| anno_start anno_end anno_text entity_type sentence section | |
| 0 43 Biochemical and structural characterization experimental_method Biochemical and structural characterization of a DNA N6-adenine methyltransferase from Helicobacter pylori TITLE | |
| 49 81 DNA N6-adenine methyltransferase protein_type Biochemical and structural characterization of a DNA N6-adenine methyltransferase from Helicobacter pylori TITLE | |
| 87 106 Helicobacter pylori species Biochemical and structural characterization of a DNA N6-adenine methyltransferase from Helicobacter pylori TITLE | |
| 0 20 DNA N6-methyladenine ptm DNA N6-methyladenine modification plays an important role in regulating a variety of biological functions in bacteria. ABSTRACT | |
| 109 117 bacteria taxonomy_domain DNA N6-methyladenine modification plays an important role in regulating a variety of biological functions in bacteria. ABSTRACT | |
| 59 75 N6-methyladenine ptm However, the mechanism of sequence-specific recognition in N6-methyladenine modification remains elusive. ABSTRACT | |
| 0 9 M1.HpyAVI protein M1.HpyAVI, a DNA N6-adenine methyltransferase from Helicobacter pylori, shows more promiscuous substrate specificity than other enzymes. ABSTRACT | |
| 13 45 DNA N6-adenine methyltransferase protein_type M1.HpyAVI, a DNA N6-adenine methyltransferase from Helicobacter pylori, shows more promiscuous substrate specificity than other enzymes. ABSTRACT | |
| 51 70 Helicobacter pylori species M1.HpyAVI, a DNA N6-adenine methyltransferase from Helicobacter pylori, shows more promiscuous substrate specificity than other enzymes. ABSTRACT | |
| 21 39 crystal structures evidence Here, we present the crystal structures of cofactor-free and AdoMet-bound structures of this enzyme, which were determined at resolutions of 3.0 Å and 3.1 Å, respectively. ABSTRACT | |
| 43 56 cofactor-free protein_state Here, we present the crystal structures of cofactor-free and AdoMet-bound structures of this enzyme, which were determined at resolutions of 3.0 Å and 3.1 Å, respectively. ABSTRACT | |
| 61 73 AdoMet-bound protein_state Here, we present the crystal structures of cofactor-free and AdoMet-bound structures of this enzyme, which were determined at resolutions of 3.0 Å and 3.1 Å, respectively. ABSTRACT | |
| 74 84 structures evidence Here, we present the crystal structures of cofactor-free and AdoMet-bound structures of this enzyme, which were determined at resolutions of 3.0 Å and 3.1 Å, respectively. ABSTRACT | |
| 22 31 M1.HpyAVI protein The core structure of M1.HpyAVI resembles the canonical AdoMet-dependent MTase fold, while the putative DNA binding regions considerably differ from those of the other MTases, which may account for the substrate promiscuity of this enzyme. ABSTRACT | |
| 56 78 AdoMet-dependent MTase protein_type The core structure of M1.HpyAVI resembles the canonical AdoMet-dependent MTase fold, while the putative DNA binding regions considerably differ from those of the other MTases, which may account for the substrate promiscuity of this enzyme. ABSTRACT | |
| 104 123 DNA binding regions site The core structure of M1.HpyAVI resembles the canonical AdoMet-dependent MTase fold, while the putative DNA binding regions considerably differ from those of the other MTases, which may account for the substrate promiscuity of this enzyme. ABSTRACT | |
| 168 174 MTases protein_type The core structure of M1.HpyAVI resembles the canonical AdoMet-dependent MTase fold, while the putative DNA binding regions considerably differ from those of the other MTases, which may account for the substrate promiscuity of this enzyme. ABSTRACT | |
| 0 25 Site-directed mutagenesis experimental_method Site-directed mutagenesis experiments identified residues D29 and E216 as crucial amino acids for cofactor binding and the methyl transfer activity of the enzyme, while P41, located in a highly flexible loop, playing a determinant role for substrate specificity. ABSTRACT | |
| 58 61 D29 residue_name_number Site-directed mutagenesis experiments identified residues D29 and E216 as crucial amino acids for cofactor binding and the methyl transfer activity of the enzyme, while P41, located in a highly flexible loop, playing a determinant role for substrate specificity. ABSTRACT | |
| 66 70 E216 residue_name_number Site-directed mutagenesis experiments identified residues D29 and E216 as crucial amino acids for cofactor binding and the methyl transfer activity of the enzyme, while P41, located in a highly flexible loop, playing a determinant role for substrate specificity. ABSTRACT | |
| 123 129 methyl chemical Site-directed mutagenesis experiments identified residues D29 and E216 as crucial amino acids for cofactor binding and the methyl transfer activity of the enzyme, while P41, located in a highly flexible loop, playing a determinant role for substrate specificity. ABSTRACT | |
| 169 172 P41 residue_name_number Site-directed mutagenesis experiments identified residues D29 and E216 as crucial amino acids for cofactor binding and the methyl transfer activity of the enzyme, while P41, located in a highly flexible loop, playing a determinant role for substrate specificity. ABSTRACT | |
| 187 202 highly flexible protein_state Site-directed mutagenesis experiments identified residues D29 and E216 as crucial amino acids for cofactor binding and the methyl transfer activity of the enzyme, while P41, located in a highly flexible loop, playing a determinant role for substrate specificity. ABSTRACT | |
| 203 207 loop structure_element Site-directed mutagenesis experiments identified residues D29 and E216 as crucial amino acids for cofactor binding and the methyl transfer activity of the enzyme, while P41, located in a highly flexible loop, playing a determinant role for substrate specificity. ABSTRACT | |
| 66 98 DNA N6-adenine methyltransferase protein_type Taken together, our data revealed the structural basis underlying DNA N6-adenine methyltransferase substrate promiscuity. ABSTRACT | |
| 0 15 DNA methylation ptm DNA methylation is a common form of modification on nucleic acids occurring in both prokaryotes and eukaryotes. INTRO | |
| 84 95 prokaryotes taxonomy_domain DNA methylation is a common form of modification on nucleic acids occurring in both prokaryotes and eukaryotes. INTRO | |
| 100 110 eukaryotes taxonomy_domain DNA methylation is a common form of modification on nucleic acids occurring in both prokaryotes and eukaryotes. INTRO | |
| 60 63 DNA chemical Such a modification creates a signature motif recognized by DNA-interacting proteins and functions as a mechanism to regulate gene expression. INTRO | |
