	protein	The locations of the α-helix α8 which is longer in SsTsr3 and of α-helix α9 which is only present in VdTsr3 are indicated. (D) Secondary structure cartoon (left) of S. pombe Trm10 (pdb4jwf)—the SPOUT-class RNA methyltransferase structurally most similar to Tsr3 and superposition of the VdTsr3 and Trm10 X-ray structures (right). (E) Analytical gel filtration profiles for VdTsr3 (red) and SsTsr3 (blue) show that both proteins are monomeric in solution.	FIG
266	279	superposition	experimental_method	The locations of the α-helix α8 which is longer in SsTsr3 and of α-helix α9 which is only present in VdTsr3 are indicated. (D) Secondary structure cartoon (left) of S. pombe Trm10 (pdb4jwf)—the SPOUT-class RNA methyltransferase structurally most similar to Tsr3 and superposition of the VdTsr3 and Trm10 X-ray structures (right). (E) Analytical gel filtration profiles for VdTsr3 (red) and SsTsr3 (blue) show that both proteins are monomeric in solution.	FIG
287	293	VdTsr3	protein	The locations of the α-helix α8 which is longer in SsTsr3 and of α-helix α9 which is only present in VdTsr3 are indicated. (D) Secondary structure cartoon (left) of S. pombe Trm10 (pdb4jwf)—the SPOUT-class RNA methyltransferase structurally most similar to Tsr3 and superposition of the VdTsr3 and Trm10 X-ray structures (right). (E) Analytical gel filtration profiles for VdTsr3 (red) and SsTsr3 (blue) show that both proteins are monomeric in solution.	FIG
298	303	Trm10	protein	The locations of the α-helix α8 which is longer in SsTsr3 and of α-helix α9 which is only present in VdTsr3 are indicated. (D) Secondary structure cartoon (left) of S. pombe Trm10 (pdb4jwf)—the SPOUT-class RNA methyltransferase structurally most similar to Tsr3 and superposition of the VdTsr3 and Trm10 X-ray structures (right). (E) Analytical gel filtration profiles for VdTsr3 (red) and SsTsr3 (blue) show that both proteins are monomeric in solution.	FIG
304	320	X-ray structures	evidence	The locations of the α-helix α8 which is longer in SsTsr3 and of α-helix α9 which is only present in VdTsr3 are indicated. (D) Secondary structure cartoon (left) of S. pombe Trm10 (pdb4jwf)—the SPOUT-class RNA methyltransferase structurally most similar to Tsr3 and superposition of the VdTsr3 and Trm10 X-ray structures (right). (E) Analytical gel filtration profiles for VdTsr3 (red) and SsTsr3 (blue) show that both proteins are monomeric in solution.	FIG
334	359	Analytical gel filtration	experimental_method	The locations of the α-helix α8 which is longer in SsTsr3 and of α-helix α9 which is only present in VdTsr3 are indicated. (D) Secondary structure cartoon (left) of S. pombe Trm10 (pdb4jwf)—the SPOUT-class RNA methyltransferase structurally most similar to Tsr3 and superposition of the VdTsr3 and Trm10 X-ray structures (right). (E) Analytical gel filtration profiles for VdTsr3 (red) and SsTsr3 (blue) show that both proteins are monomeric in solution.	FIG
360	368	profiles	evidence	The locations of the α-helix α8 which is longer in SsTsr3 and of α-helix α9 which is only present in VdTsr3 are indicated. (D) Secondary structure cartoon (left) of S. pombe Trm10 (pdb4jwf)—the SPOUT-class RNA methyltransferase structurally most similar to Tsr3 and superposition of the VdTsr3 and Trm10 X-ray structures (right). (E) Analytical gel filtration profiles for VdTsr3 (red) and SsTsr3 (blue) show that both proteins are monomeric in solution.	FIG
373	379	VdTsr3	protein	The locations of the α-helix α8 which is longer in SsTsr3 and of α-helix α9 which is only present in VdTsr3 are indicated. (D) Secondary structure cartoon (left) of S. pombe Trm10 (pdb4jwf)—the SPOUT-class RNA methyltransferase structurally most similar to Tsr3 and superposition of the VdTsr3 and Trm10 X-ray structures (right). (E) Analytical gel filtration profiles for VdTsr3 (red) and SsTsr3 (blue) show that both proteins are monomeric in solution.	FIG
390	396	SsTsr3	protein	The locations of the α-helix α8 which is longer in SsTsr3 and of α-helix α9 which is only present in VdTsr3 are indicated. (D) Secondary structure cartoon (left) of S. pombe Trm10 (pdb4jwf)—the SPOUT-class RNA methyltransferase structurally most similar to Tsr3 and superposition of the VdTsr3 and Trm10 X-ray structures (right). (E) Analytical gel filtration profiles for VdTsr3 (red) and SsTsr3 (blue) show that both proteins are monomeric in solution.	FIG
432	441	monomeric	oligomeric_state	The locations of the α-helix α8 which is longer in SsTsr3 and of α-helix α9 which is only present in VdTsr3 are indicated. (D) Secondary structure cartoon (left) of S. pombe Trm10 (pdb4jwf)—the SPOUT-class RNA methyltransferase structurally most similar to Tsr3 and superposition of the VdTsr3 and Trm10 X-ray structures (right). (E) Analytical gel filtration profiles for VdTsr3 (red) and SsTsr3 (blue) show that both proteins are monomeric in solution.	FIG
0	2	Vd	species	Vd, Vulcanisaeta distributa; Ss, Sulfolobus solfataricus.	FIG
4	27	Vulcanisaeta distributa	species	Vd, Vulcanisaeta distributa; Ss, Sulfolobus solfataricus.	FIG
29	31	Ss	species	Vd, Vulcanisaeta distributa; Ss, Sulfolobus solfataricus.	FIG
33	56	Sulfolobus solfataricus	species	Vd, Vulcanisaeta distributa; Ss, Sulfolobus solfataricus.	FIG
0	21	Structure predictions	experimental_method	Structure predictions suggested that Tsr3 might contain a so-called RLI domain which contains a ‘bacterial like’ ferredoxin fold and binds two iron-sulfur clusters through eight conserved cysteine residues.	RESULTS
37	41	Tsr3	protein	Structure predictions suggested that Tsr3 might contain a so-called RLI domain which contains a ‘bacterial like’ ferredoxin fold and binds two iron-sulfur clusters through eight conserved cysteine residues.	RESULTS
68	78	RLI domain	structure_element	Structure predictions suggested that Tsr3 might contain a so-called RLI domain which contains a ‘bacterial like’ ferredoxin fold and binds two iron-sulfur clusters through eight conserved cysteine residues.	RESULTS
97	128	bacterial like’ ferredoxin fold	structure_element	Structure predictions suggested that Tsr3 might contain a so-called RLI domain which contains a ‘bacterial like’ ferredoxin fold and binds two iron-sulfur clusters through eight conserved cysteine residues.	RESULTS
178	187	conserved	protein_state	Structure predictions suggested that Tsr3 might contain a so-called RLI domain which contains a ‘bacterial like’ ferredoxin fold and binds two iron-sulfur clusters through eight conserved cysteine residues.	RESULTS
188	196	cysteine	residue_name	Structure predictions suggested that Tsr3 might contain a so-called RLI domain which contains a ‘bacterial like’ ferredoxin fold and binds two iron-sulfur clusters through eight conserved cysteine residues.	RESULTS
40	50	RLI-domain	structure_element	However, no structural similarity to an RLI-domain was detectable.	RESULTS
54	83	alanine replacement mutations	experimental_method	This is in accordance with the functional analysis of alanine replacement mutations of cysteine residues in ScTsr3 (Supplementary Figure S3).	RESULTS
87	95	cysteine	residue_name	This is in accordance with the functional analysis of alanine replacement mutations of cysteine residues in ScTsr3 (Supplementary Figure S3).	RESULTS
108	114	ScTsr3	protein	This is in accordance with the functional analysis of alanine replacement mutations of cysteine residues in ScTsr3 (Supplementary Figure S3).	RESULTS
4	21	β-strand topology	structure_element	The β-strand topology and the deep C-terminal trefoil knot of archaeal Tsr3 are the structural hallmarks of the SPOUT-class RNA-methyltransferase fold.	RESULTS
46	58	trefoil knot	structure_element	The β-strand topology and the deep C-terminal trefoil knot of archaeal Tsr3 are the structural hallmarks of the SPOUT-class RNA-methyltransferase fold.	RESULTS
62	70	archaeal	taxonomy_domain	The β-strand topology and the deep C-terminal trefoil knot of archaeal Tsr3 are the structural hallmarks of the SPOUT-class RNA-methyltransferase fold.	RESULTS
71	75	Tsr3	protein	The β-strand topology and the deep C-terminal trefoil knot of archaeal Tsr3 are the structural hallmarks of the SPOUT-class RNA-methyltransferase fold.	RESULTS
112	145	SPOUT-class RNA-methyltransferase	protein_type	The β-strand topology and the deep C-terminal trefoil knot of archaeal Tsr3 are the structural hallmarks of the SPOUT-class RNA-methyltransferase fold.	RESULTS
47	58	DALI search	experimental_method	The closest structural homolog identified in a DALI search is the tRNA methyltransferase Trm10 (DALI Z-score 6.8) which methylates the N1 nitrogen of G9/A9 in many archaeal and eukaryotic tRNAs by using SAM as the methyl group donor.	RESULTS
66	88	tRNA methyltransferase	protein_type	The closest structural homolog identified in a DALI search is the tRNA methyltransferase Trm10 (DALI Z-score 6.8) which methylates the N1 nitrogen of G9/A9 in many archaeal and eukaryotic tRNAs by using SAM as the methyl group donor.	RESULTS
89	94	Trm10	protein	The closest structural homolog identified in a DALI search is the tRNA methyltransferase Trm10 (DALI Z-score 6.8) which methylates the N1 nitrogen of G9/A9 in many archaeal and eukaryotic tRNAs by using SAM as the methyl group donor.	RESULTS
96	108	DALI Z-score	evidence	The closest structural homolog identified in a DALI search is the tRNA methyltransferase Trm10 (DALI Z-score 6.8) which methylates the N1 nitrogen of G9/A9 in many archaeal and eukaryotic tRNAs by using SAM as the methyl group donor.	RESULTS
150	152	G9	residue_name_number	The closest structural homolog identified in a DALI search is the tRNA methyltransferase Trm10 (DALI Z-score 6.8) which methylates the N1 nitrogen of G9/A9 in many archaeal and eukaryotic tRNAs by using SAM as the methyl group donor.	RESULTS
153	155	A9	residue_name_number	The closest structural homolog identified in a DALI search is the tRNA methyltransferase Trm10 (DALI Z-score 6.8) which methylates the N1 nitrogen of G9/A9 in many archaeal and eukaryotic tRNAs by using SAM as the methyl group donor.	RESULTS
164	172	archaeal	taxonomy_domain	The closest structural homolog identified in a DALI search is the tRNA methyltransferase Trm10 (DALI Z-score 6.8) which methylates the N1 nitrogen of G9/A9 in many archaeal and eukaryotic tRNAs by using SAM as the methyl group donor.	RESULTS
177	187	eukaryotic	taxonomy_domain	The closest structural homolog identified in a DALI search is the tRNA methyltransferase Trm10 (DALI Z-score 6.8) which methylates the N1 nitrogen of G9/A9 in many archaeal and eukaryotic tRNAs by using SAM as the methyl group donor.	RESULTS
188	193	tRNAs	chemical	The closest structural homolog identified in a DALI search is the tRNA methyltransferase Trm10 (DALI Z-score 6.8) which methylates the N1 nitrogen of G9/A9 in many archaeal and eukaryotic tRNAs by using SAM as the methyl group donor.	RESULTS
203	206	SAM	chemical	The closest structural homolog identified in a DALI search is the tRNA methyltransferase Trm10 (DALI Z-score 6.8) which methylates the N1 nitrogen of G9/A9 in many archaeal and eukaryotic tRNAs by using SAM as the methyl group donor.	RESULTS
17	21	Tsr3	protein	In comparison to Tsr3 the central β-sheet element of Trm10 is extended by one additional β-strand pairing to β2.	RESULTS
34	49	β-sheet element	structure_element	In comparison to Tsr3 the central β-sheet element of Trm10 is extended by one additional β-strand pairing to β2.	RESULTS
53	58	Trm10	protein	In comparison to Tsr3 the central β-sheet element of Trm10 is extended by one additional β-strand pairing to β2.	RESULTS
89	97	β-strand	structure_element	In comparison to Tsr3 the central β-sheet element of Trm10 is extended by one additional β-strand pairing to β2.	RESULTS
109	111	β2	structure_element	In comparison to Tsr3 the central β-sheet element of Trm10 is extended by one additional β-strand pairing to β2.	RESULTS
17	29	trefoil knot	structure_element	Furthermore, the trefoil knot of Trm10 is not as deep as that of Tsr3 (Figure 4D).	RESULTS
33	38	Trm10	protein	Furthermore, the trefoil knot of Trm10 is not as deep as that of Tsr3 (Figure 4D).	RESULTS
65	69	Tsr3	protein	Furthermore, the trefoil knot of Trm10 is not as deep as that of Tsr3 (Figure 4D).	RESULTS
15	19	Nep1	protein	Interestingly, Nep1—the enzyme preceding Tsr3 in the biosynthetic pathway for the synthesis of m1acp3Ψ—also belongs to the SPOUT-class of RNA methyltransferases.	RESULTS
41	45	Tsr3	protein	Interestingly, Nep1—the enzyme preceding Tsr3 in the biosynthetic pathway for the synthesis of m1acp3Ψ—also belongs to the SPOUT-class of RNA methyltransferases.	RESULTS
95	102	m1acp3Ψ	chemical	Interestingly, Nep1—the enzyme preceding Tsr3 in the biosynthetic pathway for the synthesis of m1acp3Ψ—also belongs to the SPOUT-class of RNA methyltransferases.	RESULTS
123	160	SPOUT-class of RNA methyltransferases	protein_type	Interestingly, Nep1—the enzyme preceding Tsr3 in the biosynthetic pathway for the synthesis of m1acp3Ψ—also belongs to the SPOUT-class of RNA methyltransferases.	RESULTS
45	49	Nep1	protein	However, the structural similarities between Nep1 and Tsr3 (DALI Z-score 4.4) are less pronounced than between Tsr3 and Trm10.	RESULTS
54	58	Tsr3	protein	However, the structural similarities between Nep1 and Tsr3 (DALI Z-score 4.4) are less pronounced than between Tsr3 and Trm10.	RESULTS
60	72	DALI Z-score	evidence	However, the structural similarities between Nep1 and Tsr3 (DALI Z-score 4.4) are less pronounced than between Tsr3 and Trm10.	RESULTS
111	115	Tsr3	protein	However, the structural similarities between Nep1 and Tsr3 (DALI Z-score 4.4) are less pronounced than between Tsr3 and Trm10.	RESULTS
120	125	Trm10	protein	However, the structural similarities between Nep1 and Tsr3 (DALI Z-score 4.4) are less pronounced than between Tsr3 and Trm10.	RESULTS
5	39	SPOUT-class RNA-methyltransferases	protein_type	Most SPOUT-class RNA-methyltransferases are homodimers.	RESULTS
44	54	homodimers	oligomeric_state	Most SPOUT-class RNA-methyltransferases are homodimers.	RESULTS
23	28	Trm10	protein	A notable exception is Trm10.	RESULTS
0	14	Gel filtration	experimental_method	Gel filtration experiments with both VdTsr3 and SsTsr3 (Figure 4E) showed that both proteins are monomeric in solution thereby extending the structural similarities to Trm10.	RESULTS
37	43	VdTsr3	protein	Gel filtration experiments with both VdTsr3 and SsTsr3 (Figure 4E) showed that both proteins are monomeric in solution thereby extending the structural similarities to Trm10.	RESULTS
48	54	SsTsr3	protein	Gel filtration experiments with both VdTsr3 and SsTsr3 (Figure 4E) showed that both proteins are monomeric in solution thereby extending the structural similarities to Trm10.	RESULTS
97	106	monomeric	oligomeric_state	Gel filtration experiments with both VdTsr3 and SsTsr3 (Figure 4E) showed that both proteins are monomeric in solution thereby extending the structural similarities to Trm10.	RESULTS
168	173	Trm10	protein	Gel filtration experiments with both VdTsr3 and SsTsr3 (Figure 4E) showed that both proteins are monomeric in solution thereby extending the structural similarities to Trm10.	RESULTS
89	92	acp	chemical	So far, structural information is only available for one other enzyme that transfers the acp group from SAM to an RNA nucleotide.	RESULTS
104	107	SAM	chemical	So far, structural information is only available for one other enzyme that transfers the acp group from SAM to an RNA nucleotide.	RESULTS
114	117	RNA	chemical	So far, structural information is only available for one other enzyme that transfers the acp group from SAM to an RNA nucleotide.	RESULTS
118	128	nucleotide	chemical	So far, structural information is only available for one other enzyme that transfers the acp group from SAM to an RNA nucleotide.	RESULTS
13	17	Tyw2	protein	This enzyme, Tyw2, is part of the biosynthesis pathway of wybutosine nucleotides in tRNAs.	RESULTS
58	80	wybutosine nucleotides	chemical	This enzyme, Tyw2, is part of the biosynthesis pathway of wybutosine nucleotides in tRNAs.	RESULTS
84	89	tRNAs	chemical	This enzyme, Tyw2, is part of the biosynthesis pathway of wybutosine nucleotides in tRNAs.	RESULTS
54	58	Tsr3	protein	However, there are no structural similarities between Tsr3 and Tyw2, which contains an all-parallel β-sheet of a different topology and no knot structure.	RESULTS
63	67	Tyw2	protein	However, there are no structural similarities between Tsr3 and Tyw2, which contains an all-parallel β-sheet of a different topology and no knot structure.	RESULTS
87	107	all-parallel β-sheet	structure_element	However, there are no structural similarities between Tsr3 and Tyw2, which contains an all-parallel β-sheet of a different topology and no knot structure.	RESULTS
139	153	knot structure	structure_element	However, there are no structural similarities between Tsr3 and Tyw2, which contains an all-parallel β-sheet of a different topology and no knot structure.	RESULTS
9	13	Tyw2	protein	Instead, Tyw2 has a fold typical for the class-I-or Rossmann-fold class of methyltransferases (Supplementary Figure S5B).	RESULTS