| 0 15 DNA methylation ptm DNA methylation is mediated by DNA methyltransferases (MTases), which catalyze the transfer of a methyl group from S-adenosyl-L- methionine (AdoMet) to a given position of a particular DNA base within a specific DNA sequence. INTRO | |
| 31 53 DNA methyltransferases protein_type DNA methylation is mediated by DNA methyltransferases (MTases), which catalyze the transfer of a methyl group from S-adenosyl-L- methionine (AdoMet) to a given position of a particular DNA base within a specific DNA sequence. INTRO | |
| 55 61 MTases protein_type DNA methylation is mediated by DNA methyltransferases (MTases), which catalyze the transfer of a methyl group from S-adenosyl-L- methionine (AdoMet) to a given position of a particular DNA base within a specific DNA sequence. INTRO | |
| 97 103 methyl chemical DNA methylation is mediated by DNA methyltransferases (MTases), which catalyze the transfer of a methyl group from S-adenosyl-L- methionine (AdoMet) to a given position of a particular DNA base within a specific DNA sequence. INTRO | |
| 115 139 S-adenosyl-L- methionine chemical DNA methylation is mediated by DNA methyltransferases (MTases), which catalyze the transfer of a methyl group from S-adenosyl-L- methionine (AdoMet) to a given position of a particular DNA base within a specific DNA sequence. INTRO | |
| 141 147 AdoMet chemical DNA methylation is mediated by DNA methyltransferases (MTases), which catalyze the transfer of a methyl group from S-adenosyl-L- methionine (AdoMet) to a given position of a particular DNA base within a specific DNA sequence. INTRO | |
| 185 188 DNA chemical DNA methylation is mediated by DNA methyltransferases (MTases), which catalyze the transfer of a methyl group from S-adenosyl-L- methionine (AdoMet) to a given position of a particular DNA base within a specific DNA sequence. INTRO | |
| 212 215 DNA chemical DNA methylation is mediated by DNA methyltransferases (MTases), which catalyze the transfer of a methyl group from S-adenosyl-L- methionine (AdoMet) to a given position of a particular DNA base within a specific DNA sequence. INTRO | |
| 17 27 DNA MTases protein_type Three classes of DNA MTases have been identified to transfer a methyl group to different positions of DNA bases. INTRO | |
| 63 69 methyl chemical Three classes of DNA MTases have been identified to transfer a methyl group to different positions of DNA bases. INTRO | |
| 102 105 DNA chemical Three classes of DNA MTases have been identified to transfer a methyl group to different positions of DNA bases. INTRO | |
| 0 18 C5-cytosine MTases protein_type C5-cytosine MTases, for example, methylate C5 of cytosine (m5C). INTRO | |
| 49 57 cytosine residue_name C5-cytosine MTases, for example, methylate C5 of cytosine (m5C). INTRO | |
| 59 62 m5C ptm C5-cytosine MTases, for example, methylate C5 of cytosine (m5C). INTRO | |
| 3 13 eukaryotes taxonomy_domain In eukaryotes, m5C plays an important role in gene expression, chromatin organization, genome maintenance and parental imprinting, and is involved in a variety of human diseases including cancer. INTRO | |
| 15 18 m5C ptm In eukaryotes, m5C plays an important role in gene expression, chromatin organization, genome maintenance and parental imprinting, and is involved in a variety of human diseases including cancer. INTRO | |
| 163 168 human species In eukaryotes, m5C plays an important role in gene expression, chromatin organization, genome maintenance and parental imprinting, and is involved in a variety of human diseases including cancer. INTRO | |
| 34 45 prokaryotic taxonomy_domain By contrast, the functions of the prokaryotic DNA cytosine MTase remain unknown. INTRO | |
| 46 64 DNA cytosine MTase protein_type By contrast, the functions of the prokaryotic DNA cytosine MTase remain unknown. INTRO | |
| 0 18 N4-cytosine MTases protein_type N4-cytosine MTases, which are frequently present in thermophilic or mesophilic bacteria, transfer a methyl group to the exocyclic amino group of cytosine (4mC). INTRO | |
| 52 64 thermophilic taxonomy_domain N4-cytosine MTases, which are frequently present in thermophilic or mesophilic bacteria, transfer a methyl group to the exocyclic amino group of cytosine (4mC). INTRO | |
| 68 78 mesophilic taxonomy_domain N4-cytosine MTases, which are frequently present in thermophilic or mesophilic bacteria, transfer a methyl group to the exocyclic amino group of cytosine (4mC). INTRO | |
| 79 87 bacteria taxonomy_domain N4-cytosine MTases, which are frequently present in thermophilic or mesophilic bacteria, transfer a methyl group to the exocyclic amino group of cytosine (4mC). INTRO | |
| 100 106 methyl chemical N4-cytosine MTases, which are frequently present in thermophilic or mesophilic bacteria, transfer a methyl group to the exocyclic amino group of cytosine (4mC). INTRO | |
| 145 153 cytosine residue_name N4-cytosine MTases, which are frequently present in thermophilic or mesophilic bacteria, transfer a methyl group to the exocyclic amino group of cytosine (4mC). INTRO | |
| 155 158 4mC ptm N4-cytosine MTases, which are frequently present in thermophilic or mesophilic bacteria, transfer a methyl group to the exocyclic amino group of cytosine (4mC). INTRO | |
| 0 14 N4 methylation ptm N4 methylation seems to be primarily a component of bacterial immune system against invasion by foreign DNA, such as conjugative plasmids and bacteriophages. INTRO | |
| 52 61 bacterial taxonomy_domain N4 methylation seems to be primarily a component of bacterial immune system against invasion by foreign DNA, such as conjugative plasmids and bacteriophages. INTRO | |
| 104 107 DNA chemical N4 methylation seems to be primarily a component of bacterial immune system against invasion by foreign DNA, such as conjugative plasmids and bacteriophages. INTRO | |
| 142 156 bacteriophages taxonomy_domain N4 methylation seems to be primarily a component of bacterial immune system against invasion by foreign DNA, such as conjugative plasmids and bacteriophages. INTRO | |
| 17 34 N6-adenine MTases protein_type The third group, N6-adenine MTases methylate the exocyclic amino groups of adenine (6mA), which exists in prokaryotes as a signal for genome defense, DNA replication and repair, regulation of gene expression, control of transposition and host-pathogen interactions. INTRO | |
| 75 82 adenine residue_name The third group, N6-adenine MTases methylate the exocyclic amino groups of adenine (6mA), which exists in prokaryotes as a signal for genome defense, DNA replication and repair, regulation of gene expression, control of transposition and host-pathogen interactions. INTRO | |
| 84 87 6mA ptm The third group, N6-adenine MTases methylate the exocyclic amino groups of adenine (6mA), which exists in prokaryotes as a signal for genome defense, DNA replication and repair, regulation of gene expression, control of transposition and host-pathogen interactions. INTRO | |