41	93	class-I-or Rossmann-fold class of methyltransferases	protein_type	Instead, Tyw2 has a fold typical for the class-I-or Rossmann-fold class of methyltransferases (Supplementary Figure S5B).	RESULTS
20	24	Tsr3	protein	Cofactor binding of Tsr3	RESULTS
4	20	SAM-binding site	site	The SAM-binding site of Tsr3 is located in a deep crevice between the N- and C-terminal domains in the vicinity of the trefoil knot as typical for SPOUT-class RNA-methyltransferases (Figure 4A).	RESULTS
24	28	Tsr3	protein	The SAM-binding site of Tsr3 is located in a deep crevice between the N- and C-terminal domains in the vicinity of the trefoil knot as typical for SPOUT-class RNA-methyltransferases (Figure 4A).	RESULTS
70	95	N- and C-terminal domains	structure_element	The SAM-binding site of Tsr3 is located in a deep crevice between the N- and C-terminal domains in the vicinity of the trefoil knot as typical for SPOUT-class RNA-methyltransferases (Figure 4A).	RESULTS
119	131	trefoil knot	structure_element	The SAM-binding site of Tsr3 is located in a deep crevice between the N- and C-terminal domains in the vicinity of the trefoil knot as typical for SPOUT-class RNA-methyltransferases (Figure 4A).	RESULTS
147	181	SPOUT-class RNA-methyltransferases	protein_type	The SAM-binding site of Tsr3 is located in a deep crevice between the N- and C-terminal domains in the vicinity of the trefoil knot as typical for SPOUT-class RNA-methyltransferases (Figure 4A).	RESULTS
4	11	adenine	chemical	The adenine base of the cofactor is recognized by hydrogen bonds between its N1 nitrogen and the backbone amide of L93 directly preceding β5 as well as between its N6-amino group and the backbone carbonyl group of Y108 located in the loop connecting β5 in the N-terminal and α4 in the C-terminal domain (Figure 5A).	RESULTS
50	64	hydrogen bonds	bond_interaction	The adenine base of the cofactor is recognized by hydrogen bonds between its N1 nitrogen and the backbone amide of L93 directly preceding β5 as well as between its N6-amino group and the backbone carbonyl group of Y108 located in the loop connecting β5 in the N-terminal and α4 in the C-terminal domain (Figure 5A).	RESULTS
115	118	L93	residue_name_number	The adenine base of the cofactor is recognized by hydrogen bonds between its N1 nitrogen and the backbone amide of L93 directly preceding β5 as well as between its N6-amino group and the backbone carbonyl group of Y108 located in the loop connecting β5 in the N-terminal and α4 in the C-terminal domain (Figure 5A).	RESULTS
138	140	β5	structure_element	The adenine base of the cofactor is recognized by hydrogen bonds between its N1 nitrogen and the backbone amide of L93 directly preceding β5 as well as between its N6-amino group and the backbone carbonyl group of Y108 located in the loop connecting β5 in the N-terminal and α4 in the C-terminal domain (Figure 5A).	RESULTS
214	218	Y108	residue_name_number	The adenine base of the cofactor is recognized by hydrogen bonds between its N1 nitrogen and the backbone amide of L93 directly preceding β5 as well as between its N6-amino group and the backbone carbonyl group of Y108 located in the loop connecting β5 in the N-terminal and α4 in the C-terminal domain (Figure 5A).	RESULTS
234	238	loop	structure_element	The adenine base of the cofactor is recognized by hydrogen bonds between its N1 nitrogen and the backbone amide of L93 directly preceding β5 as well as between its N6-amino group and the backbone carbonyl group of Y108 located in the loop connecting β5 in the N-terminal and α4 in the C-terminal domain (Figure 5A).	RESULTS
250	252	β5	structure_element	The adenine base of the cofactor is recognized by hydrogen bonds between its N1 nitrogen and the backbone amide of L93 directly preceding β5 as well as between its N6-amino group and the backbone carbonyl group of Y108 located in the loop connecting β5 in the N-terminal and α4 in the C-terminal domain (Figure 5A).	RESULTS
260	270	N-terminal	structure_element	The adenine base of the cofactor is recognized by hydrogen bonds between its N1 nitrogen and the backbone amide of L93 directly preceding β5 as well as between its N6-amino group and the backbone carbonyl group of Y108 located in the loop connecting β5 in the N-terminal and α4 in the C-terminal domain (Figure 5A).	RESULTS
275	277	α4	structure_element	The adenine base of the cofactor is recognized by hydrogen bonds between its N1 nitrogen and the backbone amide of L93 directly preceding β5 as well as between its N6-amino group and the backbone carbonyl group of Y108 located in the loop connecting β5 in the N-terminal and α4 in the C-terminal domain (Figure 5A).	RESULTS
285	302	C-terminal domain	structure_element	The adenine base of the cofactor is recognized by hydrogen bonds between its N1 nitrogen and the backbone amide of L93 directly preceding β5 as well as between its N6-amino group and the backbone carbonyl group of Y108 located in the loop connecting β5 in the N-terminal and α4 in the C-terminal domain (Figure 5A).	RESULTS
17	24	adenine	chemical	Furthermore, the adenine base of SAM is involved in hydrophobic packing interactions with the side chains of L45 (β3), P47 and W73 (α3) in the N-terminal domain as well as with L93, L110 (both in the loop connecting β5 and α4) and A115 (α5) in the C-terminal domain.	RESULTS
33	36	SAM	chemical	Furthermore, the adenine base of SAM is involved in hydrophobic packing interactions with the side chains of L45 (β3), P47 and W73 (α3) in the N-terminal domain as well as with L93, L110 (both in the loop connecting β5 and α4) and A115 (α5) in the C-terminal domain.	RESULTS
52	84	hydrophobic packing interactions	bond_interaction	Furthermore, the adenine base of SAM is involved in hydrophobic packing interactions with the side chains of L45 (β3), P47 and W73 (α3) in the N-terminal domain as well as with L93, L110 (both in the loop connecting β5 and α4) and A115 (α5) in the C-terminal domain.	RESULTS
109	112	L45	residue_name_number	Furthermore, the adenine base of SAM is involved in hydrophobic packing interactions with the side chains of L45 (β3), P47 and W73 (α3) in the N-terminal domain as well as with L93, L110 (both in the loop connecting β5 and α4) and A115 (α5) in the C-terminal domain.	RESULTS
114	116	β3	structure_element	Furthermore, the adenine base of SAM is involved in hydrophobic packing interactions with the side chains of L45 (β3), P47 and W73 (α3) in the N-terminal domain as well as with L93, L110 (both in the loop connecting β5 and α4) and A115 (α5) in the C-terminal domain.	RESULTS
119	122	P47	residue_name_number	Furthermore, the adenine base of SAM is involved in hydrophobic packing interactions with the side chains of L45 (β3), P47 and W73 (α3) in the N-terminal domain as well as with L93, L110 (both in the loop connecting β5 and α4) and A115 (α5) in the C-terminal domain.	RESULTS
127	130	W73	residue_name_number	Furthermore, the adenine base of SAM is involved in hydrophobic packing interactions with the side chains of L45 (β3), P47 and W73 (α3) in the N-terminal domain as well as with L93, L110 (both in the loop connecting β5 and α4) and A115 (α5) in the C-terminal domain.	RESULTS
132	134	α3	structure_element	Furthermore, the adenine base of SAM is involved in hydrophobic packing interactions with the side chains of L45 (β3), P47 and W73 (α3) in the N-terminal domain as well as with L93, L110 (both in the loop connecting β5 and α4) and A115 (α5) in the C-terminal domain.	RESULTS
143	160	N-terminal domain	structure_element	Furthermore, the adenine base of SAM is involved in hydrophobic packing interactions with the side chains of L45 (β3), P47 and W73 (α3) in the N-terminal domain as well as with L93, L110 (both in the loop connecting β5 and α4) and A115 (α5) in the C-terminal domain.	RESULTS
177	180	L93	residue_name_number	Furthermore, the adenine base of SAM is involved in hydrophobic packing interactions with the side chains of L45 (β3), P47 and W73 (α3) in the N-terminal domain as well as with L93, L110 (both in the loop connecting β5 and α4) and A115 (α5) in the C-terminal domain.	RESULTS
182	186	L110	residue_name_number	Furthermore, the adenine base of SAM is involved in hydrophobic packing interactions with the side chains of L45 (β3), P47 and W73 (α3) in the N-terminal domain as well as with L93, L110 (both in the loop connecting β5 and α4) and A115 (α5) in the C-terminal domain.	RESULTS
200	204	loop	structure_element	Furthermore, the adenine base of SAM is involved in hydrophobic packing interactions with the side chains of L45 (β3), P47 and W73 (α3) in the N-terminal domain as well as with L93, L110 (both in the loop connecting β5 and α4) and A115 (α5) in the C-terminal domain.	RESULTS
216	218	β5	structure_element	Furthermore, the adenine base of SAM is involved in hydrophobic packing interactions with the side chains of L45 (β3), P47 and W73 (α3) in the N-terminal domain as well as with L93, L110 (both in the loop connecting β5 and α4) and A115 (α5) in the C-terminal domain.	RESULTS
223	225	α4	structure_element	Furthermore, the adenine base of SAM is involved in hydrophobic packing interactions with the side chains of L45 (β3), P47 and W73 (α3) in the N-terminal domain as well as with L93, L110 (both in the loop connecting β5 and α4) and A115 (α5) in the C-terminal domain.	RESULTS
231	235	A115	residue_name_number	Furthermore, the adenine base of SAM is involved in hydrophobic packing interactions with the side chains of L45 (β3), P47 and W73 (α3) in the N-terminal domain as well as with L93, L110 (both in the loop connecting β5 and α4) and A115 (α5) in the C-terminal domain.	RESULTS
237	239	α5	structure_element	Furthermore, the adenine base of SAM is involved in hydrophobic packing interactions with the side chains of L45 (β3), P47 and W73 (α3) in the N-terminal domain as well as with L93, L110 (both in the loop connecting β5 and α4) and A115 (α5) in the C-terminal domain.	RESULTS
248	265	C-terminal domain	structure_element	Furthermore, the adenine base of SAM is involved in hydrophobic packing interactions with the side chains of L45 (β3), P47 and W73 (α3) in the N-terminal domain as well as with L93, L110 (both in the loop connecting β5 and α4) and A115 (α5) in the C-terminal domain.	RESULTS
4	10	ribose	chemical	The ribose 2′ and 3′ hydroxyl groups of SAM are hydrogen bonded to the backbone carbonyl group of I69.	RESULTS
40	43	SAM	chemical	The ribose 2′ and 3′ hydroxyl groups of SAM are hydrogen bonded to the backbone carbonyl group of I69.	RESULTS
48	63	hydrogen bonded	bond_interaction	The ribose 2′ and 3′ hydroxyl groups of SAM are hydrogen bonded to the backbone carbonyl group of I69.	RESULTS
98	101	I69	residue_name_number	The ribose 2′ and 3′ hydroxyl groups of SAM are hydrogen bonded to the backbone carbonyl group of I69.	RESULTS
4	7	acp	chemical	The acp side chain of SAM is fixed in position by hydrogen bonding of its carboxylate group to the backbone amide and the side chain hydroxyl group of T19 in α1 as well as the backbone amide group of T112 in α4 (C-terminal domain).	RESULTS
22	25	SAM	chemical	The acp side chain of SAM is fixed in position by hydrogen bonding of its carboxylate group to the backbone amide and the side chain hydroxyl group of T19 in α1 as well as the backbone amide group of T112 in α4 (C-terminal domain).	RESULTS
50	66	hydrogen bonding	bond_interaction	The acp side chain of SAM is fixed in position by hydrogen bonding of its carboxylate group to the backbone amide and the side chain hydroxyl group of T19 in α1 as well as the backbone amide group of T112 in α4 (C-terminal domain).	RESULTS
151	154	T19	residue_name_number	The acp side chain of SAM is fixed in position by hydrogen bonding of its carboxylate group to the backbone amide and the side chain hydroxyl group of T19 in α1 as well as the backbone amide group of T112 in α4 (C-terminal domain).	RESULTS
158	160	α1	structure_element	The acp side chain of SAM is fixed in position by hydrogen bonding of its carboxylate group to the backbone amide and the side chain hydroxyl group of T19 in α1 as well as the backbone amide group of T112 in α4 (C-terminal domain).	RESULTS
200	204	T112	residue_name_number	The acp side chain of SAM is fixed in position by hydrogen bonding of its carboxylate group to the backbone amide and the side chain hydroxyl group of T19 in α1 as well as the backbone amide group of T112 in α4 (C-terminal domain).	RESULTS
208	210	α4	structure_element	The acp side chain of SAM is fixed in position by hydrogen bonding of its carboxylate group to the backbone amide and the side chain hydroxyl group of T19 in α1 as well as the backbone amide group of T112 in α4 (C-terminal domain).	RESULTS
212	229	C-terminal domain	structure_element	The acp side chain of SAM is fixed in position by hydrogen bonding of its carboxylate group to the backbone amide and the side chain hydroxyl group of T19 in α1 as well as the backbone amide group of T112 in α4 (C-terminal domain).	RESULTS
38	41	SAM	chemical	Most importantly, the methyl group of SAM is buried in a hydrophobic pocket formed by the sidechains of W73 and A76 both located in α3 (Figure 5A and B).	RESULTS
57	75	hydrophobic pocket	site	Most importantly, the methyl group of SAM is buried in a hydrophobic pocket formed by the sidechains of W73 and A76 both located in α3 (Figure 5A and B).	RESULTS
104	107	W73	residue_name_number	Most importantly, the methyl group of SAM is buried in a hydrophobic pocket formed by the sidechains of W73 and A76 both located in α3 (Figure 5A and B).	RESULTS
112	115	A76	residue_name_number	Most importantly, the methyl group of SAM is buried in a hydrophobic pocket formed by the sidechains of W73 and A76 both located in α3 (Figure 5A and B).	RESULTS
132	134	α3	structure_element	Most importantly, the methyl group of SAM is buried in a hydrophobic pocket formed by the sidechains of W73 and A76 both located in α3 (Figure 5A and B).	RESULTS
0	3	W73	residue_name_number	W73 is highly conserved in all known Tsr3 proteins, whereas A76 can be replaced by other hydrophobic amino acids.	RESULTS
7	23	highly conserved	protein_state	W73 is highly conserved in all known Tsr3 proteins, whereas A76 can be replaced by other hydrophobic amino acids.	RESULTS
37	50	Tsr3 proteins	protein_type	W73 is highly conserved in all known Tsr3 proteins, whereas A76 can be replaced by other hydrophobic amino acids.	RESULTS
60	63	A76	residue_name_number	W73 is highly conserved in all known Tsr3 proteins, whereas A76 can be replaced by other hydrophobic amino acids.	RESULTS
101	112	amino acids	chemical	W73 is highly conserved in all known Tsr3 proteins, whereas A76 can be replaced by other hydrophobic amino acids.	RESULTS
118	140	RNA-methyltransferases	protein_type	Consequently, the accessibility of this methyl group for a nucleophilic attack is strongly reduced in comparison with RNA-methyltransferases such as Trm10 (Figure 5B, C).	RESULTS
149	154	Trm10	protein	Consequently, the accessibility of this methyl group for a nucleophilic attack is strongly reduced in comparison with RNA-methyltransferases such as Trm10 (Figure 5B, C).	RESULTS
17	20	acp	chemical	In contrast, the acp side chain of SAM is accessible for reactions in the Tsr3-bound state (Figure 5B).	RESULTS
35	38	SAM	chemical	In contrast, the acp side chain of SAM is accessible for reactions in the Tsr3-bound state (Figure 5B).	RESULTS
74	84	Tsr3-bound	protein_state	In contrast, the acp side chain of SAM is accessible for reactions in the Tsr3-bound state (Figure 5B).	RESULTS
0	3	SAM	chemical	SAM-binding by Tsr3.	FIG
15	19	Tsr3	protein	SAM-binding by Tsr3.	FIG
25	43	SAM-binding pocket	site	(A) Close-up view of the SAM-binding pocket of VdTsr3.	FIG
47	53	VdTsr3	protein	(A) Close-up view of the SAM-binding pocket of VdTsr3.	FIG
48	54	sulfur	chemical	Nitrogen atoms are dark blue, oxygen atoms red, sulfur atoms orange, carbon atoms of the protein light blue and carbon atoms of SAM yellow.	FIG
128	131	SAM	chemical	Nitrogen atoms are dark blue, oxygen atoms red, sulfur atoms orange, carbon atoms of the protein light blue and carbon atoms of SAM yellow.	FIG
0	14	Hydrogen bonds	bond_interaction	Hydrogen bonds are indicated by dashed lines.	FIG
33	36	acp	chemical	(B) Solvent accessibility of the acp group of SAM bound to VdTsr3.	FIG
46	49	SAM	chemical	(B) Solvent accessibility of the acp group of SAM bound to VdTsr3.	FIG
50	58	bound to	protein_state	(B) Solvent accessibility of the acp group of SAM bound to VdTsr3.	FIG
59	65	VdTsr3	protein	(B) Solvent accessibility of the acp group of SAM bound to VdTsr3.	FIG
87	90	SAM	chemical	The solvent accessible surface of the protein is shown in semitransparent gray whereas SAM is show in a stick representation.	FIG
53	56	acp	chemical	A red arrow indicates the reactive CH2-moiety of the acp group. (C) Solvent accessibility of the SAM methyl group for SAM bound to the RNA methyltransferase Trm10.	FIG
97	100	SAM	chemical	A red arrow indicates the reactive CH2-moiety of the acp group. (C) Solvent accessibility of the SAM methyl group for SAM bound to the RNA methyltransferase Trm10.	FIG