| 106 117 prokaryotes taxonomy_domain The third group, N6-adenine MTases methylate the exocyclic amino groups of adenine (6mA), which exists in prokaryotes as a signal for genome defense, DNA replication and repair, regulation of gene expression, control of transposition and host-pathogen interactions. INTRO | |
| 150 153 DNA chemical The third group, N6-adenine MTases methylate the exocyclic amino groups of adenine (6mA), which exists in prokaryotes as a signal for genome defense, DNA replication and repair, regulation of gene expression, control of transposition and host-pathogen interactions. INTRO | |
| 80 83 6mA ptm Recent studies utilizing new sequencing approaches have showed the existence of 6mA in several eukaryotic species. INTRO | |
| 95 105 eukaryotic taxonomy_domain Recent studies utilizing new sequencing approaches have showed the existence of 6mA in several eukaryotic species. INTRO | |
| 0 3 DNA chemical DNA 6mA modification is associated with important biological processes including nucleosome distribution close to the transcription start sites in Chlamydomonas, carrying heritable epigenetic information in C.elegans or controlling development of Drosophila. INTRO | |
| 4 7 6mA ptm DNA 6mA modification is associated with important biological processes including nucleosome distribution close to the transcription start sites in Chlamydomonas, carrying heritable epigenetic information in C.elegans or controlling development of Drosophila. INTRO | |
| 147 160 Chlamydomonas taxonomy_domain DNA 6mA modification is associated with important biological processes including nucleosome distribution close to the transcription start sites in Chlamydomonas, carrying heritable epigenetic information in C.elegans or controlling development of Drosophila. INTRO | |
| 207 216 C.elegans species DNA 6mA modification is associated with important biological processes including nucleosome distribution close to the transcription start sites in Chlamydomonas, carrying heritable epigenetic information in C.elegans or controlling development of Drosophila. INTRO | |
| 247 257 Drosophila taxonomy_domain DNA 6mA modification is associated with important biological processes including nucleosome distribution close to the transcription start sites in Chlamydomonas, carrying heritable epigenetic information in C.elegans or controlling development of Drosophila. INTRO | |
| 23 34 methylation ptm All the three types of methylation exist in prokaryotes, and most DNA MTases are components of the restriction-modification (R-M) systems. INTRO | |
| 44 55 prokaryotes taxonomy_domain All the three types of methylation exist in prokaryotes, and most DNA MTases are components of the restriction-modification (R-M) systems. INTRO | |
| 66 76 DNA MTases protein_type All the three types of methylation exist in prokaryotes, and most DNA MTases are components of the restriction-modification (R-M) systems. INTRO | |
| 17 41 restriction endonuclease protein_type “R” stands for a restriction endonuclease cleaving specific DNA sequences, while “M” symbolizes a modification methyltransferase rendering these sequences resistant to cleavage. INTRO | |
| 60 63 DNA chemical “R” stands for a restriction endonuclease cleaving specific DNA sequences, while “M” symbolizes a modification methyltransferase rendering these sequences resistant to cleavage. INTRO | |
| 98 128 modification methyltransferase protein_type “R” stands for a restriction endonuclease cleaving specific DNA sequences, while “M” symbolizes a modification methyltransferase rendering these sequences resistant to cleavage. INTRO | |
| 79 87 bacteria taxonomy_domain The cooperation of these two enzymes provides a defensive mechanism to protect bacteria from infection by bacteriophages. INTRO | |
| 106 120 bacteriophages taxonomy_domain The cooperation of these two enzymes provides a defensive mechanism to protect bacteria from infection by bacteriophages. INTRO | |
| 99 102 DNA chemical The R-M systems are classified into three types based on specific structural features, position of DNA cleavage and cofactor requirements. INTRO | |
| 24 65 DNA adenine or cytosine methyltransferase protein_type In types I and III, the DNA adenine or cytosine methyltransferase is part of a multi-subunit enzyme that catalyzes both restriction and modification. INTRO | |
| 68 92 restriction endonuclease protein_type By contrast, two separate enzymes exist in type II systems, where a restriction endonuclease and a DNA adenine or cytosine methyltransferase recognize the same targets. INTRO | |
| 99 140 DNA adenine or cytosine methyltransferase protein_type By contrast, two separate enzymes exist in type II systems, where a restriction endonuclease and a DNA adenine or cytosine methyltransferase recognize the same targets. INTRO | |
| 21 30 bacterial taxonomy_domain To date, a number of bacterial DNA MTases have been structurally characterized, covering enzymes from all the three classes. INTRO | |
| 31 41 DNA MTases protein_type To date, a number of bacterial DNA MTases have been structurally characterized, covering enzymes from all the three classes. INTRO | |
| 52 78 structurally characterized experimental_method To date, a number of bacterial DNA MTases have been structurally characterized, covering enzymes from all the three classes. INTRO | |
| 10 16 MTases protein_type All these MTases exhibit high similarity in their overall architectures, which are generally folded into two domains: a conserved larger catalytic domain comprising an active site for methyl transfer and a site for AdoMet-binding, and a smaller target (DNA)-recognition domain (TRD) containing variable regions implicated in sequence-specific DNA recognition and the infiltration of the DNA to flip the target base. INTRO | |
| 120 129 conserved protein_state All these MTases exhibit high similarity in their overall architectures, which are generally folded into two domains: a conserved larger catalytic domain comprising an active site for methyl transfer and a site for AdoMet-binding, and a smaller target (DNA)-recognition domain (TRD) containing variable regions implicated in sequence-specific DNA recognition and the infiltration of the DNA to flip the target base. INTRO | |
| 137 153 catalytic domain structure_element All these MTases exhibit high similarity in their overall architectures, which are generally folded into two domains: a conserved larger catalytic domain comprising an active site for methyl transfer and a site for AdoMet-binding, and a smaller target (DNA)-recognition domain (TRD) containing variable regions implicated in sequence-specific DNA recognition and the infiltration of the DNA to flip the target base. INTRO | |