118	121	SAM	chemical	A red arrow indicates the reactive CH2-moiety of the acp group. (C) Solvent accessibility of the SAM methyl group for SAM bound to the RNA methyltransferase Trm10.	FIG
122	130	bound to	protein_state	A red arrow indicates the reactive CH2-moiety of the acp group. (C) Solvent accessibility of the SAM methyl group for SAM bound to the RNA methyltransferase Trm10.	FIG
135	156	RNA methyltransferase	protein_type	A red arrow indicates the reactive CH2-moiety of the acp group. (C) Solvent accessibility of the SAM methyl group for SAM bound to the RNA methyltransferase Trm10.	FIG
157	162	Trm10	protein	A red arrow indicates the reactive CH2-moiety of the acp group. (C) Solvent accessibility of the SAM methyl group for SAM bound to the RNA methyltransferase Trm10.	FIG
0	5	Bound	protein_state	Bound SAM was modelled based on the X-ray structure of the Trm10/SAH-complex (pdb4jwf).	FIG
6	9	SAM	chemical	Bound SAM was modelled based on the X-ray structure of the Trm10/SAH-complex (pdb4jwf).	FIG
36	51	X-ray structure	evidence	Bound SAM was modelled based on the X-ray structure of the Trm10/SAH-complex (pdb4jwf).	FIG
59	68	Trm10/SAH	complex_assembly	Bound SAM was modelled based on the X-ray structure of the Trm10/SAH-complex (pdb4jwf).	FIG
26	29	SAM	chemical	A red arrow indicates the SAM methyl group. (D) Binding of SAM analogs to SsTsr3.	FIG
59	62	SAM	chemical	A red arrow indicates the SAM methyl group. (D) Binding of SAM analogs to SsTsr3.	FIG
74	80	SsTsr3	protein	A red arrow indicates the SAM methyl group. (D) Binding of SAM analogs to SsTsr3.	FIG
0	40	Tryptophan fluorescence quenching curves	evidence	Tryptophan fluorescence quenching curves upon addition of SAM (blue), 5′-methyl-thioadenosine (red) and SAH (black).	FIG
58	61	SAM	chemical	Tryptophan fluorescence quenching curves upon addition of SAM (blue), 5′-methyl-thioadenosine (red) and SAH (black).	FIG
70	93	5′-methyl-thioadenosine	chemical	Tryptophan fluorescence quenching curves upon addition of SAM (blue), 5′-methyl-thioadenosine (red) and SAH (black).	FIG
104	107	SAH	chemical	Tryptophan fluorescence quenching curves upon addition of SAM (blue), 5′-methyl-thioadenosine (red) and SAH (black).	FIG
15	30	14C-labeled SAM	chemical	(E) Binding of 14C-labeled SAM to SsTsr3.	FIG
34	40	SsTsr3	protein	(E) Binding of 14C-labeled SAM to SsTsr3.	FIG
22	25	SAM	chemical	Radioactively labeled SAM is retained on a filter in the presence of SsTsr3.	FIG
57	68	presence of	protein_state	Radioactively labeled SAM is retained on a filter in the presence of SsTsr3.	FIG
69	75	SsTsr3	protein	Radioactively labeled SAM is retained on a filter in the presence of SsTsr3.	FIG
22	25	SAM	chemical	Addition of unlabeled SAM competes with the binding of labeled SAM.	FIG
63	66	SAM	chemical	Addition of unlabeled SAM competes with the binding of labeled SAM.	FIG
2	6	W66A	mutant	A W66A-mutant of SsTsr3 (W73 in VdTsr3) does not bind SAM.	FIG
7	13	mutant	protein_state	A W66A-mutant of SsTsr3 (W73 in VdTsr3) does not bind SAM.	FIG
17	23	SsTsr3	protein	A W66A-mutant of SsTsr3 (W73 in VdTsr3) does not bind SAM.	FIG
25	28	W73	residue_name_number	A W66A-mutant of SsTsr3 (W73 in VdTsr3) does not bind SAM.	FIG
32	38	VdTsr3	protein	A W66A-mutant of SsTsr3 (W73 in VdTsr3) does not bind SAM.	FIG
54	57	SAM	chemical	A W66A-mutant of SsTsr3 (W73 in VdTsr3) does not bind SAM.	FIG
4	20	Primer extension	experimental_method	(F) Primer extension (upper left) shows a strongly reduced acp modification of yeast 18S rRNA in Δtsr3 cells expressing Tsr3-S62D, -E111A or –W114A.	FIG
59	62	acp	chemical	(F) Primer extension (upper left) shows a strongly reduced acp modification of yeast 18S rRNA in Δtsr3 cells expressing Tsr3-S62D, -E111A or –W114A.	FIG
79	84	yeast	taxonomy_domain	(F) Primer extension (upper left) shows a strongly reduced acp modification of yeast 18S rRNA in Δtsr3 cells expressing Tsr3-S62D, -E111A or –W114A.	FIG
85	93	18S rRNA	chemical	(F) Primer extension (upper left) shows a strongly reduced acp modification of yeast 18S rRNA in Δtsr3 cells expressing Tsr3-S62D, -E111A or –W114A.	FIG
97	102	Δtsr3	mutant	(F) Primer extension (upper left) shows a strongly reduced acp modification of yeast 18S rRNA in Δtsr3 cells expressing Tsr3-S62D, -E111A or –W114A.	FIG
120	129	Tsr3-S62D	mutant	(F) Primer extension (upper left) shows a strongly reduced acp modification of yeast 18S rRNA in Δtsr3 cells expressing Tsr3-S62D, -E111A or –W114A.	FIG
131	137	-E111A	mutant	(F) Primer extension (upper left) shows a strongly reduced acp modification of yeast 18S rRNA in Δtsr3 cells expressing Tsr3-S62D, -E111A or –W114A.	FIG
141	147	–W114A	mutant	(F) Primer extension (upper left) shows a strongly reduced acp modification of yeast 18S rRNA in Δtsr3 cells expressing Tsr3-S62D, -E111A or –W114A.	FIG
23	35	20S pre-rRNA	chemical	This correlates with a 20S pre-rRNA accumulation comparable to the Δtsr3 deletion (right: northern blot).	FIG
67	72	Δtsr3	mutant	This correlates with a 20S pre-rRNA accumulation comparable to the Δtsr3 deletion (right: northern blot).	FIG
90	103	northern blot	experimental_method	This correlates with a 20S pre-rRNA accumulation comparable to the Δtsr3 deletion (right: northern blot).	FIG
0	11	3xHA tagged	protein_state	3xHA tagged Tsr3 mutants are expressed comparable to the wild type as shown by western blot (lower left).	FIG
12	16	Tsr3	protein	3xHA tagged Tsr3 mutants are expressed comparable to the wild type as shown by western blot (lower left).	FIG
17	24	mutants	protein_state	3xHA tagged Tsr3 mutants are expressed comparable to the wild type as shown by western blot (lower left).	FIG
57	66	wild type	protein_state	3xHA tagged Tsr3 mutants are expressed comparable to the wild type as shown by western blot (lower left).	FIG
79	91	western blot	experimental_method	3xHA tagged Tsr3 mutants are expressed comparable to the wild type as shown by western blot (lower left).	FIG
0	18	Binding affinities	evidence	Binding affinities for SAM and its analogs 5′-methylthioadenosin and SAH to SsTsr3 were measured using tryptophan fluorescence quenching.	RESULTS
23	26	SAM	chemical	Binding affinities for SAM and its analogs 5′-methylthioadenosin and SAH to SsTsr3 were measured using tryptophan fluorescence quenching.	RESULTS
43	64	5′-methylthioadenosin	chemical	Binding affinities for SAM and its analogs 5′-methylthioadenosin and SAH to SsTsr3 were measured using tryptophan fluorescence quenching.	RESULTS
69	72	SAH	chemical	Binding affinities for SAM and its analogs 5′-methylthioadenosin and SAH to SsTsr3 were measured using tryptophan fluorescence quenching.	RESULTS
76	82	SsTsr3	protein	Binding affinities for SAM and its analogs 5′-methylthioadenosin and SAH to SsTsr3 were measured using tryptophan fluorescence quenching.	RESULTS
103	136	tryptophan fluorescence quenching	experimental_method	Binding affinities for SAM and its analogs 5′-methylthioadenosin and SAH to SsTsr3 were measured using tryptophan fluorescence quenching.	RESULTS
0	6	VdTsr3	protein	VdTsr3 could not be used in these experiments since we could not purify it in a stable SAM-free form.	RESULTS
80	86	stable	protein_state	VdTsr3 could not be used in these experiments since we could not purify it in a stable SAM-free form.	RESULTS
87	95	SAM-free	protein_state	VdTsr3 could not be used in these experiments since we could not purify it in a stable SAM-free form.	RESULTS
0	6	SsTsr3	protein	SsTsr3 bound SAM with a KD of 6.5 μM, which is similar to SAM-KD's reported for several SPOUT-class methyltransferases.	RESULTS
7	12	bound	protein_state	SsTsr3 bound SAM with a KD of 6.5 μM, which is similar to SAM-KD's reported for several SPOUT-class methyltransferases.	RESULTS
13	16	SAM	chemical	SsTsr3 bound SAM with a KD of 6.5 μM, which is similar to SAM-KD's reported for several SPOUT-class methyltransferases.	RESULTS
24	26	KD	evidence	SsTsr3 bound SAM with a KD of 6.5 μM, which is similar to SAM-KD's reported for several SPOUT-class methyltransferases.	RESULTS
58	66	SAM-KD's	evidence	SsTsr3 bound SAM with a KD of 6.5 μM, which is similar to SAM-KD's reported for several SPOUT-class methyltransferases.	RESULTS
88	118	SPOUT-class methyltransferases	protein_type	SsTsr3 bound SAM with a KD of 6.5 μM, which is similar to SAM-KD's reported for several SPOUT-class methyltransferases.	RESULTS
0	21	5′-methylthioadenosin	chemical	5′-methylthioadenosin—the reaction product after the acp-transfer—binds only ∼2.5-fold weaker (KD = 16.7 μM) compared to SAM.	RESULTS
53	56	acp	chemical	5′-methylthioadenosin—the reaction product after the acp-transfer—binds only ∼2.5-fold weaker (KD = 16.7 μM) compared to SAM.	RESULTS
121	124	SAM	chemical	5′-methylthioadenosin—the reaction product after the acp-transfer—binds only ∼2.5-fold weaker (KD = 16.7 μM) compared to SAM.	RESULTS
0	22	S-adenosylhomocysteine	chemical	S-adenosylhomocysteine which lacks the methyl group of SAM binds with significantly lower affinity (KD = 55.5 μM) (Figure 5D).	RESULTS
55	58	SAM	chemical	S-adenosylhomocysteine which lacks the methyl group of SAM binds with significantly lower affinity (KD = 55.5 μM) (Figure 5D).	RESULTS
90	98	affinity	evidence	S-adenosylhomocysteine which lacks the methyl group of SAM binds with significantly lower affinity (KD = 55.5 μM) (Figure 5D).	RESULTS
100	102	KD	evidence	S-adenosylhomocysteine which lacks the methyl group of SAM binds with significantly lower affinity (KD = 55.5 μM) (Figure 5D).	RESULTS
23	46	hydrophobic interaction	bond_interaction	This suggests that the hydrophobic interaction between SAM's methyl group and the hydrophobic pocket of Tsr3 is thermodynamically important for the interaction.	RESULTS
55	58	SAM	chemical	This suggests that the hydrophobic interaction between SAM's methyl group and the hydrophobic pocket of Tsr3 is thermodynamically important for the interaction.	RESULTS
82	100	hydrophobic pocket	site	This suggests that the hydrophobic interaction between SAM's methyl group and the hydrophobic pocket of Tsr3 is thermodynamically important for the interaction.	RESULTS
104	108	Tsr3	protein	This suggests that the hydrophobic interaction between SAM's methyl group and the hydrophobic pocket of Tsr3 is thermodynamically important for the interaction.	RESULTS
31	45	hydrogen bonds	bond_interaction	On the other hand, the loss of hydrogen bonds between the acp sidechain carboxylate group and the protein appears to be thermodynamically less important but these hydrogen bonds might play a crucial role for the proper orientation of the cofactor side chain in the substrate binding pocket.	RESULTS
58	61	acp	chemical	On the other hand, the loss of hydrogen bonds between the acp sidechain carboxylate group and the protein appears to be thermodynamically less important but these hydrogen bonds might play a crucial role for the proper orientation of the cofactor side chain in the substrate binding pocket.	RESULTS
163	177	hydrogen bonds	bond_interaction	On the other hand, the loss of hydrogen bonds between the acp sidechain carboxylate group and the protein appears to be thermodynamically less important but these hydrogen bonds might play a crucial role for the proper orientation of the cofactor side chain in the substrate binding pocket.	RESULTS
265	289	substrate binding pocket	site	On the other hand, the loss of hydrogen bonds between the acp sidechain carboxylate group and the protein appears to be thermodynamically less important but these hydrogen bonds might play a crucial role for the proper orientation of the cofactor side chain in the substrate binding pocket.	RESULTS
15	19	W66A	mutant	Accordingly, a W66A-mutation (W73 in VdTsr3) of SsTsr3 significantly diminished SAM-binding in a filter binding assay compared to the wild type (Figure 5E).	RESULTS
20	28	mutation	experimental_method	Accordingly, a W66A-mutation (W73 in VdTsr3) of SsTsr3 significantly diminished SAM-binding in a filter binding assay compared to the wild type (Figure 5E).	RESULTS
30	33	W73	residue_name_number	Accordingly, a W66A-mutation (W73 in VdTsr3) of SsTsr3 significantly diminished SAM-binding in a filter binding assay compared to the wild type (Figure 5E).	RESULTS
37	43	VdTsr3	protein	Accordingly, a W66A-mutation (W73 in VdTsr3) of SsTsr3 significantly diminished SAM-binding in a filter binding assay compared to the wild type (Figure 5E).	RESULTS
48	54	SsTsr3	protein	Accordingly, a W66A-mutation (W73 in VdTsr3) of SsTsr3 significantly diminished SAM-binding in a filter binding assay compared to the wild type (Figure 5E).	RESULTS
80	91	SAM-binding	evidence	Accordingly, a W66A-mutation (W73 in VdTsr3) of SsTsr3 significantly diminished SAM-binding in a filter binding assay compared to the wild type (Figure 5E).	RESULTS
97	117	filter binding assay	experimental_method	Accordingly, a W66A-mutation (W73 in VdTsr3) of SsTsr3 significantly diminished SAM-binding in a filter binding assay compared to the wild type (Figure 5E).	RESULTS
134	143	wild type	protein_state	Accordingly, a W66A-mutation (W73 in VdTsr3) of SsTsr3 significantly diminished SAM-binding in a filter binding assay compared to the wild type (Figure 5E).	RESULTS
15	30	W to A mutation	experimental_method	Furthermore, a W to A mutation at the equivalent position W114 in ScTsr3 strongly reduced the in vivo acp transferase activity (Figure 5F).	RESULTS
58	62	W114	residue_name_number	Furthermore, a W to A mutation at the equivalent position W114 in ScTsr3 strongly reduced the in vivo acp transferase activity (Figure 5F).	RESULTS
66	72	ScTsr3	protein	Furthermore, a W to A mutation at the equivalent position W114 in ScTsr3 strongly reduced the in vivo acp transferase activity (Figure 5F).	RESULTS
102	117	acp transferase	protein_type	Furthermore, a W to A mutation at the equivalent position W114 in ScTsr3 strongly reduced the in vivo acp transferase activity (Figure 5F).	RESULTS
33	36	T19	residue_name_number	The side chain hydroxyl group of T19 seems of minor importance for SAM binding since mutations of T17 (T19 in VdTsr3) to either A or D did not significantly influence the SAM-binding affinity of SsTsr3 (KD's = 3.9 or 11.2 mM, respectively).	RESULTS
67	70	SAM	chemical	The side chain hydroxyl group of T19 seems of minor importance for SAM binding since mutations of T17 (T19 in VdTsr3) to either A or D did not significantly influence the SAM-binding affinity of SsTsr3 (KD's = 3.9 or 11.2 mM, respectively).	RESULTS
85	94	mutations	experimental_method	The side chain hydroxyl group of T19 seems of minor importance for SAM binding since mutations of T17 (T19 in VdTsr3) to either A or D did not significantly influence the SAM-binding affinity of SsTsr3 (KD's = 3.9 or 11.2 mM, respectively).	RESULTS
98	101	T17	residue_name_number	The side chain hydroxyl group of T19 seems of minor importance for SAM binding since mutations of T17 (T19 in VdTsr3) to either A or D did not significantly influence the SAM-binding affinity of SsTsr3 (KD's = 3.9 or 11.2 mM, respectively).	RESULTS
103	106	T19	residue_name_number	The side chain hydroxyl group of T19 seems of minor importance for SAM binding since mutations of T17 (T19 in VdTsr3) to either A or D did not significantly influence the SAM-binding affinity of SsTsr3 (KD's = 3.9 or 11.2 mM, respectively).	RESULTS
110	116	VdTsr3	protein	The side chain hydroxyl group of T19 seems of minor importance for SAM binding since mutations of T17 (T19 in VdTsr3) to either A or D did not significantly influence the SAM-binding affinity of SsTsr3 (KD's = 3.9 or 11.2 mM, respectively).	RESULTS
128	129	A	residue_name	The side chain hydroxyl group of T19 seems of minor importance for SAM binding since mutations of T17 (T19 in VdTsr3) to either A or D did not significantly influence the SAM-binding affinity of SsTsr3 (KD's = 3.9 or 11.2 mM, respectively).	RESULTS
133	134	D	residue_name	The side chain hydroxyl group of T19 seems of minor importance for SAM binding since mutations of T17 (T19 in VdTsr3) to either A or D did not significantly influence the SAM-binding affinity of SsTsr3 (KD's = 3.9 or 11.2 mM, respectively).	RESULTS
171	191	SAM-binding affinity	evidence	The side chain hydroxyl group of T19 seems of minor importance for SAM binding since mutations of T17 (T19 in VdTsr3) to either A or D did not significantly influence the SAM-binding affinity of SsTsr3 (KD's = 3.9 or 11.2 mM, respectively).	RESULTS
195	201	SsTsr3	protein	The side chain hydroxyl group of T19 seems of minor importance for SAM binding since mutations of T17 (T19 in VdTsr3) to either A or D did not significantly influence the SAM-binding affinity of SsTsr3 (KD's = 3.9 or 11.2 mM, respectively).	RESULTS
203	205	KD	evidence	The side chain hydroxyl group of T19 seems of minor importance for SAM binding since mutations of T17 (T19 in VdTsr3) to either A or D did not significantly influence the SAM-binding affinity of SsTsr3 (KD's = 3.9 or 11.2 mM, respectively).	RESULTS
16	24	mutation	experimental_method	Nevertheless, a mutation of the equivalent position S62 of ScTsr3 to D, but not to A, resulted in reduced acp modification in vivo, as shown by primer extension analysis (Figure 5F).	RESULTS
52	55	S62	residue_name_number	Nevertheless, a mutation of the equivalent position S62 of ScTsr3 to D, but not to A, resulted in reduced acp modification in vivo, as shown by primer extension analysis (Figure 5F).	RESULTS
59	65	ScTsr3	protein	Nevertheless, a mutation of the equivalent position S62 of ScTsr3 to D, but not to A, resulted in reduced acp modification in vivo, as shown by primer extension analysis (Figure 5F).	RESULTS
69	70	D	residue_name	Nevertheless, a mutation of the equivalent position S62 of ScTsr3 to D, but not to A, resulted in reduced acp modification in vivo, as shown by primer extension analysis (Figure 5F).	RESULTS
83	84	A	residue_name	Nevertheless, a mutation of the equivalent position S62 of ScTsr3 to D, but not to A, resulted in reduced acp modification in vivo, as shown by primer extension analysis (Figure 5F).	RESULTS
106	109	acp	chemical	Nevertheless, a mutation of the equivalent position S62 of ScTsr3 to D, but not to A, resulted in reduced acp modification in vivo, as shown by primer extension analysis (Figure 5F).	RESULTS
144	169	primer extension analysis	experimental_method	Nevertheless, a mutation of the equivalent position S62 of ScTsr3 to D, but not to A, resulted in reduced acp modification in vivo, as shown by primer extension analysis (Figure 5F).	RESULTS
4	7	acp	chemical	The acp-transfer reaction catalyzed by Tsr3 most likely requires the presence of a catalytic base in order to abstract a proton from the N3 imino group of the modified pseudouridine.	RESULTS
39	43	Tsr3	protein	The acp-transfer reaction catalyzed by Tsr3 most likely requires the presence of a catalytic base in order to abstract a proton from the N3 imino group of the modified pseudouridine.	RESULTS
168	181	pseudouridine	chemical	The acp-transfer reaction catalyzed by Tsr3 most likely requires the presence of a catalytic base in order to abstract a proton from the N3 imino group of the modified pseudouridine.	RESULTS
18	21	D70	residue_name_number	The side chain of D70 (VdTsr3) located in β4 is ∼5 Å away from the SAM sulfur atom.	RESULTS
23	29	VdTsr3	protein	The side chain of D70 (VdTsr3) located in β4 is ∼5 Å away from the SAM sulfur atom.	RESULTS
42	44	β4	structure_element	The side chain of D70 (VdTsr3) located in β4 is ∼5 Å away from the SAM sulfur atom.	RESULTS
67	70	SAM	chemical	The side chain of D70 (VdTsr3) located in β4 is ∼5 Å away from the SAM sulfur atom.	RESULTS
16	28	conserved as	protein_state	This residue is conserved as D or E both in archaeal and eukaryotic Tsr3 homologs.	RESULTS
29	30	D	residue_name	This residue is conserved as D or E both in archaeal and eukaryotic Tsr3 homologs.	RESULTS
34	35	E	residue_name	This residue is conserved as D or E both in archaeal and eukaryotic Tsr3 homologs.	RESULTS
44	52	archaeal	taxonomy_domain	This residue is conserved as D or E both in archaeal and eukaryotic Tsr3 homologs.	RESULTS
57	67	eukaryotic	taxonomy_domain	This residue is conserved as D or E both in archaeal and eukaryotic Tsr3 homologs.	RESULTS
68	72	Tsr3	protein	This residue is conserved as D or E both in archaeal and eukaryotic Tsr3 homologs.	RESULTS
0	9	Mutations	experimental_method	Mutations of the corresponding residue in SsTsr3 to A (D63) does not significantly alter the SAM-binding affinity of the protein (KD = 11.0 μM).	RESULTS
42	48	SsTsr3	protein	Mutations of the corresponding residue in SsTsr3 to A (D63) does not significantly alter the SAM-binding affinity of the protein (KD = 11.0 μM).	RESULTS
52	53	A	residue_name	Mutations of the corresponding residue in SsTsr3 to A (D63) does not significantly alter the SAM-binding affinity of the protein (KD = 11.0 μM).	RESULTS
55	58	D63	residue_name_number	Mutations of the corresponding residue in SsTsr3 to A (D63) does not significantly alter the SAM-binding affinity of the protein (KD = 11.0 μM).	RESULTS
93	113	SAM-binding affinity	evidence	Mutations of the corresponding residue in SsTsr3 to A (D63) does not significantly alter the SAM-binding affinity of the protein (KD = 11.0 μM).	RESULTS
130	132	KD	evidence	Mutations of the corresponding residue in SsTsr3 to A (D63) does not significantly alter the SAM-binding affinity of the protein (KD = 11.0 μM).	RESULTS
13	21	mutation	experimental_method	However, the mutation of the corresponding residue of ScTsr3 (E111A) leads to a significant decrease of the acp transferase activity in vivo (Figure 5F).	RESULTS
54	60	ScTsr3	protein	However, the mutation of the corresponding residue of ScTsr3 (E111A) leads to a significant decrease of the acp transferase activity in vivo (Figure 5F).	RESULTS
62	67	E111A	mutant	However, the mutation of the corresponding residue of ScTsr3 (E111A) leads to a significant decrease of the acp transferase activity in vivo (Figure 5F).	RESULTS
108	123	acp transferase	protein_type	However, the mutation of the corresponding residue of ScTsr3 (E111A) leads to a significant decrease of the acp transferase activity in vivo (Figure 5F).	RESULTS
0	3	RNA	chemical	RNA-binding of Tsr3	RESULTS
15	19	Tsr3	protein	RNA-binding of Tsr3	RESULTS
0	48	Analysis of the electrostatic surface properties	experimental_method	Analysis of the electrostatic surface properties of VdTsr3 clearly identified positively charged surface patches in the vicinity of the SAM-binding site suggesting a putative RNA-binding site (Figure 6A).	RESULTS
52	58	VdTsr3	protein	Analysis of the electrostatic surface properties of VdTsr3 clearly identified positively charged surface patches in the vicinity of the SAM-binding site suggesting a putative RNA-binding site (Figure 6A).	RESULTS
78	112	positively charged surface patches	site	Analysis of the electrostatic surface properties of VdTsr3 clearly identified positively charged surface patches in the vicinity of the SAM-binding site suggesting a putative RNA-binding site (Figure 6A).	RESULTS
136	152	SAM-binding site	site	Analysis of the electrostatic surface properties of VdTsr3 clearly identified positively charged surface patches in the vicinity of the SAM-binding site suggesting a putative RNA-binding site (Figure 6A).	RESULTS
175	191	RNA-binding site	site	Analysis of the electrostatic surface properties of VdTsr3 clearly identified positively charged surface patches in the vicinity of the SAM-binding site suggesting a putative RNA-binding site (Figure 6A).	RESULTS
34	37	MES	chemical	Furthermore, a negatively charged MES-ion is found in the crystal structure of VdTsr3 complexed to the side chain of K22 in helix α1.	RESULTS
58	75	crystal structure	evidence	Furthermore, a negatively charged MES-ion is found in the crystal structure of VdTsr3 complexed to the side chain of K22 in helix α1.	RESULTS
79	85	VdTsr3	protein	Furthermore, a negatively charged MES-ion is found in the crystal structure of VdTsr3 complexed to the side chain of K22 in helix α1.	RESULTS
86	98	complexed to	protein_state	Furthermore, a negatively charged MES-ion is found in the crystal structure of VdTsr3 complexed to the side chain of K22 in helix α1.	RESULTS
117	120	K22	residue_name_number	Furthermore, a negatively charged MES-ion is found in the crystal structure of VdTsr3 complexed to the side chain of K22 in helix α1.	RESULTS
124	129	helix	structure_element	Furthermore, a negatively charged MES-ion is found in the crystal structure of VdTsr3 complexed to the side chain of K22 in helix α1.	RESULTS
130	132	α1	structure_element	Furthermore, a negatively charged MES-ion is found in the crystal structure of VdTsr3 complexed to the side chain of K22 in helix α1.	RESULTS
23	30	sulfate	chemical	Its negatively charged sulfate group might mimic an RNA backbone phosphate.	RESULTS
52	55	RNA	chemical	Its negatively charged sulfate group might mimic an RNA backbone phosphate.	RESULTS
0	5	Helix	structure_element	Helix α1 contains two more positively charged amino acids K17 and R25 as does the loop preceding it (R9).	RESULTS
6	8	α1	structure_element	Helix α1 contains two more positively charged amino acids K17 and R25 as does the loop preceding it (R9).	RESULTS
58	61	K17	residue_name_number	Helix α1 contains two more positively charged amino acids K17 and R25 as does the loop preceding it (R9).	RESULTS
66	69	R25	residue_name_number	Helix α1 contains two more positively charged amino acids K17 and R25 as does the loop preceding it (R9).	RESULTS
82	86	loop	structure_element	Helix α1 contains two more positively charged amino acids K17 and R25 as does the loop preceding it (R9).	RESULTS
101	103	R9	residue_name_number	Helix α1 contains two more positively charged amino acids K17 and R25 as does the loop preceding it (R9).	RESULTS
68	73	helix	structure_element	A second cluster of positively charged residues is found in or near helix α3 (K74, R75, K82, R85 and K87).	RESULTS
74	76	α3	structure_element	A second cluster of positively charged residues is found in or near helix α3 (K74, R75, K82, R85 and K87).	RESULTS
78	81	K74	residue_name_number	A second cluster of positively charged residues is found in or near helix α3 (K74, R75, K82, R85 and K87).	RESULTS
83	86	R75	residue_name_number	A second cluster of positively charged residues is found in or near helix α3 (K74, R75, K82, R85 and K87).	RESULTS
88	91	K82	residue_name_number	A second cluster of positively charged residues is found in or near helix α3 (K74, R75, K82, R85 and K87).	RESULTS
93	96	R85	residue_name_number	A second cluster of positively charged residues is found in or near helix α3 (K74, R75, K82, R85 and K87).	RESULTS
101	104	K87	residue_name_number	A second cluster of positively charged residues is found in or near helix α3 (K74, R75, K82, R85 and K87).	RESULTS
30	39	conserved	protein_state	Some of these amino acids are conserved between archaeal and eukaryotic Tsr3 (Supplementary Figure S1A).	RESULTS
48	56	archaeal	taxonomy_domain	Some of these amino acids are conserved between archaeal and eukaryotic Tsr3 (Supplementary Figure S1A).	RESULTS
61	71	eukaryotic	taxonomy_domain	Some of these amino acids are conserved between archaeal and eukaryotic Tsr3 (Supplementary Figure S1A).	RESULTS
72	76	Tsr3	protein	Some of these amino acids are conserved between archaeal and eukaryotic Tsr3 (Supplementary Figure S1A).	RESULTS
7	24	C-terminal domain	structure_element	In the C-terminal domain, the surface exposed α-helices α5 and α7 carry a significant amount of positively charged amino acids.	RESULTS
46	55	α-helices	structure_element	In the C-terminal domain, the surface exposed α-helices α5 and α7 carry a significant amount of positively charged amino acids.	RESULTS
56	58	α5	structure_element	In the C-terminal domain, the surface exposed α-helices α5 and α7 carry a significant amount of positively charged amino acids.	RESULTS
63	65	α7	structure_element	In the C-terminal domain, the surface exposed α-helices α5 and α7 carry a significant amount of positively charged amino acids.	RESULTS
2	17	triple mutation	experimental_method	A triple mutation of the conserved positively charged residues R60, K65 and R131 to A in ScTsr3 resulted in a protein with a significantly impaired acp transferase activity in vivo (Figure 6D) in line with an important functional role for these positively charged residues.	RESULTS
25	34	conserved	protein_state	A triple mutation of the conserved positively charged residues R60, K65 and R131 to A in ScTsr3 resulted in a protein with a significantly impaired acp transferase activity in vivo (Figure 6D) in line with an important functional role for these positively charged residues.	RESULTS
63	66	R60	residue_name_number	A triple mutation of the conserved positively charged residues R60, K65 and R131 to A in ScTsr3 resulted in a protein with a significantly impaired acp transferase activity in vivo (Figure 6D) in line with an important functional role for these positively charged residues.	RESULTS
68	71	K65	residue_name_number	A triple mutation of the conserved positively charged residues R60, K65 and R131 to A in ScTsr3 resulted in a protein with a significantly impaired acp transferase activity in vivo (Figure 6D) in line with an important functional role for these positively charged residues.	RESULTS
76	80	R131	residue_name_number	A triple mutation of the conserved positively charged residues R60, K65 and R131 to A in ScTsr3 resulted in a protein with a significantly impaired acp transferase activity in vivo (Figure 6D) in line with an important functional role for these positively charged residues.	RESULTS
84	85	A	residue_name	A triple mutation of the conserved positively charged residues R60, K65 and R131 to A in ScTsr3 resulted in a protein with a significantly impaired acp transferase activity in vivo (Figure 6D) in line with an important functional role for these positively charged residues.	RESULTS
89	95	ScTsr3	protein	A triple mutation of the conserved positively charged residues R60, K65 and R131 to A in ScTsr3 resulted in a protein with a significantly impaired acp transferase activity in vivo (Figure 6D) in line with an important functional role for these positively charged residues.	RESULTS
148	163	acp transferase	protein_type	A triple mutation of the conserved positively charged residues R60, K65 and R131 to A in ScTsr3 resulted in a protein with a significantly impaired acp transferase activity in vivo (Figure 6D) in line with an important functional role for these positively charged residues.	RESULTS
15	19	Tsr3	protein	RNA-binding of Tsr3.	FIG
56	62	VdTsr3	protein	(A) Electrostatic charge distribution on the surface of VdTsr3.	FIG
0	3	SAM	chemical	SAM is shown in a stick representation.	FIG
59	62	MES	chemical	Also shown in stick representation is a negatively charged MES ion.	FIG
0	9	Conserved	protein_state	Conserved basic amino acids are labeled. (B) Comparison of the secondary structures of helix 31 from the small ribosomal subunit rRNAs in S. cerevisiae and S. solfataricus with the location of the hypermodified nucleotide indicated in red.	FIG
16	27	amino acids	chemical	Conserved basic amino acids are labeled. (B) Comparison of the secondary structures of helix 31 from the small ribosomal subunit rRNAs in S. cerevisiae and S. solfataricus with the location of the hypermodified nucleotide indicated in red.	FIG
87	95	helix 31	structure_element	Conserved basic amino acids are labeled. (B) Comparison of the secondary structures of helix 31 from the small ribosomal subunit rRNAs in S. cerevisiae and S. solfataricus with the location of the hypermodified nucleotide indicated in red.	FIG
129	134	rRNAs	chemical	Conserved basic amino acids are labeled. (B) Comparison of the secondary structures of helix 31 from the small ribosomal subunit rRNAs in S. cerevisiae and S. solfataricus with the location of the hypermodified nucleotide indicated in red.	FIG
138	151	S. cerevisiae	species	Conserved basic amino acids are labeled. (B) Comparison of the secondary structures of helix 31 from the small ribosomal subunit rRNAs in S. cerevisiae and S. solfataricus with the location of the hypermodified nucleotide indicated in red.	FIG
156	171	S. solfataricus	species	Conserved basic amino acids are labeled. (B) Comparison of the secondary structures of helix 31 from the small ribosomal subunit rRNAs in S. cerevisiae and S. solfataricus with the location of the hypermodified nucleotide indicated in red.	FIG
197	210	hypermodified	protein_state	Conserved basic amino acids are labeled. (B) Comparison of the secondary structures of helix 31 from the small ribosomal subunit rRNAs in S. cerevisiae and S. solfataricus with the location of the hypermodified nucleotide indicated in red.	FIG
211	221	nucleotide	chemical	Conserved basic amino acids are labeled. (B) Comparison of the secondary structures of helix 31 from the small ribosomal subunit rRNAs in S. cerevisiae and S. solfataricus with the location of the hypermodified nucleotide indicated in red.	FIG
4	19	S. solfataricus	species	For S. solfataricus the chemical identity of the hypermodified nucleotide is not known but the existence of NEP1 and TSR3 homologs suggest that it is indeed N1-methyl-N3-acp-pseudouridine.	FIG
49	62	hypermodified	protein_state	For S. solfataricus the chemical identity of the hypermodified nucleotide is not known but the existence of NEP1 and TSR3 homologs suggest that it is indeed N1-methyl-N3-acp-pseudouridine.	FIG
63	73	nucleotide	chemical	For S. solfataricus the chemical identity of the hypermodified nucleotide is not known but the existence of NEP1 and TSR3 homologs suggest that it is indeed N1-methyl-N3-acp-pseudouridine.	FIG
108	112	NEP1	protein	For S. solfataricus the chemical identity of the hypermodified nucleotide is not known but the existence of NEP1 and TSR3 homologs suggest that it is indeed N1-methyl-N3-acp-pseudouridine.	FIG
117	121	TSR3	protein	For S. solfataricus the chemical identity of the hypermodified nucleotide is not known but the existence of NEP1 and TSR3 homologs suggest that it is indeed N1-methyl-N3-acp-pseudouridine.	FIG