| 168 179 active site site All these MTases exhibit high similarity in their overall architectures, which are generally folded into two domains: a conserved larger catalytic domain comprising an active site for methyl transfer and a site for AdoMet-binding, and a smaller target (DNA)-recognition domain (TRD) containing variable regions implicated in sequence-specific DNA recognition and the infiltration of the DNA to flip the target base. INTRO | |
| 184 190 methyl chemical All these MTases exhibit high similarity in their overall architectures, which are generally folded into two domains: a conserved larger catalytic domain comprising an active site for methyl transfer and a site for AdoMet-binding, and a smaller target (DNA)-recognition domain (TRD) containing variable regions implicated in sequence-specific DNA recognition and the infiltration of the DNA to flip the target base. INTRO | |
| 215 221 AdoMet chemical All these MTases exhibit high similarity in their overall architectures, which are generally folded into two domains: a conserved larger catalytic domain comprising an active site for methyl transfer and a site for AdoMet-binding, and a smaller target (DNA)-recognition domain (TRD) containing variable regions implicated in sequence-specific DNA recognition and the infiltration of the DNA to flip the target base. INTRO | |
| 245 276 target (DNA)-recognition domain structure_element All these MTases exhibit high similarity in their overall architectures, which are generally folded into two domains: a conserved larger catalytic domain comprising an active site for methyl transfer and a site for AdoMet-binding, and a smaller target (DNA)-recognition domain (TRD) containing variable regions implicated in sequence-specific DNA recognition and the infiltration of the DNA to flip the target base. INTRO | |
| 278 281 TRD structure_element All these MTases exhibit high similarity in their overall architectures, which are generally folded into two domains: a conserved larger catalytic domain comprising an active site for methyl transfer and a site for AdoMet-binding, and a smaller target (DNA)-recognition domain (TRD) containing variable regions implicated in sequence-specific DNA recognition and the infiltration of the DNA to flip the target base. INTRO | |
| 343 346 DNA chemical All these MTases exhibit high similarity in their overall architectures, which are generally folded into two domains: a conserved larger catalytic domain comprising an active site for methyl transfer and a site for AdoMet-binding, and a smaller target (DNA)-recognition domain (TRD) containing variable regions implicated in sequence-specific DNA recognition and the infiltration of the DNA to flip the target base. INTRO | |
| 387 390 DNA chemical All these MTases exhibit high similarity in their overall architectures, which are generally folded into two domains: a conserved larger catalytic domain comprising an active site for methyl transfer and a site for AdoMet-binding, and a smaller target (DNA)-recognition domain (TRD) containing variable regions implicated in sequence-specific DNA recognition and the infiltration of the DNA to flip the target base. INTRO | |
| 0 9 Conserved protein_state Conserved amino acid motifs have been identified from reported structures, including ten motifs (I-X) in cytosine MTases and nine motifs (I-VIII and X) in adenine MTases, all of which are arranged in an almost constant order. INTRO | |
| 63 73 structures evidence Conserved amino acid motifs have been identified from reported structures, including ten motifs (I-X) in cytosine MTases and nine motifs (I-VIII and X) in adenine MTases, all of which are arranged in an almost constant order. INTRO | |
| 97 100 I-X structure_element Conserved amino acid motifs have been identified from reported structures, including ten motifs (I-X) in cytosine MTases and nine motifs (I-VIII and X) in adenine MTases, all of which are arranged in an almost constant order. INTRO | |
| 105 120 cytosine MTases protein_type Conserved amino acid motifs have been identified from reported structures, including ten motifs (I-X) in cytosine MTases and nine motifs (I-VIII and X) in adenine MTases, all of which are arranged in an almost constant order. INTRO | |
| 138 144 I-VIII structure_element Conserved amino acid motifs have been identified from reported structures, including ten motifs (I-X) in cytosine MTases and nine motifs (I-VIII and X) in adenine MTases, all of which are arranged in an almost constant order. INTRO | |
| 149 150 X structure_element Conserved amino acid motifs have been identified from reported structures, including ten motifs (I-X) in cytosine MTases and nine motifs (I-VIII and X) in adenine MTases, all of which are arranged in an almost constant order. INTRO | |
| 155 169 adenine MTases protein_type Conserved amino acid motifs have been identified from reported structures, including ten motifs (I-X) in cytosine MTases and nine motifs (I-VIII and X) in adenine MTases, all of which are arranged in an almost constant order. INTRO | |
| 45 54 conserved protein_state According to the linear arrangement of three conserved domains, exocyclic amino MTases are subdivided into six groups (namely α, β, γ, ζ, δ and ε). INTRO | |
| 64 86 exocyclic amino MTases protein_type According to the linear arrangement of three conserved domains, exocyclic amino MTases are subdivided into six groups (namely α, β, γ, ζ, δ and ε). INTRO | |
| 126 127 α protein_type According to the linear arrangement of three conserved domains, exocyclic amino MTases are subdivided into six groups (namely α, β, γ, ζ, δ and ε). INTRO | |
| 129 130 β protein_type According to the linear arrangement of three conserved domains, exocyclic amino MTases are subdivided into six groups (namely α, β, γ, ζ, δ and ε). INTRO | |
| 132 133 γ protein_type According to the linear arrangement of three conserved domains, exocyclic amino MTases are subdivided into six groups (namely α, β, γ, ζ, δ and ε). INTRO | |
| 135 136 ζ protein_type According to the linear arrangement of three conserved domains, exocyclic amino MTases are subdivided into six groups (namely α, β, γ, ζ, δ and ε). INTRO | |
| 138 139 δ protein_type According to the linear arrangement of three conserved domains, exocyclic amino MTases are subdivided into six groups (namely α, β, γ, ζ, δ and ε). INTRO | |
| 144 145 ε protein_type According to the linear arrangement of three conserved domains, exocyclic amino MTases are subdivided into six groups (namely α, β, γ, ζ, δ and ε). INTRO | |
| 0 33 N6-adenine and N4-cytosine MTases protein_type N6-adenine and N4-cytosine MTases, in particular, are closely related by sharing common structural features. RESULTS | |
| 0 33 N6-adenine and N4-cytosine MTases protein_type N6-adenine and N4-cytosine MTases, in particular, are closely related by sharing common structural features. RESULTS | |
| 42 51 bacterial taxonomy_domain Despite the considerable similarity among bacterial MTases, some differences were observed among the enzymes from various species. INTRO | |
| 52 58 MTases protein_type Despite the considerable similarity among bacterial MTases, some differences were observed among the enzymes from various species. INTRO | |
| 39 45 MTases protein_type For example, the structural regions of MTases beyond the catalytic domain are rather variable, such as the C-terminal domain of M.TaqI, the extended arm of M.MboIIA and M.RsrI, the helix bundle of EcoDam, and so on. INTRO | |
| 57 73 catalytic domain structure_element For example, the structural regions of MTases beyond the catalytic domain are rather variable, such as the C-terminal domain of M.TaqI, the extended arm of M.MboIIA and M.RsrI, the helix bundle of EcoDam, and so on. INTRO | |
| 107 124 C-terminal domain structure_element For example, the structural regions of MTases beyond the catalytic domain are rather variable, such as the C-terminal domain of M.TaqI, the extended arm of M.MboIIA and M.RsrI, the helix bundle of EcoDam, and so on. INTRO | |
| 128 134 M.TaqI protein For example, the structural regions of MTases beyond the catalytic domain are rather variable, such as the C-terminal domain of M.TaqI, the extended arm of M.MboIIA and M.RsrI, the helix bundle of EcoDam, and so on. INTRO | |
| 156 164 M.MboIIA protein For example, the structural regions of MTases beyond the catalytic domain are rather variable, such as the C-terminal domain of M.TaqI, the extended arm of M.MboIIA and M.RsrI, the helix bundle of EcoDam, and so on. INTRO | |
| 169 175 M.RsrI protein For example, the structural regions of MTases beyond the catalytic domain are rather variable, such as the C-terminal domain of M.TaqI, the extended arm of M.MboIIA and M.RsrI, the helix bundle of EcoDam, and so on. INTRO | |
| 181 193 helix bundle structure_element For example, the structural regions of MTases beyond the catalytic domain are rather variable, such as the C-terminal domain of M.TaqI, the extended arm of M.MboIIA and M.RsrI, the helix bundle of EcoDam, and so on. INTRO | |
| 197 203 EcoDam protein For example, the structural regions of MTases beyond the catalytic domain are rather variable, such as the C-terminal domain of M.TaqI, the extended arm of M.MboIIA and M.RsrI, the helix bundle of EcoDam, and so on. INTRO | |
| 0 15 DNA methylation ptm DNA methylation is thought to influence bacterial virulence. INTRO | |
| 40 49 bacterial taxonomy_domain DNA methylation is thought to influence bacterial virulence. INTRO | |
| 0 29 DNA adenine methyltransferase protein_type DNA adenine methyltransferase has been shown to play a crucial role in colonization of deep tissue sites in Salmonella typhimurium and Aeromonas hydrophila. INTRO | |
| 108 130 Salmonella typhimurium species DNA adenine methyltransferase has been shown to play a crucial role in colonization of deep tissue sites in Salmonella typhimurium and Aeromonas hydrophila. INTRO | |
| 135 155 Aeromonas hydrophila species DNA adenine methyltransferase has been shown to play a crucial role in colonization of deep tissue sites in Salmonella typhimurium and Aeromonas hydrophila. INTRO | |
| 13 36 DNA adenine methylation ptm Importantly, DNA adenine methylation is a global regulator of genes expressed during infection and inhibitors of DNA adenine methylation are likely to have a broad antimicrobial action. INTRO | |
| 113 136 DNA adenine methylation ptm Importantly, DNA adenine methylation is a global regulator of genes expressed during infection and inhibitors of DNA adenine methylation are likely to have a broad antimicrobial action. INTRO | |
| 0 3 Dam protein_type Dam was considered a promising target for antimicrobial drug development. INTRO | |
| 0 19 Helicobacter pylori species Helicobacter pylori is a Gram-negative bacterium that persistently colonizes in human stomach worldwide. INTRO | |
| 25 48 Gram-negative bacterium taxonomy_domain Helicobacter pylori is a Gram-negative bacterium that persistently colonizes in human stomach worldwide. INTRO | |
| 80 85 human species Helicobacter pylori is a Gram-negative bacterium that persistently colonizes in human stomach worldwide. INTRO | |
| 0 9 H. pylori species H. pylori is involved in 90% of all gastric malignancies, infecting nearly 50% of the world's population and is the most crucial etiologic agent for gastric adenocarcinoma. INTRO | |
| 0 9 H. pylori species H. pylori strains possess a few R-M systems like other bacteria to function as defensive systems. INTRO | |
| 55 63 bacteria taxonomy_domain H. pylori strains possess a few R-M systems like other bacteria to function as defensive systems. INTRO | |
| 0 15 H. pylori 26695 species H. pylori 26695, for example, has 23 R-M systems. INTRO | |
| 0 18 Methyltransferases protein_type Methyltransferases were suggested to be involved in H. pylori pathogenicity. INTRO | |
| 52 61 H. pylori species Methyltransferases were suggested to be involved in H. pylori pathogenicity. INTRO | |
| 0 9 M1.HpyAVI protein M1.HpyAVI is a DNA adenine MTase that belongs to the type II R-M system. INTRO | |
| 15 32 DNA adenine MTase protein_type M1.HpyAVI is a DNA adenine MTase that belongs to the type II R-M system. INTRO | |
| 25 35 DNA MTases protein_type This system contains two DNA MTases named M1.HpyAVI and M2.HpyAVI, and a putative restriction enzyme. INTRO | |
| 42 51 M1.HpyAVI protein This system contains two DNA MTases named M1.HpyAVI and M2.HpyAVI, and a putative restriction enzyme. INTRO | |
| 56 65 M2.HpyAVI protein This system contains two DNA MTases named M1.HpyAVI and M2.HpyAVI, and a putative restriction enzyme. INTRO | |
| 82 100 restriction enzyme protein_type This system contains two DNA MTases named M1.HpyAVI and M2.HpyAVI, and a putative restriction enzyme. INTRO | |
| 0 9 M1.HpyAVI protein M1.HpyAVI encoded by ORF hp0050 is an N6-adenine methyltransferase belonging to the β-class MTase. INTRO | |
| 25 31 hp0050 gene M1.HpyAVI encoded by ORF hp0050 is an N6-adenine methyltransferase belonging to the β-class MTase. INTRO | |
| 38 66 N6-adenine methyltransferase protein_type M1.HpyAVI encoded by ORF hp0050 is an N6-adenine methyltransferase belonging to the β-class MTase. INTRO | |
| 84 97 β-class MTase protein_type M1.HpyAVI encoded by ORF hp0050 is an N6-adenine methyltransferase belonging to the β-class MTase. INTRO | |