157	187	N1-methyl-N3-acp-pseudouridine	chemical	For S. solfataricus the chemical identity of the hypermodified nucleotide is not known but the existence of NEP1 and TSR3 homologs suggest that it is indeed N1-methyl-N3-acp-pseudouridine.	FIG
15	21	SsTsr3	protein	(C) Binding of SsTsr3 to RNA.	FIG
25	28	RNA	chemical	(C) Binding of SsTsr3 to RNA.	FIG
3	15	fluoresceine	chemical	5′-fluoresceine labeled RNA oligonucleotides corresponding either to the native (20mer – see inset) or a stabilized (20mer_GC - inset) helix 31 of the small ribosomal subunit rRNA from S. solfataricus were titrated with increasing amounts of SsTsr3 and the changes in the fluoresceine fluorescence anisotropy were measured and fitted to a binding curve (20mer – red, 20mer_GC – blue).	FIG
24	27	RNA	chemical	5′-fluoresceine labeled RNA oligonucleotides corresponding either to the native (20mer – see inset) or a stabilized (20mer_GC - inset) helix 31 of the small ribosomal subunit rRNA from S. solfataricus were titrated with increasing amounts of SsTsr3 and the changes in the fluoresceine fluorescence anisotropy were measured and fitted to a binding curve (20mer – red, 20mer_GC – blue).	FIG
73	79	native	protein_state	5′-fluoresceine labeled RNA oligonucleotides corresponding either to the native (20mer – see inset) or a stabilized (20mer_GC - inset) helix 31 of the small ribosomal subunit rRNA from S. solfataricus were titrated with increasing amounts of SsTsr3 and the changes in the fluoresceine fluorescence anisotropy were measured and fitted to a binding curve (20mer – red, 20mer_GC – blue).	FIG
81	86	20mer	oligomeric_state	5′-fluoresceine labeled RNA oligonucleotides corresponding either to the native (20mer – see inset) or a stabilized (20mer_GC - inset) helix 31 of the small ribosomal subunit rRNA from S. solfataricus were titrated with increasing amounts of SsTsr3 and the changes in the fluoresceine fluorescence anisotropy were measured and fitted to a binding curve (20mer – red, 20mer_GC – blue).	FIG
105	115	stabilized	protein_state	5′-fluoresceine labeled RNA oligonucleotides corresponding either to the native (20mer – see inset) or a stabilized (20mer_GC - inset) helix 31 of the small ribosomal subunit rRNA from S. solfataricus were titrated with increasing amounts of SsTsr3 and the changes in the fluoresceine fluorescence anisotropy were measured and fitted to a binding curve (20mer – red, 20mer_GC – blue).	FIG
117	125	20mer_GC	oligomeric_state	5′-fluoresceine labeled RNA oligonucleotides corresponding either to the native (20mer – see inset) or a stabilized (20mer_GC - inset) helix 31 of the small ribosomal subunit rRNA from S. solfataricus were titrated with increasing amounts of SsTsr3 and the changes in the fluoresceine fluorescence anisotropy were measured and fitted to a binding curve (20mer – red, 20mer_GC – blue).	FIG
135	143	helix 31	structure_element	5′-fluoresceine labeled RNA oligonucleotides corresponding either to the native (20mer – see inset) or a stabilized (20mer_GC - inset) helix 31 of the small ribosomal subunit rRNA from S. solfataricus were titrated with increasing amounts of SsTsr3 and the changes in the fluoresceine fluorescence anisotropy were measured and fitted to a binding curve (20mer – red, 20mer_GC – blue).	FIG
175	179	rRNA	chemical	5′-fluoresceine labeled RNA oligonucleotides corresponding either to the native (20mer – see inset) or a stabilized (20mer_GC - inset) helix 31 of the small ribosomal subunit rRNA from S. solfataricus were titrated with increasing amounts of SsTsr3 and the changes in the fluoresceine fluorescence anisotropy were measured and fitted to a binding curve (20mer – red, 20mer_GC – blue).	FIG
185	200	S. solfataricus	species	5′-fluoresceine labeled RNA oligonucleotides corresponding either to the native (20mer – see inset) or a stabilized (20mer_GC - inset) helix 31 of the small ribosomal subunit rRNA from S. solfataricus were titrated with increasing amounts of SsTsr3 and the changes in the fluoresceine fluorescence anisotropy were measured and fitted to a binding curve (20mer – red, 20mer_GC – blue).	FIG
206	238	titrated with increasing amounts	experimental_method	5′-fluoresceine labeled RNA oligonucleotides corresponding either to the native (20mer – see inset) or a stabilized (20mer_GC - inset) helix 31 of the small ribosomal subunit rRNA from S. solfataricus were titrated with increasing amounts of SsTsr3 and the changes in the fluoresceine fluorescence anisotropy were measured and fitted to a binding curve (20mer – red, 20mer_GC – blue).	FIG
242	248	SsTsr3	protein	5′-fluoresceine labeled RNA oligonucleotides corresponding either to the native (20mer – see inset) or a stabilized (20mer_GC - inset) helix 31 of the small ribosomal subunit rRNA from S. solfataricus were titrated with increasing amounts of SsTsr3 and the changes in the fluoresceine fluorescence anisotropy were measured and fitted to a binding curve (20mer – red, 20mer_GC – blue).	FIG
272	284	fluoresceine	chemical	5′-fluoresceine labeled RNA oligonucleotides corresponding either to the native (20mer – see inset) or a stabilized (20mer_GC - inset) helix 31 of the small ribosomal subunit rRNA from S. solfataricus were titrated with increasing amounts of SsTsr3 and the changes in the fluoresceine fluorescence anisotropy were measured and fitted to a binding curve (20mer – red, 20mer_GC – blue).	FIG
285	308	fluorescence anisotropy	evidence	5′-fluoresceine labeled RNA oligonucleotides corresponding either to the native (20mer – see inset) or a stabilized (20mer_GC - inset) helix 31 of the small ribosomal subunit rRNA from S. solfataricus were titrated with increasing amounts of SsTsr3 and the changes in the fluoresceine fluorescence anisotropy were measured and fitted to a binding curve (20mer – red, 20mer_GC – blue).	FIG
339	352	binding curve	evidence	5′-fluoresceine labeled RNA oligonucleotides corresponding either to the native (20mer – see inset) or a stabilized (20mer_GC - inset) helix 31 of the small ribosomal subunit rRNA from S. solfataricus were titrated with increasing amounts of SsTsr3 and the changes in the fluoresceine fluorescence anisotropy were measured and fitted to a binding curve (20mer – red, 20mer_GC – blue).	FIG
354	359	20mer	oligomeric_state	5′-fluoresceine labeled RNA oligonucleotides corresponding either to the native (20mer – see inset) or a stabilized (20mer_GC - inset) helix 31 of the small ribosomal subunit rRNA from S. solfataricus were titrated with increasing amounts of SsTsr3 and the changes in the fluoresceine fluorescence anisotropy were measured and fitted to a binding curve (20mer – red, 20mer_GC – blue).	FIG
367	375	20mer_GC	oligomeric_state	5′-fluoresceine labeled RNA oligonucleotides corresponding either to the native (20mer – see inset) or a stabilized (20mer_GC - inset) helix 31 of the small ribosomal subunit rRNA from S. solfataricus were titrated with increasing amounts of SsTsr3 and the changes in the fluoresceine fluorescence anisotropy were measured and fitted to a binding curve (20mer – red, 20mer_GC – blue).	FIG
0	12	Oligo-U9-RNA	chemical	Oligo-U9-RNA was used for comparison (black).	FIG
4	12	20mer_GC	oligomeric_state	The 20mer_GC RNA was also titrated with SsTsr3 in the presence of 2 mM SAM (purple). (D) Mutants of ScTsr3 R60, K65 or R131 (equivalent to K17, K22 and R91 in VdTsr3) expressed in Δtsr3 yeast cells show a primer extension stop comparable to the wild type.	FIG
13	16	RNA	chemical	The 20mer_GC RNA was also titrated with SsTsr3 in the presence of 2 mM SAM (purple). (D) Mutants of ScTsr3 R60, K65 or R131 (equivalent to K17, K22 and R91 in VdTsr3) expressed in Δtsr3 yeast cells show a primer extension stop comparable to the wild type.	FIG
26	34	titrated	experimental_method	The 20mer_GC RNA was also titrated with SsTsr3 in the presence of 2 mM SAM (purple). (D) Mutants of ScTsr3 R60, K65 or R131 (equivalent to K17, K22 and R91 in VdTsr3) expressed in Δtsr3 yeast cells show a primer extension stop comparable to the wild type.	FIG
40	46	SsTsr3	protein	The 20mer_GC RNA was also titrated with SsTsr3 in the presence of 2 mM SAM (purple). (D) Mutants of ScTsr3 R60, K65 or R131 (equivalent to K17, K22 and R91 in VdTsr3) expressed in Δtsr3 yeast cells show a primer extension stop comparable to the wild type.	FIG
71	74	SAM	chemical	The 20mer_GC RNA was also titrated with SsTsr3 in the presence of 2 mM SAM (purple). (D) Mutants of ScTsr3 R60, K65 or R131 (equivalent to K17, K22 and R91 in VdTsr3) expressed in Δtsr3 yeast cells show a primer extension stop comparable to the wild type.	FIG
89	96	Mutants	protein_state	The 20mer_GC RNA was also titrated with SsTsr3 in the presence of 2 mM SAM (purple). (D) Mutants of ScTsr3 R60, K65 or R131 (equivalent to K17, K22 and R91 in VdTsr3) expressed in Δtsr3 yeast cells show a primer extension stop comparable to the wild type.	FIG
100	106	ScTsr3	protein	The 20mer_GC RNA was also titrated with SsTsr3 in the presence of 2 mM SAM (purple). (D) Mutants of ScTsr3 R60, K65 or R131 (equivalent to K17, K22 and R91 in VdTsr3) expressed in Δtsr3 yeast cells show a primer extension stop comparable to the wild type.	FIG
107	110	R60	residue_name_number	The 20mer_GC RNA was also titrated with SsTsr3 in the presence of 2 mM SAM (purple). (D) Mutants of ScTsr3 R60, K65 or R131 (equivalent to K17, K22 and R91 in VdTsr3) expressed in Δtsr3 yeast cells show a primer extension stop comparable to the wild type.	FIG
112	115	K65	residue_name_number	The 20mer_GC RNA was also titrated with SsTsr3 in the presence of 2 mM SAM (purple). (D) Mutants of ScTsr3 R60, K65 or R131 (equivalent to K17, K22 and R91 in VdTsr3) expressed in Δtsr3 yeast cells show a primer extension stop comparable to the wild type.	FIG
119	123	R131	residue_name_number	The 20mer_GC RNA was also titrated with SsTsr3 in the presence of 2 mM SAM (purple). (D) Mutants of ScTsr3 R60, K65 or R131 (equivalent to K17, K22 and R91 in VdTsr3) expressed in Δtsr3 yeast cells show a primer extension stop comparable to the wild type.	FIG
139	142	K17	residue_name_number	The 20mer_GC RNA was also titrated with SsTsr3 in the presence of 2 mM SAM (purple). (D) Mutants of ScTsr3 R60, K65 or R131 (equivalent to K17, K22 and R91 in VdTsr3) expressed in Δtsr3 yeast cells show a primer extension stop comparable to the wild type.	FIG
144	147	K22	residue_name_number	The 20mer_GC RNA was also titrated with SsTsr3 in the presence of 2 mM SAM (purple). (D) Mutants of ScTsr3 R60, K65 or R131 (equivalent to K17, K22 and R91 in VdTsr3) expressed in Δtsr3 yeast cells show a primer extension stop comparable to the wild type.	FIG
152	155	R91	residue_name_number	The 20mer_GC RNA was also titrated with SsTsr3 in the presence of 2 mM SAM (purple). (D) Mutants of ScTsr3 R60, K65 or R131 (equivalent to K17, K22 and R91 in VdTsr3) expressed in Δtsr3 yeast cells show a primer extension stop comparable to the wild type.	FIG
159	165	VdTsr3	protein	The 20mer_GC RNA was also titrated with SsTsr3 in the presence of 2 mM SAM (purple). (D) Mutants of ScTsr3 R60, K65 or R131 (equivalent to K17, K22 and R91 in VdTsr3) expressed in Δtsr3 yeast cells show a primer extension stop comparable to the wild type.	FIG
167	176	expressed	experimental_method	The 20mer_GC RNA was also titrated with SsTsr3 in the presence of 2 mM SAM (purple). (D) Mutants of ScTsr3 R60, K65 or R131 (equivalent to K17, K22 and R91 in VdTsr3) expressed in Δtsr3 yeast cells show a primer extension stop comparable to the wild type.	FIG
180	185	Δtsr3	mutant	The 20mer_GC RNA was also titrated with SsTsr3 in the presence of 2 mM SAM (purple). (D) Mutants of ScTsr3 R60, K65 or R131 (equivalent to K17, K22 and R91 in VdTsr3) expressed in Δtsr3 yeast cells show a primer extension stop comparable to the wild type.	FIG
186	191	yeast	taxonomy_domain	The 20mer_GC RNA was also titrated with SsTsr3 in the presence of 2 mM SAM (purple). (D) Mutants of ScTsr3 R60, K65 or R131 (equivalent to K17, K22 and R91 in VdTsr3) expressed in Δtsr3 yeast cells show a primer extension stop comparable to the wild type.	FIG
205	226	primer extension stop	evidence	The 20mer_GC RNA was also titrated with SsTsr3 in the presence of 2 mM SAM (purple). (D) Mutants of ScTsr3 R60, K65 or R131 (equivalent to K17, K22 and R91 in VdTsr3) expressed in Δtsr3 yeast cells show a primer extension stop comparable to the wild type.	FIG
245	254	wild type	protein_state	The 20mer_GC RNA was also titrated with SsTsr3 in the presence of 2 mM SAM (purple). (D) Mutants of ScTsr3 R60, K65 or R131 (equivalent to K17, K22 and R91 in VdTsr3) expressed in Δtsr3 yeast cells show a primer extension stop comparable to the wild type.	FIG
0	40	Combination of the three point mutations	experimental_method	Combination of the three point mutations (R60A/K65A/R131A) leads to a strongly reduced acp modification of 18S rRNA.	FIG
42	46	R60A	mutant	Combination of the three point mutations (R60A/K65A/R131A) leads to a strongly reduced acp modification of 18S rRNA.	FIG
47	51	K65A	mutant	Combination of the three point mutations (R60A/K65A/R131A) leads to a strongly reduced acp modification of 18S rRNA.	FIG
52	57	R131A	mutant	Combination of the three point mutations (R60A/K65A/R131A) leads to a strongly reduced acp modification of 18S rRNA.	FIG
87	90	acp	chemical	Combination of the three point mutations (R60A/K65A/R131A) leads to a strongly reduced acp modification of 18S rRNA.	FIG
107	115	18S rRNA	chemical	Combination of the three point mutations (R60A/K65A/R131A) leads to a strongly reduced acp modification of 18S rRNA.	FIG
50	54	Tsr3	protein	In order to explore the RNA-ligand specificity of Tsr3 we titrated SsTsr3 prepared in RNase-free form with 5′-fluoresceine-labeled RNA and determined the affinity by fluorescence anisotropy measurements.	RESULTS
58	66	titrated	experimental_method	In order to explore the RNA-ligand specificity of Tsr3 we titrated SsTsr3 prepared in RNase-free form with 5′-fluoresceine-labeled RNA and determined the affinity by fluorescence anisotropy measurements.	RESULTS
67	73	SsTsr3	protein	In order to explore the RNA-ligand specificity of Tsr3 we titrated SsTsr3 prepared in RNase-free form with 5′-fluoresceine-labeled RNA and determined the affinity by fluorescence anisotropy measurements.	RESULTS
86	96	RNase-free	protein_state	In order to explore the RNA-ligand specificity of Tsr3 we titrated SsTsr3 prepared in RNase-free form with 5′-fluoresceine-labeled RNA and determined the affinity by fluorescence anisotropy measurements.	RESULTS
110	122	fluoresceine	chemical	In order to explore the RNA-ligand specificity of Tsr3 we titrated SsTsr3 prepared in RNase-free form with 5′-fluoresceine-labeled RNA and determined the affinity by fluorescence anisotropy measurements.	RESULTS
131	134	RNA	chemical	In order to explore the RNA-ligand specificity of Tsr3 we titrated SsTsr3 prepared in RNase-free form with 5′-fluoresceine-labeled RNA and determined the affinity by fluorescence anisotropy measurements.	RESULTS
154	162	affinity	evidence	In order to explore the RNA-ligand specificity of Tsr3 we titrated SsTsr3 prepared in RNase-free form with 5′-fluoresceine-labeled RNA and determined the affinity by fluorescence anisotropy measurements.	RESULTS
166	202	fluorescence anisotropy measurements	experimental_method	In order to explore the RNA-ligand specificity of Tsr3 we titrated SsTsr3 prepared in RNase-free form with 5′-fluoresceine-labeled RNA and determined the affinity by fluorescence anisotropy measurements.	RESULTS
0	6	SsTsr3	protein	SsTsr3 in the apo state bound a 20mer RNA corresponding to helix 31 of S. solfataricus 16S rRNA (Figure 6B) with a KD of 1.9 μM and to a version of this hairpin stabilized by additional GC base pairs (20mer-GC) with a KD of 0.6 μM (Figure 6C).	RESULTS
14	17	apo	protein_state	SsTsr3 in the apo state bound a 20mer RNA corresponding to helix 31 of S. solfataricus 16S rRNA (Figure 6B) with a KD of 1.9 μM and to a version of this hairpin stabilized by additional GC base pairs (20mer-GC) with a KD of 0.6 μM (Figure 6C).	RESULTS
24	29	bound	protein_state	SsTsr3 in the apo state bound a 20mer RNA corresponding to helix 31 of S. solfataricus 16S rRNA (Figure 6B) with a KD of 1.9 μM and to a version of this hairpin stabilized by additional GC base pairs (20mer-GC) with a KD of 0.6 μM (Figure 6C).	RESULTS
32	37	20mer	oligomeric_state	SsTsr3 in the apo state bound a 20mer RNA corresponding to helix 31 of S. solfataricus 16S rRNA (Figure 6B) with a KD of 1.9 μM and to a version of this hairpin stabilized by additional GC base pairs (20mer-GC) with a KD of 0.6 μM (Figure 6C).	RESULTS
38	41	RNA	chemical	SsTsr3 in the apo state bound a 20mer RNA corresponding to helix 31 of S. solfataricus 16S rRNA (Figure 6B) with a KD of 1.9 μM and to a version of this hairpin stabilized by additional GC base pairs (20mer-GC) with a KD of 0.6 μM (Figure 6C).	RESULTS
59	67	helix 31	structure_element	SsTsr3 in the apo state bound a 20mer RNA corresponding to helix 31 of S. solfataricus 16S rRNA (Figure 6B) with a KD of 1.9 μM and to a version of this hairpin stabilized by additional GC base pairs (20mer-GC) with a KD of 0.6 μM (Figure 6C).	RESULTS