| 74 85 5′-GAGG-3′, chemical It has been reported recently that this enzyme recognizes the sequence of 5′-GAGG-3′, 5′-GGAG-3′ or 5′-GAAG-3′ and methylates adenines in these sequences. INTRO | |
| 86 96 5′-GGAG-3′ chemical It has been reported recently that this enzyme recognizes the sequence of 5′-GAGG-3′, 5′-GGAG-3′ or 5′-GAAG-3′ and methylates adenines in these sequences. INTRO | |
| 100 110 5′-GAAG-3′ chemical It has been reported recently that this enzyme recognizes the sequence of 5′-GAGG-3′, 5′-GGAG-3′ or 5′-GAAG-3′ and methylates adenines in these sequences. INTRO | |
| 126 134 adenines residue_name It has been reported recently that this enzyme recognizes the sequence of 5′-GAGG-3′, 5′-GGAG-3′ or 5′-GAAG-3′ and methylates adenines in these sequences. INTRO | |
| 11 22 methylation ptm Given that methylation of two adjacent adenines on the same strand have never been observed for other N6-adenine MTases, the methylation activity on 5′-GAAG-3′ seems to be a unique feature of M1.HpyAVI, compared with the homologs from other strains of H.pylori which is able to methylate only 5′-GAGG-3′. The structural basis and the catalytic mechanism underlying such a distinct activity are not well understood due to the lack of an available 3D structure of this enzyme. INTRO | |
| 39 47 adenines residue_name Given that methylation of two adjacent adenines on the same strand have never been observed for other N6-adenine MTases, the methylation activity on 5′-GAAG-3′ seems to be a unique feature of M1.HpyAVI, compared with the homologs from other strains of H.pylori which is able to methylate only 5′-GAGG-3′. The structural basis and the catalytic mechanism underlying such a distinct activity are not well understood due to the lack of an available 3D structure of this enzyme. INTRO | |
| 102 119 N6-adenine MTases protein_type Given that methylation of two adjacent adenines on the same strand have never been observed for other N6-adenine MTases, the methylation activity on 5′-GAAG-3′ seems to be a unique feature of M1.HpyAVI, compared with the homologs from other strains of H.pylori which is able to methylate only 5′-GAGG-3′. The structural basis and the catalytic mechanism underlying such a distinct activity are not well understood due to the lack of an available 3D structure of this enzyme. INTRO | |
| 125 136 methylation ptm Given that methylation of two adjacent adenines on the same strand have never been observed for other N6-adenine MTases, the methylation activity on 5′-GAAG-3′ seems to be a unique feature of M1.HpyAVI, compared with the homologs from other strains of H.pylori which is able to methylate only 5′-GAGG-3′. The structural basis and the catalytic mechanism underlying such a distinct activity are not well understood due to the lack of an available 3D structure of this enzyme. INTRO | |
| 149 159 5′-GAAG-3′ chemical Given that methylation of two adjacent adenines on the same strand have never been observed for other N6-adenine MTases, the methylation activity on 5′-GAAG-3′ seems to be a unique feature of M1.HpyAVI, compared with the homologs from other strains of H.pylori which is able to methylate only 5′-GAGG-3′. The structural basis and the catalytic mechanism underlying such a distinct activity are not well understood due to the lack of an available 3D structure of this enzyme. INTRO | |
| 192 201 M1.HpyAVI protein Given that methylation of two adjacent adenines on the same strand have never been observed for other N6-adenine MTases, the methylation activity on 5′-GAAG-3′ seems to be a unique feature of M1.HpyAVI, compared with the homologs from other strains of H.pylori which is able to methylate only 5′-GAGG-3′. The structural basis and the catalytic mechanism underlying such a distinct activity are not well understood due to the lack of an available 3D structure of this enzyme. INTRO | |
| 252 260 H.pylori species Given that methylation of two adjacent adenines on the same strand have never been observed for other N6-adenine MTases, the methylation activity on 5′-GAAG-3′ seems to be a unique feature of M1.HpyAVI, compared with the homologs from other strains of H.pylori which is able to methylate only 5′-GAGG-3′. The structural basis and the catalytic mechanism underlying such a distinct activity are not well understood due to the lack of an available 3D structure of this enzyme. INTRO | |
| 293 303 5′-GAGG-3′ chemical Given that methylation of two adjacent adenines on the same strand have never been observed for other N6-adenine MTases, the methylation activity on 5′-GAAG-3′ seems to be a unique feature of M1.HpyAVI, compared with the homologs from other strains of H.pylori which is able to methylate only 5′-GAGG-3′. The structural basis and the catalytic mechanism underlying such a distinct activity are not well understood due to the lack of an available 3D structure of this enzyme. INTRO | |
| 449 458 structure evidence Given that methylation of two adjacent adenines on the same strand have never been observed for other N6-adenine MTases, the methylation activity on 5′-GAAG-3′ seems to be a unique feature of M1.HpyAVI, compared with the homologs from other strains of H.pylori which is able to methylate only 5′-GAGG-3′. The structural basis and the catalytic mechanism underlying such a distinct activity are not well understood due to the lack of an available 3D structure of this enzyme. INTRO | |
| 20 37 crystal structure evidence Here, we report the crystal structure of M1.HpyAVI from H. pylori 26695, which is the first determined N6-adenine MTase structure in H. pylori. INTRO | |
| 41 50 M1.HpyAVI protein Here, we report the crystal structure of M1.HpyAVI from H. pylori 26695, which is the first determined N6-adenine MTase structure in H. pylori. INTRO | |
| 56 71 H. pylori 26695 species Here, we report the crystal structure of M1.HpyAVI from H. pylori 26695, which is the first determined N6-adenine MTase structure in H. pylori. INTRO | |
| 103 119 N6-adenine MTase protein_type Here, we report the crystal structure of M1.HpyAVI from H. pylori 26695, which is the first determined N6-adenine MTase structure in H. pylori. INTRO | |
| 120 129 structure evidence Here, we report the crystal structure of M1.HpyAVI from H. pylori 26695, which is the first determined N6-adenine MTase structure in H. pylori. INTRO | |
| 133 142 H. pylori species Here, we report the crystal structure of M1.HpyAVI from H. pylori 26695, which is the first determined N6-adenine MTase structure in H. pylori. INTRO | |
| 4 13 structure evidence The structure reveals a similar architecture as the canonical fold of homologous proteins, but displays several differences in the loop regions and TRD. INTRO | |
| 131 135 loop structure_element The structure reveals a similar architecture as the canonical fold of homologous proteins, but displays several differences in the loop regions and TRD. INTRO | |
| 148 151 TRD structure_element The structure reveals a similar architecture as the canonical fold of homologous proteins, but displays several differences in the loop regions and TRD. INTRO | |
| 9 44 structural and biochemical analyses experimental_method Based on structural and biochemical analyses, we then identified two conserved amino acids, D29 at the catalytic site and E216 close to the C-terminus, as crucial residues for cofactor binding and methyltransferase activity of M1.HpyAVI. INTRO | |
| 69 78 conserved protein_state Based on structural and biochemical analyses, we then identified two conserved amino acids, D29 at the catalytic site and E216 close to the C-terminus, as crucial residues for cofactor binding and methyltransferase activity of M1.HpyAVI. INTRO | |
| 92 95 D29 residue_name_number Based on structural and biochemical analyses, we then identified two conserved amino acids, D29 at the catalytic site and E216 close to the C-terminus, as crucial residues for cofactor binding and methyltransferase activity of M1.HpyAVI. INTRO | |
| 103 117 catalytic site site Based on structural and biochemical analyses, we then identified two conserved amino acids, D29 at the catalytic site and E216 close to the C-terminus, as crucial residues for cofactor binding and methyltransferase activity of M1.HpyAVI. INTRO | |
| 122 126 E216 residue_name_number Based on structural and biochemical analyses, we then identified two conserved amino acids, D29 at the catalytic site and E216 close to the C-terminus, as crucial residues for cofactor binding and methyltransferase activity of M1.HpyAVI. INTRO | |
| 197 214 methyltransferase protein_type Based on structural and biochemical analyses, we then identified two conserved amino acids, D29 at the catalytic site and E216 close to the C-terminus, as crucial residues for cofactor binding and methyltransferase activity of M1.HpyAVI. INTRO | |
| 227 236 M1.HpyAVI protein Based on structural and biochemical analyses, we then identified two conserved amino acids, D29 at the catalytic site and E216 close to the C-terminus, as crucial residues for cofactor binding and methyltransferase activity of M1.HpyAVI. INTRO | |
| 15 28 non-conserved protein_state In addition, a non-conserved amino acid, P41, seems to play a key role in substrate recognition. INTRO | |
| 41 44 P41 residue_name_number In addition, a non-conserved amino acid, P41, seems to play a key role in substrate recognition. INTRO | |
| 8 17 structure evidence Overall structure RESULTS | |
| 12 23 full-length protein_state Recombinant full-length M1.HpyAVI was produced as a soluble protein in Escherichia coli, but was quite unstable and tended to aggregate in low salt environment. RESULTS | |
| 24 33 M1.HpyAVI protein Recombinant full-length M1.HpyAVI was produced as a soluble protein in Escherichia coli, but was quite unstable and tended to aggregate in low salt environment. RESULTS | |
| 71 87 Escherichia coli species Recombinant full-length M1.HpyAVI was produced as a soluble protein in Escherichia coli, but was quite unstable and tended to aggregate in low salt environment. RESULTS | |
| 92 107 sodium chloride chemical The protein, however, remained fully soluble in a buffer containing higher concentration of sodium chloride (>300 mM), which prompted that M1.HpyAVI is likely a halophilic protein. RESULTS | |
| 139 148 M1.HpyAVI protein The protein, however, remained fully soluble in a buffer containing higher concentration of sodium chloride (>300 mM), which prompted that M1.HpyAVI is likely a halophilic protein. RESULTS | |
| 161 171 halophilic protein_state The protein, however, remained fully soluble in a buffer containing higher concentration of sodium chloride (>300 mM), which prompted that M1.HpyAVI is likely a halophilic protein. RESULTS | |
| 4 17 cofactor-free protein_state The cofactor-free and AdoMet-bound proteins were crystallized at different conditions. RESULTS | |
| 22 34 AdoMet-bound protein_state The cofactor-free and AdoMet-bound proteins were crystallized at different conditions. RESULTS | |
| 49 61 crystallized experimental_method The cofactor-free and AdoMet-bound proteins were crystallized at different conditions. RESULTS | |
| 5 15 structures evidence Both structures were determined by means of molecular replacement, and refined to 3.0 Å and 3.1 Å, respectively. RESULTS | |
| 44 65 molecular replacement experimental_method Both structures were determined by means of molecular replacement, and refined to 3.0 Å and 3.1 Å, respectively. RESULTS | |
| 14 35 X-ray data collection experimental_method Statistics of X-ray data collection and structure refinement were summarized in Table 1. RESULTS | |
| 40 60 structure refinement experimental_method Statistics of X-ray data collection and structure refinement were summarized in Table 1. RESULTS | |
| 20 51 structure refinement statistics evidence Data collection and structure refinement statistics of M1.HpyAVI TABLE | |
| 55 64 M1.HpyAVI protein Data collection and structure refinement statistics of M1.HpyAVI TABLE | |
| 1 10 M1.HpyAVI protein " M1.HpyAVI M1.HpyAVI-AdoMet complex Data collection Wavelength (Å) 1.0000 0.97772 Space group P43212 P65 Unit-cell parameters (Å, ˚) a = b = 69.73, c = 532.75α = β = γ = 90 a = b = 135.60, c = 265.15α = β = 90, γ = 120 Resolution range (Å) a 49.09-3.00 (3.09-3.00) 48.91-3.10 (3.18-3.10) Unique reflections a 27243 49833 Multiplicity a 3.7 (3.8) 5.6 (4.0) Completeness (%)a 98.7 (98.9) 99.7 (97.8) Mean I/δ (I) a 12.1 (3.4) 14.0 (1.9) Solvent content (%) 58.67 61.96 Rmergea 0.073 (0.378) 0.106 (0.769) Structure refinement Rwork 0.251 0.221 Rfree 0.308 0.276 R.m.s.d., bond lengths (Å) 0.007 0.007 R.m.s.d., bond angles (˚) 1.408 1.651 Ramachandran plot Favoured region (%) 89.44 91.44 Allowed region (%) 9.58 7.11 Outliers (%) 0.99 1.45 " TABLE | |
| 11 27 M1.HpyAVI-AdoMet complex_assembly " M1.HpyAVI M1.HpyAVI-AdoMet complex Data collection Wavelength (Å) 1.0000 0.97772 Space group P43212 P65 Unit-cell parameters (Å, ˚) a = b = 69.73, c = 532.75α = β = γ = 90 a = b = 135.60, c = 265.15α = β = 90, γ = 120 Resolution range (Å) a 49.09-3.00 (3.09-3.00) 48.91-3.10 (3.18-3.10) Unique reflections a 27243 49833 Multiplicity a 3.7 (3.8) 5.6 (4.0) Completeness (%)a 98.7 (98.9) 99.7 (97.8) Mean I/δ (I) a 12.1 (3.4) 14.0 (1.9) Solvent content (%) 58.67 61.96 Rmergea 0.073 (0.378) 0.106 (0.769) Structure refinement Rwork 0.251 0.221 Rfree 0.308 0.276 R.m.s.d., bond lengths (Å) 0.007 0.007 R.m.s.d., bond angles (˚) 1.408 1.651 Ramachandran plot Favoured region (%) 89.44 91.44 Allowed region (%) 9.58 7.11 Outliers (%) 0.99 1.45 " TABLE | |