71	86	S. solfataricus	species	SsTsr3 in the apo state bound a 20mer RNA corresponding to helix 31 of S. solfataricus 16S rRNA (Figure 6B) with a KD of 1.9 μM and to a version of this hairpin stabilized by additional GC base pairs (20mer-GC) with a KD of 0.6 μM (Figure 6C).	RESULTS
87	95	16S rRNA	chemical	SsTsr3 in the apo state bound a 20mer RNA corresponding to helix 31 of S. solfataricus 16S rRNA (Figure 6B) with a KD of 1.9 μM and to a version of this hairpin stabilized by additional GC base pairs (20mer-GC) with a KD of 0.6 μM (Figure 6C).	RESULTS
115	117	KD	evidence	SsTsr3 in the apo state bound a 20mer RNA corresponding to helix 31 of S. solfataricus 16S rRNA (Figure 6B) with a KD of 1.9 μM and to a version of this hairpin stabilized by additional GC base pairs (20mer-GC) with a KD of 0.6 μM (Figure 6C).	RESULTS
153	160	hairpin	structure_element	SsTsr3 in the apo state bound a 20mer RNA corresponding to helix 31 of S. solfataricus 16S rRNA (Figure 6B) with a KD of 1.9 μM and to a version of this hairpin stabilized by additional GC base pairs (20mer-GC) with a KD of 0.6 μM (Figure 6C).	RESULTS
201	209	20mer-GC	oligomeric_state	SsTsr3 in the apo state bound a 20mer RNA corresponding to helix 31 of S. solfataricus 16S rRNA (Figure 6B) with a KD of 1.9 μM and to a version of this hairpin stabilized by additional GC base pairs (20mer-GC) with a KD of 0.6 μM (Figure 6C).	RESULTS
218	220	KD	evidence	SsTsr3 in the apo state bound a 20mer RNA corresponding to helix 31 of S. solfataricus 16S rRNA (Figure 6B) with a KD of 1.9 μM and to a version of this hairpin stabilized by additional GC base pairs (20mer-GC) with a KD of 0.6 μM (Figure 6C).	RESULTS
18	28	oligoU-RNA	chemical	A single stranded oligoU-RNA bound with a 10-fold-reduced affinity (6.0 μM).	RESULTS
29	34	bound	protein_state	A single stranded oligoU-RNA bound with a 10-fold-reduced affinity (6.0 μM).	RESULTS
58	66	affinity	evidence	A single stranded oligoU-RNA bound with a 10-fold-reduced affinity (6.0 μM).	RESULTS
38	41	SAM	chemical	The presence of saturating amounts of SAM (2 mM) did not have a significant influence on the RNA-affinity of SsTsr3 (KD of 1.7 μM for the 20mer-GC-RNA) suggesting no cooperativity in substrate binding.	RESULTS
93	105	RNA-affinity	evidence	The presence of saturating amounts of SAM (2 mM) did not have a significant influence on the RNA-affinity of SsTsr3 (KD of 1.7 μM for the 20mer-GC-RNA) suggesting no cooperativity in substrate binding.	RESULTS
109	115	SsTsr3	protein	The presence of saturating amounts of SAM (2 mM) did not have a significant influence on the RNA-affinity of SsTsr3 (KD of 1.7 μM for the 20mer-GC-RNA) suggesting no cooperativity in substrate binding.	RESULTS
117	119	KD	evidence	The presence of saturating amounts of SAM (2 mM) did not have a significant influence on the RNA-affinity of SsTsr3 (KD of 1.7 μM for the 20mer-GC-RNA) suggesting no cooperativity in substrate binding.	RESULTS
138	146	20mer-GC	oligomeric_state	The presence of saturating amounts of SAM (2 mM) did not have a significant influence on the RNA-affinity of SsTsr3 (KD of 1.7 μM for the 20mer-GC-RNA) suggesting no cooperativity in substrate binding.	RESULTS
147	150	RNA	chemical	The presence of saturating amounts of SAM (2 mM) did not have a significant influence on the RNA-affinity of SsTsr3 (KD of 1.7 μM for the 20mer-GC-RNA) suggesting no cooperativity in substrate binding.	RESULTS
0	5	U1191	residue_name_number	U1191 is the only hypermodified base in the yeast 18S rRNA and is strongly conserved in eukaryotes.	DISCUSS
18	31	hypermodified	protein_state	U1191 is the only hypermodified base in the yeast 18S rRNA and is strongly conserved in eukaryotes.	DISCUSS
44	49	yeast	taxonomy_domain	U1191 is the only hypermodified base in the yeast 18S rRNA and is strongly conserved in eukaryotes.	DISCUSS
50	58	18S rRNA	chemical	U1191 is the only hypermodified base in the yeast 18S rRNA and is strongly conserved in eukaryotes.	DISCUSS
66	84	strongly conserved	protein_state	U1191 is the only hypermodified base in the yeast 18S rRNA and is strongly conserved in eukaryotes.	DISCUSS
88	98	eukaryotes	taxonomy_domain	U1191 is the only hypermodified base in the yeast 18S rRNA and is strongly conserved in eukaryotes.	DISCUSS
17	67	1-methyl-3-(3-amino-3-carboxypropyl)-pseudouridine	chemical	The formation of 1-methyl-3-(3-amino-3-carboxypropyl)-pseudouridine (m1acp3Ψ) is very complex requiring three successive modification reactions involving one H/ACA snoRNP (snR35) and two protein enzymes (Nep1/Emg1 and Tsr3).	DISCUSS
69	76	m1acp3Ψ	chemical	The formation of 1-methyl-3-(3-amino-3-carboxypropyl)-pseudouridine (m1acp3Ψ) is very complex requiring three successive modification reactions involving one H/ACA snoRNP (snR35) and two protein enzymes (Nep1/Emg1 and Tsr3).	DISCUSS
158	163	H/ACA	structure_element	The formation of 1-methyl-3-(3-amino-3-carboxypropyl)-pseudouridine (m1acp3Ψ) is very complex requiring three successive modification reactions involving one H/ACA snoRNP (snR35) and two protein enzymes (Nep1/Emg1 and Tsr3).	DISCUSS
164	170	snoRNP	complex_assembly	The formation of 1-methyl-3-(3-amino-3-carboxypropyl)-pseudouridine (m1acp3Ψ) is very complex requiring three successive modification reactions involving one H/ACA snoRNP (snR35) and two protein enzymes (Nep1/Emg1 and Tsr3).	DISCUSS
172	177	snR35	protein	The formation of 1-methyl-3-(3-amino-3-carboxypropyl)-pseudouridine (m1acp3Ψ) is very complex requiring three successive modification reactions involving one H/ACA snoRNP (snR35) and two protein enzymes (Nep1/Emg1 and Tsr3).	DISCUSS
204	208	Nep1	protein	The formation of 1-methyl-3-(3-amino-3-carboxypropyl)-pseudouridine (m1acp3Ψ) is very complex requiring three successive modification reactions involving one H/ACA snoRNP (snR35) and two protein enzymes (Nep1/Emg1 and Tsr3).	DISCUSS
209	213	Emg1	protein	The formation of 1-methyl-3-(3-amino-3-carboxypropyl)-pseudouridine (m1acp3Ψ) is very complex requiring three successive modification reactions involving one H/ACA snoRNP (snR35) and two protein enzymes (Nep1/Emg1 and Tsr3).	DISCUSS
218	222	Tsr3	protein	The formation of 1-methyl-3-(3-amino-3-carboxypropyl)-pseudouridine (m1acp3Ψ) is very complex requiring three successive modification reactions involving one H/ACA snoRNP (snR35) and two protein enzymes (Nep1/Emg1 and Tsr3).	DISCUSS
24	34	eukaryotic	taxonomy_domain	This makes it unique in eukaryotic rRNA modification.	DISCUSS
35	39	rRNA	chemical	This makes it unique in eukaryotic rRNA modification.	DISCUSS
4	11	m1acp3Ψ	chemical	The m1acp3Ψ base is located at the tip of helix 31 on the 18S rRNA (Supplementary Figure S1B) which, together with helices 18, 24, 34 and 44, contribute to building the decoding center of the small ribosomal subunit.	DISCUSS
42	50	helix 31	structure_element	The m1acp3Ψ base is located at the tip of helix 31 on the 18S rRNA (Supplementary Figure S1B) which, together with helices 18, 24, 34 and 44, contribute to building the decoding center of the small ribosomal subunit.	DISCUSS
58	66	18S rRNA	chemical	The m1acp3Ψ base is located at the tip of helix 31 on the 18S rRNA (Supplementary Figure S1B) which, together with helices 18, 24, 34 and 44, contribute to building the decoding center of the small ribosomal subunit.	DISCUSS
115	140	helices 18, 24, 34 and 44	structure_element	The m1acp3Ψ base is located at the tip of helix 31 on the 18S rRNA (Supplementary Figure S1B) which, together with helices 18, 24, 34 and 44, contribute to building the decoding center of the small ribosomal subunit.	DISCUSS
24	29	acp3U	chemical	A similar modification (acp3U) was identified in Haloferax volcanii and corresponding modified nucleotides were also shown to occur in other archaea.	DISCUSS
49	67	Haloferax volcanii	species	A similar modification (acp3U) was identified in Haloferax volcanii and corresponding modified nucleotides were also shown to occur in other archaea.	DISCUSS
95	106	nucleotides	chemical	A similar modification (acp3U) was identified in Haloferax volcanii and corresponding modified nucleotides were also shown to occur in other archaea.	DISCUSS
141	148	archaea	taxonomy_domain	A similar modification (acp3U) was identified in Haloferax volcanii and corresponding modified nucleotides were also shown to occur in other archaea.	DISCUSS
14	18	TSR3	protein	As shown here TSR3 encodes the transferase catalyzing the acp modification as the last step in the biosynthesis of m1acp3Ψ in yeast and human cells.	DISCUSS
58	61	acp	chemical	As shown here TSR3 encodes the transferase catalyzing the acp modification as the last step in the biosynthesis of m1acp3Ψ in yeast and human cells.	DISCUSS
115	122	m1acp3Ψ	chemical	As shown here TSR3 encodes the transferase catalyzing the acp modification as the last step in the biosynthesis of m1acp3Ψ in yeast and human cells.	DISCUSS
126	131	yeast	taxonomy_domain	As shown here TSR3 encodes the transferase catalyzing the acp modification as the last step in the biosynthesis of m1acp3Ψ in yeast and human cells.	DISCUSS
136	141	human	species	As shown here TSR3 encodes the transferase catalyzing the acp modification as the last step in the biosynthesis of m1acp3Ψ in yeast and human cells.	DISCUSS
14	22	archaeal	taxonomy_domain	Unexpectedly, archaeal Tsr3 has a structure similar to SPOUT-class RNA methyltransferases, and it is the first example for an enzyme of this class transferring an acp group, due to a modified SAM-binding pocket that exposes the acp instead of the methyl group of SAM to its RNA substrate.	DISCUSS
23	27	Tsr3	protein	Unexpectedly, archaeal Tsr3 has a structure similar to SPOUT-class RNA methyltransferases, and it is the first example for an enzyme of this class transferring an acp group, due to a modified SAM-binding pocket that exposes the acp instead of the methyl group of SAM to its RNA substrate.	DISCUSS
34	43	structure	evidence	Unexpectedly, archaeal Tsr3 has a structure similar to SPOUT-class RNA methyltransferases, and it is the first example for an enzyme of this class transferring an acp group, due to a modified SAM-binding pocket that exposes the acp instead of the methyl group of SAM to its RNA substrate.	DISCUSS
55	89	SPOUT-class RNA methyltransferases	protein_type	Unexpectedly, archaeal Tsr3 has a structure similar to SPOUT-class RNA methyltransferases, and it is the first example for an enzyme of this class transferring an acp group, due to a modified SAM-binding pocket that exposes the acp instead of the methyl group of SAM to its RNA substrate.	DISCUSS
163	166	acp	chemical	Unexpectedly, archaeal Tsr3 has a structure similar to SPOUT-class RNA methyltransferases, and it is the first example for an enzyme of this class transferring an acp group, due to a modified SAM-binding pocket that exposes the acp instead of the methyl group of SAM to its RNA substrate.	DISCUSS
192	210	SAM-binding pocket	site	Unexpectedly, archaeal Tsr3 has a structure similar to SPOUT-class RNA methyltransferases, and it is the first example for an enzyme of this class transferring an acp group, due to a modified SAM-binding pocket that exposes the acp instead of the methyl group of SAM to its RNA substrate.	DISCUSS
228	231	acp	chemical	Unexpectedly, archaeal Tsr3 has a structure similar to SPOUT-class RNA methyltransferases, and it is the first example for an enzyme of this class transferring an acp group, due to a modified SAM-binding pocket that exposes the acp instead of the methyl group of SAM to its RNA substrate.	DISCUSS
263	266	SAM	chemical	Unexpectedly, archaeal Tsr3 has a structure similar to SPOUT-class RNA methyltransferases, and it is the first example for an enzyme of this class transferring an acp group, due to a modified SAM-binding pocket that exposes the acp instead of the methyl group of SAM to its RNA substrate.	DISCUSS
274	277	RNA	chemical	Unexpectedly, archaeal Tsr3 has a structure similar to SPOUT-class RNA methyltransferases, and it is the first example for an enzyme of this class transferring an acp group, due to a modified SAM-binding pocket that exposes the acp instead of the methyl group of SAM to its RNA substrate.	DISCUSS
38	72	Rossmann-fold Tyw2 acp transferase	protein_type	Similar to the structurally unrelated Rossmann-fold Tyw2 acp transferase, the SAM methyl group of Tsr3 is bound in an inaccessible hydrophobic pocket whereas the acp side chain becomes accessible for a nucleophilic attack by the N3 of pseudouridine.	DISCUSS
78	81	SAM	chemical	Similar to the structurally unrelated Rossmann-fold Tyw2 acp transferase, the SAM methyl group of Tsr3 is bound in an inaccessible hydrophobic pocket whereas the acp side chain becomes accessible for a nucleophilic attack by the N3 of pseudouridine.	DISCUSS
98	102	Tsr3	protein	Similar to the structurally unrelated Rossmann-fold Tyw2 acp transferase, the SAM methyl group of Tsr3 is bound in an inaccessible hydrophobic pocket whereas the acp side chain becomes accessible for a nucleophilic attack by the N3 of pseudouridine.	DISCUSS
131	149	hydrophobic pocket	site	Similar to the structurally unrelated Rossmann-fold Tyw2 acp transferase, the SAM methyl group of Tsr3 is bound in an inaccessible hydrophobic pocket whereas the acp side chain becomes accessible for a nucleophilic attack by the N3 of pseudouridine.	DISCUSS
162	165	acp	chemical	Similar to the structurally unrelated Rossmann-fold Tyw2 acp transferase, the SAM methyl group of Tsr3 is bound in an inaccessible hydrophobic pocket whereas the acp side chain becomes accessible for a nucleophilic attack by the N3 of pseudouridine.	DISCUSS
235	248	pseudouridine	chemical	Similar to the structurally unrelated Rossmann-fold Tyw2 acp transferase, the SAM methyl group of Tsr3 is bound in an inaccessible hydrophobic pocket whereas the acp side chain becomes accessible for a nucleophilic attack by the N3 of pseudouridine.	DISCUSS
49	70	RNA methyltransferase	protein_type	In contrast, in the structurally closely related RNA methyltransferase Trm10 the methyl group of the cofactor SAM is accessible whereas its acp side chain is buried inside the protein.	DISCUSS
71	76	Trm10	protein	In contrast, in the structurally closely related RNA methyltransferase Trm10 the methyl group of the cofactor SAM is accessible whereas its acp side chain is buried inside the protein.	DISCUSS
110	113	SAM	chemical	In contrast, in the structurally closely related RNA methyltransferase Trm10 the methyl group of the cofactor SAM is accessible whereas its acp side chain is buried inside the protein.	DISCUSS
140	143	acp	chemical	In contrast, in the structurally closely related RNA methyltransferase Trm10 the methyl group of the cofactor SAM is accessible whereas its acp side chain is buried inside the protein.	DISCUSS
34	63	SAM-dependent acp transferase	protein_type	This suggests that enzymes with a SAM-dependent acp transferase activity might have evolved from SAM-dependent methyltransferases by slight modifications of the SAM-binding pocket.	DISCUSS
97	129	SAM-dependent methyltransferases	protein_type	This suggests that enzymes with a SAM-dependent acp transferase activity might have evolved from SAM-dependent methyltransferases by slight modifications of the SAM-binding pocket.	DISCUSS
161	179	SAM-binding pocket	site	This suggests that enzymes with a SAM-dependent acp transferase activity might have evolved from SAM-dependent methyltransferases by slight modifications of the SAM-binding pocket.	DISCUSS
30	45	acp transferase	protein_type	Thus, additional examples for acp transferase enzymes might be found with similarities to other structural classes of methyltransferases.	DISCUSS
118	136	methyltransferases	protein_type	Thus, additional examples for acp transferase enzymes might be found with similarities to other structural classes of methyltransferases.	DISCUSS
15	19	Nep1	protein	In contrast to Nep1, the enzyme preceding Tsr3 in the m1acp3Ψ biosynthesis pathway, Tsr3 binds rather weakly and with little specificity to its isolated substrate RNA.	DISCUSS
42	46	Tsr3	protein	In contrast to Nep1, the enzyme preceding Tsr3 in the m1acp3Ψ biosynthesis pathway, Tsr3 binds rather weakly and with little specificity to its isolated substrate RNA.	DISCUSS
54	61	m1acp3Ψ	chemical	In contrast to Nep1, the enzyme preceding Tsr3 in the m1acp3Ψ biosynthesis pathway, Tsr3 binds rather weakly and with little specificity to its isolated substrate RNA.	DISCUSS
84	88	Tsr3	protein	In contrast to Nep1, the enzyme preceding Tsr3 in the m1acp3Ψ biosynthesis pathway, Tsr3 binds rather weakly and with little specificity to its isolated substrate RNA.	DISCUSS
163	166	RNA	chemical	In contrast to Nep1, the enzyme preceding Tsr3 in the m1acp3Ψ biosynthesis pathway, Tsr3 binds rather weakly and with little specificity to its isolated substrate RNA.	DISCUSS
19	23	Tsr3	protein	This suggests that Tsr3 is not stably incorporated into pre-ribosomal particles and that its binding to the nascent ribosomal subunit possibly requires additional interactions with other pre-ribosomal components.	DISCUSS
56	79	pre-ribosomal particles	complex_assembly	This suggests that Tsr3 is not stably incorporated into pre-ribosomal particles and that its binding to the nascent ribosomal subunit possibly requires additional interactions with other pre-ribosomal components.	DISCUSS
116	133	ribosomal subunit	complex_assembly	This suggests that Tsr3 is not stably incorporated into pre-ribosomal particles and that its binding to the nascent ribosomal subunit possibly requires additional interactions with other pre-ribosomal components.	DISCUSS
17	42	sucrose gradient analysis	experimental_method	Consistently, in sucrose gradient analysis, Tsr3 was found in low-molecular weight fractions rather than with pre-ribosome containing high-molecular weight fractions.	DISCUSS
44	48	Tsr3	protein	Consistently, in sucrose gradient analysis, Tsr3 was found in low-molecular weight fractions rather than with pre-ribosome containing high-molecular weight fractions.	DISCUSS
110	122	pre-ribosome	complex_assembly	Consistently, in sucrose gradient analysis, Tsr3 was found in low-molecular weight fractions rather than with pre-ribosome containing high-molecular weight fractions.	DISCUSS
76	81	rRNAs	chemical	In contrast to several enzymes that catalyze base specific modifications in rRNAs Tsr3 is not an essential protein.	DISCUSS
82	86	Tsr3	protein	In contrast to several enzymes that catalyze base specific modifications in rRNAs Tsr3 is not an essential protein.	DISCUSS
17	54	small subunit rRNA methyltransferases	protein_type	Typically, other small subunit rRNA methyltransferases as Dim1, Bud23 and Nep1/Emg1 carry dual functions, in ribosome biogenesis and rRNA modification, and it is their involvement in pre-RNA processing that is essential rather than their RNA-methylating activity (, discussed in 7).	DISCUSS
58	62	Dim1	protein	Typically, other small subunit rRNA methyltransferases as Dim1, Bud23 and Nep1/Emg1 carry dual functions, in ribosome biogenesis and rRNA modification, and it is their involvement in pre-RNA processing that is essential rather than their RNA-methylating activity (, discussed in 7).	DISCUSS
64	69	Bud23	protein	Typically, other small subunit rRNA methyltransferases as Dim1, Bud23 and Nep1/Emg1 carry dual functions, in ribosome biogenesis and rRNA modification, and it is their involvement in pre-RNA processing that is essential rather than their RNA-methylating activity (, discussed in 7).	DISCUSS
74	78	Nep1	protein	Typically, other small subunit rRNA methyltransferases as Dim1, Bud23 and Nep1/Emg1 carry dual functions, in ribosome biogenesis and rRNA modification, and it is their involvement in pre-RNA processing that is essential rather than their RNA-methylating activity (, discussed in 7).	DISCUSS
79	83	Emg1	protein	Typically, other small subunit rRNA methyltransferases as Dim1, Bud23 and Nep1/Emg1 carry dual functions, in ribosome biogenesis and rRNA modification, and it is their involvement in pre-RNA processing that is essential rather than their RNA-methylating activity (, discussed in 7).	DISCUSS
133	137	rRNA	chemical	Typically, other small subunit rRNA methyltransferases as Dim1, Bud23 and Nep1/Emg1 carry dual functions, in ribosome biogenesis and rRNA modification, and it is their involvement in pre-RNA processing that is essential rather than their RNA-methylating activity (, discussed in 7).	DISCUSS
183	190	pre-RNA	chemical	Typically, other small subunit rRNA methyltransferases as Dim1, Bud23 and Nep1/Emg1 carry dual functions, in ribosome biogenesis and rRNA modification, and it is their involvement in pre-RNA processing that is essential rather than their RNA-methylating activity (, discussed in 7).	DISCUSS
25	29	Tsr3	protein	In contrast, for several Tsr3 mutants (SAM-binding and cysteine mutations) we found a systematic correlation between the loss of acp modification and the efficiency of 18S rRNA maturation.	DISCUSS
39	50	SAM-binding	protein_state	In contrast, for several Tsr3 mutants (SAM-binding and cysteine mutations) we found a systematic correlation between the loss of acp modification and the efficiency of 18S rRNA maturation.	DISCUSS
55	73	cysteine mutations	protein_state	In contrast, for several Tsr3 mutants (SAM-binding and cysteine mutations) we found a systematic correlation between the loss of acp modification and the efficiency of 18S rRNA maturation.	DISCUSS
129	132	acp	chemical	In contrast, for several Tsr3 mutants (SAM-binding and cysteine mutations) we found a systematic correlation between the loss of acp modification and the efficiency of 18S rRNA maturation.	DISCUSS
168	176	18S rRNA	chemical	In contrast, for several Tsr3 mutants (SAM-binding and cysteine mutations) we found a systematic correlation between the loss of acp modification and the efficiency of 18S rRNA maturation.	DISCUSS
55	59	rRNA	chemical	This demonstrates that, unlike the other small subunit rRNA base modifications, the acp modification is required for efficient pre-rRNA processing.	DISCUSS
84	87	acp	chemical	This demonstrates that, unlike the other small subunit rRNA base modifications, the acp modification is required for efficient pre-rRNA processing.	DISCUSS
127	135	pre-rRNA	chemical	This demonstrates that, unlike the other small subunit rRNA base modifications, the acp modification is required for efficient pre-rRNA processing.	DISCUSS
10	88	structural, functional, and CRAC (cross-linking and cDNA analysis) experiments	experimental_method	Recently, structural, functional, and CRAC (cross-linking and cDNA analysis) experiments of late assembly factors involved in cytoplasmic processing of 40S subunits, along with cryo-EM studies of the late pre-40S subunits have provided important insights into late pre-40S processing.	DISCUSS
152	164	40S subunits	complex_assembly	Recently, structural, functional, and CRAC (cross-linking and cDNA analysis) experiments of late assembly factors involved in cytoplasmic processing of 40S subunits, along with cryo-EM studies of the late pre-40S subunits have provided important insights into late pre-40S processing.	DISCUSS
177	184	cryo-EM	experimental_method	Recently, structural, functional, and CRAC (cross-linking and cDNA analysis) experiments of late assembly factors involved in cytoplasmic processing of 40S subunits, along with cryo-EM studies of the late pre-40S subunits have provided important insights into late pre-40S processing.	DISCUSS
200	204	late	protein_state	Recently, structural, functional, and CRAC (cross-linking and cDNA analysis) experiments of late assembly factors involved in cytoplasmic processing of 40S subunits, along with cryo-EM studies of the late pre-40S subunits have provided important insights into late pre-40S processing.	DISCUSS
205	221	pre-40S subunits	complex_assembly	Recently, structural, functional, and CRAC (cross-linking and cDNA analysis) experiments of late assembly factors involved in cytoplasmic processing of 40S subunits, along with cryo-EM studies of the late pre-40S subunits have provided important insights into late pre-40S processing.	DISCUSS
265	272	pre-40S	complex_assembly	Recently, structural, functional, and CRAC (cross-linking and cDNA analysis) experiments of late assembly factors involved in cytoplasmic processing of 40S subunits, along with cryo-EM studies of the late pre-40S subunits have provided important insights into late pre-40S processing.	DISCUSS
55	72	pre-40S particles	complex_assembly	Apart from most of the ribosomal proteins, cytoplasmic pre-40S particles contain 20S rRNA and at least seven non-ribosomal proteins including the D-site endonuclease Nob1 as well as Tsr1, a putative GTPase and Rio2 which block the mRNA channel and the initiator tRNA binding site, respectively, thus preventing translation initiation.	DISCUSS
81	89	20S rRNA	chemical	Apart from most of the ribosomal proteins, cytoplasmic pre-40S particles contain 20S rRNA and at least seven non-ribosomal proteins including the D-site endonuclease Nob1 as well as Tsr1, a putative GTPase and Rio2 which block the mRNA channel and the initiator tRNA binding site, respectively, thus preventing translation initiation.	DISCUSS
109	131	non-ribosomal proteins	protein_type	Apart from most of the ribosomal proteins, cytoplasmic pre-40S particles contain 20S rRNA and at least seven non-ribosomal proteins including the D-site endonuclease Nob1 as well as Tsr1, a putative GTPase and Rio2 which block the mRNA channel and the initiator tRNA binding site, respectively, thus preventing translation initiation.	DISCUSS
146	165	D-site endonuclease	protein_type	Apart from most of the ribosomal proteins, cytoplasmic pre-40S particles contain 20S rRNA and at least seven non-ribosomal proteins including the D-site endonuclease Nob1 as well as Tsr1, a putative GTPase and Rio2 which block the mRNA channel and the initiator tRNA binding site, respectively, thus preventing translation initiation.	DISCUSS
166	170	Nob1	protein	Apart from most of the ribosomal proteins, cytoplasmic pre-40S particles contain 20S rRNA and at least seven non-ribosomal proteins including the D-site endonuclease Nob1 as well as Tsr1, a putative GTPase and Rio2 which block the mRNA channel and the initiator tRNA binding site, respectively, thus preventing translation initiation.	DISCUSS
182	186	Tsr1	protein	Apart from most of the ribosomal proteins, cytoplasmic pre-40S particles contain 20S rRNA and at least seven non-ribosomal proteins including the D-site endonuclease Nob1 as well as Tsr1, a putative GTPase and Rio2 which block the mRNA channel and the initiator tRNA binding site, respectively, thus preventing translation initiation.	DISCUSS
199	205	GTPase	protein_type	Apart from most of the ribosomal proteins, cytoplasmic pre-40S particles contain 20S rRNA and at least seven non-ribosomal proteins including the D-site endonuclease Nob1 as well as Tsr1, a putative GTPase and Rio2 which block the mRNA channel and the initiator tRNA binding site, respectively, thus preventing translation initiation.	DISCUSS
210	214	Rio2	protein	Apart from most of the ribosomal proteins, cytoplasmic pre-40S particles contain 20S rRNA and at least seven non-ribosomal proteins including the D-site endonuclease Nob1 as well as Tsr1, a putative GTPase and Rio2 which block the mRNA channel and the initiator tRNA binding site, respectively, thus preventing translation initiation.	DISCUSS
231	243	mRNA channel	site	Apart from most of the ribosomal proteins, cytoplasmic pre-40S particles contain 20S rRNA and at least seven non-ribosomal proteins including the D-site endonuclease Nob1 as well as Tsr1, a putative GTPase and Rio2 which block the mRNA channel and the initiator tRNA binding site, respectively, thus preventing translation initiation.	DISCUSS
252	279	initiator tRNA binding site	site	Apart from most of the ribosomal proteins, cytoplasmic pre-40S particles contain 20S rRNA and at least seven non-ribosomal proteins including the D-site endonuclease Nob1 as well as Tsr1, a putative GTPase and Rio2 which block the mRNA channel and the initiator tRNA binding site, respectively, thus preventing translation initiation.	DISCUSS
45	48	GTP	chemical	After structural changes, possibly driven by GTP hydrolysis, which go together with the formation of the decoding site, the 20S pre-rRNA becomes accessible for Nob1 cleavage at site D. This also involves joining of pre-40S and 60S subunits to 80S-like particles in a translation-like cycle promoted by eIF5B.	DISCUSS
105	118	decoding site	site	After structural changes, possibly driven by GTP hydrolysis, which go together with the formation of the decoding site, the 20S pre-rRNA becomes accessible for Nob1 cleavage at site D. This also involves joining of pre-40S and 60S subunits to 80S-like particles in a translation-like cycle promoted by eIF5B.	DISCUSS
124	136	20S pre-rRNA	chemical	After structural changes, possibly driven by GTP hydrolysis, which go together with the formation of the decoding site, the 20S pre-rRNA becomes accessible for Nob1 cleavage at site D. This also involves joining of pre-40S and 60S subunits to 80S-like particles in a translation-like cycle promoted by eIF5B.	DISCUSS
160	164	Nob1	protein	After structural changes, possibly driven by GTP hydrolysis, which go together with the formation of the decoding site, the 20S pre-rRNA becomes accessible for Nob1 cleavage at site D. This also involves joining of pre-40S and 60S subunits to 80S-like particles in a translation-like cycle promoted by eIF5B.	DISCUSS
177	183	site D	site	After structural changes, possibly driven by GTP hydrolysis, which go together with the formation of the decoding site, the 20S pre-rRNA becomes accessible for Nob1 cleavage at site D. This also involves joining of pre-40S and 60S subunits to 80S-like particles in a translation-like cycle promoted by eIF5B.	DISCUSS
215	222	pre-40S	complex_assembly	After structural changes, possibly driven by GTP hydrolysis, which go together with the formation of the decoding site, the 20S pre-rRNA becomes accessible for Nob1 cleavage at site D. This also involves joining of pre-40S and 60S subunits to 80S-like particles in a translation-like cycle promoted by eIF5B.	DISCUSS
227	239	60S subunits	complex_assembly	After structural changes, possibly driven by GTP hydrolysis, which go together with the formation of the decoding site, the 20S pre-rRNA becomes accessible for Nob1 cleavage at site D. This also involves joining of pre-40S and 60S subunits to 80S-like particles in a translation-like cycle promoted by eIF5B.	DISCUSS
243	261	80S-like particles	complex_assembly	After structural changes, possibly driven by GTP hydrolysis, which go together with the formation of the decoding site, the 20S pre-rRNA becomes accessible for Nob1 cleavage at site D. This also involves joining of pre-40S and 60S subunits to 80S-like particles in a translation-like cycle promoted by eIF5B.	DISCUSS
302	307	eIF5B	protein	After structural changes, possibly driven by GTP hydrolysis, which go together with the formation of the decoding site, the 20S pre-rRNA becomes accessible for Nob1 cleavage at site D. This also involves joining of pre-40S and 60S subunits to 80S-like particles in a translation-like cycle promoted by eIF5B.	DISCUSS
86	97	40S subunit	complex_assembly	The cleavage step most likely acts as a quality control check that ensures the proper 40S subunit assembly with only completely processed precursors.	DISCUSS
9	27	termination factor	protein_type	Finally, termination factor Rli1, an ATPase, promotes the dissociation of assembly factors and the 80S-like complex dissociates and releases the mature 40S subunit.	DISCUSS
28	32	Rli1	protein	Finally, termination factor Rli1, an ATPase, promotes the dissociation of assembly factors and the 80S-like complex dissociates and releases the mature 40S subunit.	DISCUSS
37	43	ATPase	protein_type	Finally, termination factor Rli1, an ATPase, promotes the dissociation of assembly factors and the 80S-like complex dissociates and releases the mature 40S subunit.	DISCUSS
99	115	80S-like complex	complex_assembly	Finally, termination factor Rli1, an ATPase, promotes the dissociation of assembly factors and the 80S-like complex dissociates and releases the mature 40S subunit.	DISCUSS
145	151	mature	protein_state	Finally, termination factor Rli1, an ATPase, promotes the dissociation of assembly factors and the 80S-like complex dissociates and releases the mature 40S subunit.	DISCUSS
152	163	40S subunit	complex_assembly	Finally, termination factor Rli1, an ATPase, promotes the dissociation of assembly factors and the 80S-like complex dissociates and releases the mature 40S subunit.	DISCUSS
43	46	acp	chemical	Interestingly, differences in the level of acp modification were demonstrated for different steps of the cytoplasmic pre-40S subunit maturation after analyzing purified 20S pre-rRNAs using different purification bait proteins.	DISCUSS
117	132	pre-40S subunit	complex_assembly	Interestingly, differences in the level of acp modification were demonstrated for different steps of the cytoplasmic pre-40S subunit maturation after analyzing purified 20S pre-rRNAs using different purification bait proteins.	DISCUSS
169	182	20S pre-rRNAs	chemical	Interestingly, differences in the level of acp modification were demonstrated for different steps of the cytoplasmic pre-40S subunit maturation after analyzing purified 20S pre-rRNAs using different purification bait proteins.	DISCUSS
18	34	pre-40S subunits	complex_assembly	Early cytoplasmic pre-40S subunits still containing the ribosome assembly factors Tsr1, Ltv1, Enp1 and Rio2 were not or only partially acp modified.	DISCUSS
56	81	ribosome assembly factors	protein_type	Early cytoplasmic pre-40S subunits still containing the ribosome assembly factors Tsr1, Ltv1, Enp1 and Rio2 were not or only partially acp modified.	DISCUSS
82	86	Tsr1	protein	Early cytoplasmic pre-40S subunits still containing the ribosome assembly factors Tsr1, Ltv1, Enp1 and Rio2 were not or only partially acp modified.	DISCUSS
88	92	Ltv1	protein	Early cytoplasmic pre-40S subunits still containing the ribosome assembly factors Tsr1, Ltv1, Enp1 and Rio2 were not or only partially acp modified.	DISCUSS
94	98	Enp1	protein	Early cytoplasmic pre-40S subunits still containing the ribosome assembly factors Tsr1, Ltv1, Enp1 and Rio2 were not or only partially acp modified.	DISCUSS
103	107	Rio2	protein	Early cytoplasmic pre-40S subunits still containing the ribosome assembly factors Tsr1, Ltv1, Enp1 and Rio2 were not or only partially acp modified.	DISCUSS
135	147	acp modified	protein_state	Early cytoplasmic pre-40S subunits still containing the ribosome assembly factors Tsr1, Ltv1, Enp1 and Rio2 were not or only partially acp modified.	DISCUSS
18	34	pre-40S subunits	complex_assembly	In contrast, late pre-40S subunits containing Nob1 and Rio1 or already associated with 60S subunits in 80S-like particles showed acp modification levels comparable to mature 40S subunits.	DISCUSS
46	50	Nob1	protein	In contrast, late pre-40S subunits containing Nob1 and Rio1 or already associated with 60S subunits in 80S-like particles showed acp modification levels comparable to mature 40S subunits.	DISCUSS
55	59	Rio1	protein	In contrast, late pre-40S subunits containing Nob1 and Rio1 or already associated with 60S subunits in 80S-like particles showed acp modification levels comparable to mature 40S subunits.	DISCUSS
87	99	60S subunits	complex_assembly	In contrast, late pre-40S subunits containing Nob1 and Rio1 or already associated with 60S subunits in 80S-like particles showed acp modification levels comparable to mature 40S subunits.	DISCUSS
103	121	80S-like particles	complex_assembly	In contrast, late pre-40S subunits containing Nob1 and Rio1 or already associated with 60S subunits in 80S-like particles showed acp modification levels comparable to mature 40S subunits.	DISCUSS
129	132	acp	chemical	In contrast, late pre-40S subunits containing Nob1 and Rio1 or already associated with 60S subunits in 80S-like particles showed acp modification levels comparable to mature 40S subunits.	DISCUSS
167	173	mature	protein_state	In contrast, late pre-40S subunits containing Nob1 and Rio1 or already associated with 60S subunits in 80S-like particles showed acp modification levels comparable to mature 40S subunits.	DISCUSS
174	186	40S subunits	complex_assembly	In contrast, late pre-40S subunits containing Nob1 and Rio1 or already associated with 60S subunits in 80S-like particles showed acp modification levels comparable to mature 40S subunits.	DISCUSS
10	13	acp	chemical	Thus, the acp transfer to m1Ψ1191 occurs during the step at which Rio2 leaves the pre-40S particle.	DISCUSS
26	33	m1Ψ1191	residue_name_number	Thus, the acp transfer to m1Ψ1191 occurs during the step at which Rio2 leaves the pre-40S particle.	DISCUSS
66	70	Rio2	protein	Thus, the acp transfer to m1Ψ1191 occurs during the step at which Rio2 leaves the pre-40S particle.	DISCUSS
82	98	pre-40S particle	complex_assembly	Thus, the acp transfer to m1Ψ1191 occurs during the step at which Rio2 leaves the pre-40S particle.	DISCUSS
42	45	acp	chemical	These data and the finding that a missing acp modification hinders pre-20S rRNA processing, suggest that the acp modification together with the release of Rio2 promotes the formation of the decoding site and thus D-site cleavage by Nob1.	DISCUSS
67	79	pre-20S rRNA	chemical	These data and the finding that a missing acp modification hinders pre-20S rRNA processing, suggest that the acp modification together with the release of Rio2 promotes the formation of the decoding site and thus D-site cleavage by Nob1.	DISCUSS
109	112	acp	chemical	These data and the finding that a missing acp modification hinders pre-20S rRNA processing, suggest that the acp modification together with the release of Rio2 promotes the formation of the decoding site and thus D-site cleavage by Nob1.	DISCUSS
155	159	Rio2	protein	These data and the finding that a missing acp modification hinders pre-20S rRNA processing, suggest that the acp modification together with the release of Rio2 promotes the formation of the decoding site and thus D-site cleavage by Nob1.	DISCUSS
190	203	decoding site	site	These data and the finding that a missing acp modification hinders pre-20S rRNA processing, suggest that the acp modification together with the release of Rio2 promotes the formation of the decoding site and thus D-site cleavage by Nob1.	DISCUSS
213	219	D-site	site	These data and the finding that a missing acp modification hinders pre-20S rRNA processing, suggest that the acp modification together with the release of Rio2 promotes the formation of the decoding site and thus D-site cleavage by Nob1.	DISCUSS
232	236	Nob1	protein	These data and the finding that a missing acp modification hinders pre-20S rRNA processing, suggest that the acp modification together with the release of Rio2 promotes the formation of the decoding site and thus D-site cleavage by Nob1.	DISCUSS
26	29	acp	chemical	The interrelation between acp modification and Rio2 release is also supported by CRAC analysis showing that Rio2 binds to helix 31 next to the Ψ1191 residue that receives the acp modification.	DISCUSS
47	51	Rio2	protein	The interrelation between acp modification and Rio2 release is also supported by CRAC analysis showing that Rio2 binds to helix 31 next to the Ψ1191 residue that receives the acp modification.	DISCUSS
81	94	CRAC analysis	experimental_method	The interrelation between acp modification and Rio2 release is also supported by CRAC analysis showing that Rio2 binds to helix 31 next to the Ψ1191 residue that receives the acp modification.	DISCUSS
108	112	Rio2	protein	The interrelation between acp modification and Rio2 release is also supported by CRAC analysis showing that Rio2 binds to helix 31 next to the Ψ1191 residue that receives the acp modification.	DISCUSS
122	130	helix 31	structure_element	The interrelation between acp modification and Rio2 release is also supported by CRAC analysis showing that Rio2 binds to helix 31 next to the Ψ1191 residue that receives the acp modification.	DISCUSS
143	148	Ψ1191	residue_name_number	The interrelation between acp modification and Rio2 release is also supported by CRAC analysis showing that Rio2 binds to helix 31 next to the Ψ1191 residue that receives the acp modification.	DISCUSS
175	178	acp	chemical	The interrelation between acp modification and Rio2 release is also supported by CRAC analysis showing that Rio2 binds to helix 31 next to the Ψ1191 residue that receives the acp modification.	DISCUSS
11	15	Rio2	protein	Therefore, Rio2 either blocks the access of Tsr3 to helix 31, and acp modification can only occur after Rio2 is released, or the acp modification of m1Ψ1191 and putative subsequent conformational changes of 20S rRNA weaken the binding of Rio2 to helix 31 and support its release from the pre-rRNA.	DISCUSS
44	48	Tsr3	protein	Therefore, Rio2 either blocks the access of Tsr3 to helix 31, and acp modification can only occur after Rio2 is released, or the acp modification of m1Ψ1191 and putative subsequent conformational changes of 20S rRNA weaken the binding of Rio2 to helix 31 and support its release from the pre-rRNA.	DISCUSS
52	60	helix 31	structure_element	Therefore, Rio2 either blocks the access of Tsr3 to helix 31, and acp modification can only occur after Rio2 is released, or the acp modification of m1Ψ1191 and putative subsequent conformational changes of 20S rRNA weaken the binding of Rio2 to helix 31 and support its release from the pre-rRNA.	DISCUSS
66	69	acp	chemical	Therefore, Rio2 either blocks the access of Tsr3 to helix 31, and acp modification can only occur after Rio2 is released, or the acp modification of m1Ψ1191 and putative subsequent conformational changes of 20S rRNA weaken the binding of Rio2 to helix 31 and support its release from the pre-rRNA.	DISCUSS
104	108	Rio2	protein	Therefore, Rio2 either blocks the access of Tsr3 to helix 31, and acp modification can only occur after Rio2 is released, or the acp modification of m1Ψ1191 and putative subsequent conformational changes of 20S rRNA weaken the binding of Rio2 to helix 31 and support its release from the pre-rRNA.	DISCUSS
129	132	acp	chemical	Therefore, Rio2 either blocks the access of Tsr3 to helix 31, and acp modification can only occur after Rio2 is released, or the acp modification of m1Ψ1191 and putative subsequent conformational changes of 20S rRNA weaken the binding of Rio2 to helix 31 and support its release from the pre-rRNA.	DISCUSS
149	156	m1Ψ1191	residue_name_number	Therefore, Rio2 either blocks the access of Tsr3 to helix 31, and acp modification can only occur after Rio2 is released, or the acp modification of m1Ψ1191 and putative subsequent conformational changes of 20S rRNA weaken the binding of Rio2 to helix 31 and support its release from the pre-rRNA.	DISCUSS
207	215	20S rRNA	chemical	Therefore, Rio2 either blocks the access of Tsr3 to helix 31, and acp modification can only occur after Rio2 is released, or the acp modification of m1Ψ1191 and putative subsequent conformational changes of 20S rRNA weaken the binding of Rio2 to helix 31 and support its release from the pre-rRNA.	DISCUSS
238	242	Rio2	protein	Therefore, Rio2 either blocks the access of Tsr3 to helix 31, and acp modification can only occur after Rio2 is released, or the acp modification of m1Ψ1191 and putative subsequent conformational changes of 20S rRNA weaken the binding of Rio2 to helix 31 and support its release from the pre-rRNA.	DISCUSS
246	254	helix 31	structure_element	Therefore, Rio2 either blocks the access of Tsr3 to helix 31, and acp modification can only occur after Rio2 is released, or the acp modification of m1Ψ1191 and putative subsequent conformational changes of 20S rRNA weaken the binding of Rio2 to helix 31 and support its release from the pre-rRNA.	DISCUSS
288	296	pre-rRNA	chemical	Therefore, Rio2 either blocks the access of Tsr3 to helix 31, and acp modification can only occur after Rio2 is released, or the acp modification of m1Ψ1191 and putative subsequent conformational changes of 20S rRNA weaken the binding of Rio2 to helix 31 and support its release from the pre-rRNA.	DISCUSS
27	31	Tsr3	protein	In summary, by identifying Tsr3 as the enzyme responsible for introducing the acp group to the hypermodified m1acp3Ψ nucleotide at position 1191 (yeast)/ 1248 (humans) of 18S rRNA we added one of the last remaining pieces to the puzzle of eukaryotic small ribosomal subunit rRNA modifications.	DISCUSS
78	81	acp	chemical	In summary, by identifying Tsr3 as the enzyme responsible for introducing the acp group to the hypermodified m1acp3Ψ nucleotide at position 1191 (yeast)/ 1248 (humans) of 18S rRNA we added one of the last remaining pieces to the puzzle of eukaryotic small ribosomal subunit rRNA modifications.	DISCUSS
95	108	hypermodified	protein_state	In summary, by identifying Tsr3 as the enzyme responsible for introducing the acp group to the hypermodified m1acp3Ψ nucleotide at position 1191 (yeast)/ 1248 (humans) of 18S rRNA we added one of the last remaining pieces to the puzzle of eukaryotic small ribosomal subunit rRNA modifications.	DISCUSS
109	116	m1acp3Ψ	chemical	In summary, by identifying Tsr3 as the enzyme responsible for introducing the acp group to the hypermodified m1acp3Ψ nucleotide at position 1191 (yeast)/ 1248 (humans) of 18S rRNA we added one of the last remaining pieces to the puzzle of eukaryotic small ribosomal subunit rRNA modifications.	DISCUSS
117	127	nucleotide	chemical	In summary, by identifying Tsr3 as the enzyme responsible for introducing the acp group to the hypermodified m1acp3Ψ nucleotide at position 1191 (yeast)/ 1248 (humans) of 18S rRNA we added one of the last remaining pieces to the puzzle of eukaryotic small ribosomal subunit rRNA modifications.	DISCUSS
140	144	1191	residue_number	In summary, by identifying Tsr3 as the enzyme responsible for introducing the acp group to the hypermodified m1acp3Ψ nucleotide at position 1191 (yeast)/ 1248 (humans) of 18S rRNA we added one of the last remaining pieces to the puzzle of eukaryotic small ribosomal subunit rRNA modifications.	DISCUSS
146	151	yeast	taxonomy_domain	In summary, by identifying Tsr3 as the enzyme responsible for introducing the acp group to the hypermodified m1acp3Ψ nucleotide at position 1191 (yeast)/ 1248 (humans) of 18S rRNA we added one of the last remaining pieces to the puzzle of eukaryotic small ribosomal subunit rRNA modifications.	DISCUSS
154	158	1248	residue_number	In summary, by identifying Tsr3 as the enzyme responsible for introducing the acp group to the hypermodified m1acp3Ψ nucleotide at position 1191 (yeast)/ 1248 (humans) of 18S rRNA we added one of the last remaining pieces to the puzzle of eukaryotic small ribosomal subunit rRNA modifications.	DISCUSS
160	166	humans	species	In summary, by identifying Tsr3 as the enzyme responsible for introducing the acp group to the hypermodified m1acp3Ψ nucleotide at position 1191 (yeast)/ 1248 (humans) of 18S rRNA we added one of the last remaining pieces to the puzzle of eukaryotic small ribosomal subunit rRNA modifications.	DISCUSS
171	179	18S rRNA	chemical	In summary, by identifying Tsr3 as the enzyme responsible for introducing the acp group to the hypermodified m1acp3Ψ nucleotide at position 1191 (yeast)/ 1248 (humans) of 18S rRNA we added one of the last remaining pieces to the puzzle of eukaryotic small ribosomal subunit rRNA modifications.	DISCUSS
239	249	eukaryotic	taxonomy_domain	In summary, by identifying Tsr3 as the enzyme responsible for introducing the acp group to the hypermodified m1acp3Ψ nucleotide at position 1191 (yeast)/ 1248 (humans) of 18S rRNA we added one of the last remaining pieces to the puzzle of eukaryotic small ribosomal subunit rRNA modifications.	DISCUSS
250	278	small ribosomal subunit rRNA	chemical	In summary, by identifying Tsr3 as the enzyme responsible for introducing the acp group to the hypermodified m1acp3Ψ nucleotide at position 1191 (yeast)/ 1248 (humans) of 18S rRNA we added one of the last remaining pieces to the puzzle of eukaryotic small ribosomal subunit rRNA modifications.	DISCUSS
48	51	acp	chemical	The current data together with the finding that acp modification takes place at the very last step in pre-40S subunit maturation indicate that the acp modification probably supports the formation of the decoding site and efficient 20S pre-rRNA D-site cleavage.	DISCUSS
102	117	pre-40S subunit	complex_assembly	The current data together with the finding that acp modification takes place at the very last step in pre-40S subunit maturation indicate that the acp modification probably supports the formation of the decoding site and efficient 20S pre-rRNA D-site cleavage.	DISCUSS
147	150	acp	chemical	The current data together with the finding that acp modification takes place at the very last step in pre-40S subunit maturation indicate that the acp modification probably supports the formation of the decoding site and efficient 20S pre-rRNA D-site cleavage.	DISCUSS
203	216	decoding site	site	The current data together with the finding that acp modification takes place at the very last step in pre-40S subunit maturation indicate that the acp modification probably supports the formation of the decoding site and efficient 20S pre-rRNA D-site cleavage.	DISCUSS
231	243	20S pre-rRNA	chemical	The current data together with the finding that acp modification takes place at the very last step in pre-40S subunit maturation indicate that the acp modification probably supports the formation of the decoding site and efficient 20S pre-rRNA D-site cleavage.	DISCUSS
244	250	D-site	site	The current data together with the finding that acp modification takes place at the very last step in pre-40S subunit maturation indicate that the acp modification probably supports the formation of the decoding site and efficient 20S pre-rRNA D-site cleavage.	DISCUSS
17	32	structural data	evidence	Furthermore, our structural data unravelled how the regioselectivity of SAM-dependent group transfer reactions can be tuned by distinct small evolutionary adaptions of the ligand binding pocket of SAM-binding enzymes.	DISCUSS
72	75	SAM	chemical	Furthermore, our structural data unravelled how the regioselectivity of SAM-dependent group transfer reactions can be tuned by distinct small evolutionary adaptions of the ligand binding pocket of SAM-binding enzymes.	DISCUSS
172	193	ligand binding pocket	site	Furthermore, our structural data unravelled how the regioselectivity of SAM-dependent group transfer reactions can be tuned by distinct small evolutionary adaptions of the ligand binding pocket of SAM-binding enzymes.	DISCUSS
197	216	SAM-binding enzymes	protein_type	Furthermore, our structural data unravelled how the regioselectivity of SAM-dependent group transfer reactions can be tuned by distinct small evolutionary adaptions of the ligand binding pocket of SAM-binding enzymes.	DISCUSS