| 594 601 R.m.s.d evidence " M1.HpyAVI M1.HpyAVI-AdoMet complex Data collection Wavelength (Å) 1.0000 0.97772 Space group P43212 P65 Unit-cell parameters (Å, ˚) a = b = 69.73, c = 532.75α = β = γ = 90 a = b = 135.60, c = 265.15α = β = 90, γ = 120 Resolution range (Å) a 49.09-3.00 (3.09-3.00) 48.91-3.10 (3.18-3.10) Unique reflections a 27243 49833 Multiplicity a 3.7 (3.8) 5.6 (4.0) Completeness (%)a 98.7 (98.9) 99.7 (97.8) Mean I/δ (I) a 12.1 (3.4) 14.0 (1.9) Solvent content (%) 58.67 61.96 Rmergea 0.073 (0.378) 0.106 (0.769) Structure refinement Rwork 0.251 0.221 Rfree 0.308 0.276 R.m.s.d., bond lengths (Å) 0.007 0.007 R.m.s.d., bond angles (˚) 1.408 1.651 Ramachandran plot Favoured region (%) 89.44 91.44 Allowed region (%) 9.58 7.11 Outliers (%) 0.99 1.45 " TABLE | |
| 635 642 R.m.s.d evidence " M1.HpyAVI M1.HpyAVI-AdoMet complex Data collection Wavelength (Å) 1.0000 0.97772 Space group P43212 P65 Unit-cell parameters (Å, ˚) a = b = 69.73, c = 532.75α = β = γ = 90 a = b = 135.60, c = 265.15α = β = 90, γ = 120 Resolution range (Å) a 49.09-3.00 (3.09-3.00) 48.91-3.10 (3.18-3.10) Unique reflections a 27243 49833 Multiplicity a 3.7 (3.8) 5.6 (4.0) Completeness (%)a 98.7 (98.9) 99.7 (97.8) Mean I/δ (I) a 12.1 (3.4) 14.0 (1.9) Solvent content (%) 58.67 61.96 Rmergea 0.073 (0.378) 0.106 (0.769) Structure refinement Rwork 0.251 0.221 Rfree 0.308 0.276 R.m.s.d., bond lengths (Å) 0.007 0.007 R.m.s.d., bond angles (˚) 1.408 1.651 Ramachandran plot Favoured region (%) 89.44 91.44 Allowed region (%) 9.58 7.11 Outliers (%) 0.99 1.45 " TABLE | |
| 23 31 monomers oligomeric_state Four and eight protein monomers resided in the asymmetric units of the two crystal structures. RESULTS | |
| 75 93 crystal structures evidence Four and eight protein monomers resided in the asymmetric units of the two crystal structures. RESULTS | |
| 48 53 loops structure_element Some amino acids, particularly those within two loops (residues 32-61 and 152-172) in both structures, were poorly defined in electron density and had to be omitted from the refined models. RESULTS | |
| 64 69 32-61 residue_range Some amino acids, particularly those within two loops (residues 32-61 and 152-172) in both structures, were poorly defined in electron density and had to be omitted from the refined models. RESULTS | |
| 74 81 152-172 residue_range Some amino acids, particularly those within two loops (residues 32-61 and 152-172) in both structures, were poorly defined in electron density and had to be omitted from the refined models. RESULTS | |
| 91 101 structures evidence Some amino acids, particularly those within two loops (residues 32-61 and 152-172) in both structures, were poorly defined in electron density and had to be omitted from the refined models. RESULTS | |
| 126 142 electron density evidence Some amino acids, particularly those within two loops (residues 32-61 and 152-172) in both structures, were poorly defined in electron density and had to be omitted from the refined models. RESULTS | |
| 8 18 structures evidence The two structures are very similar to each other (Figure 1) and could be well overlaid with an RMSD of 0.76 Å on 191 Cα atoms. RESULTS | |
| 96 100 RMSD evidence The two structures are very similar to each other (Figure 1) and could be well overlaid with an RMSD of 0.76 Å on 191 Cα atoms. RESULTS | |
| 28 37 M1.HpyAVI protein The overall architecture of M1.HpyAVI revealed in these structures resembles the AdoMet-dependent MTase fold in which a twisted seven-stranded β-sheet flanked by six α-helices forms the structural core. RESULTS | |
| 56 66 structures evidence The overall architecture of M1.HpyAVI revealed in these structures resembles the AdoMet-dependent MTase fold in which a twisted seven-stranded β-sheet flanked by six α-helices forms the structural core. RESULTS | |
| 81 103 AdoMet-dependent MTase protein_type The overall architecture of M1.HpyAVI revealed in these structures resembles the AdoMet-dependent MTase fold in which a twisted seven-stranded β-sheet flanked by six α-helices forms the structural core. RESULTS | |
| 143 150 β-sheet structure_element The overall architecture of M1.HpyAVI revealed in these structures resembles the AdoMet-dependent MTase fold in which a twisted seven-stranded β-sheet flanked by six α-helices forms the structural core. RESULTS | |
| 166 175 α-helices structure_element The overall architecture of M1.HpyAVI revealed in these structures resembles the AdoMet-dependent MTase fold in which a twisted seven-stranded β-sheet flanked by six α-helices forms the structural core. RESULTS | |
| 18 28 structures evidence Like the reported structures of the larger domain of MTases, three helices (αA, αB and αZ) are located at one face of the central β-sheet, while the other three αD, αE and αC sit at the other side. RESULTS | |
| 53 59 MTases protein_type Like the reported structures of the larger domain of MTases, three helices (αA, αB and αZ) are located at one face of the central β-sheet, while the other three αD, αE and αC sit at the other side. RESULTS | |
| 67 74 helices structure_element Like the reported structures of the larger domain of MTases, three helices (αA, αB and αZ) are located at one face of the central β-sheet, while the other three αD, αE and αC sit at the other side. RESULTS | |
| 76 78 αA structure_element Like the reported structures of the larger domain of MTases, three helices (αA, αB and αZ) are located at one face of the central β-sheet, while the other three αD, αE and αC sit at the other side. RESULTS | |
| 80 82 αB structure_element Like the reported structures of the larger domain of MTases, three helices (αA, αB and αZ) are located at one face of the central β-sheet, while the other three αD, αE and αC sit at the other side. RESULTS | |
| 87 89 αZ structure_element Like the reported structures of the larger domain of MTases, three helices (αA, αB and αZ) are located at one face of the central β-sheet, while the other three αD, αE and αC sit at the other side. RESULTS | |
| 130 137 β-sheet structure_element Like the reported structures of the larger domain of MTases, three helices (αA, αB and αZ) are located at one face of the central β-sheet, while the other three αD, αE and αC sit at the other side. RESULTS | |
| 161 163 αD structure_element Like the reported structures of the larger domain of MTases, three helices (αA, αB and αZ) are located at one face of the central β-sheet, while the other three αD, αE and αC sit at the other side. RESULTS | |
| 165 167 αE structure_element Like the reported structures of the larger domain of MTases, three helices (αA, αB and αZ) are located at one face of the central β-sheet, while the other three αD, αE and αC sit at the other side. RESULTS | |
| 172 174 αC structure_element Like the reported structures of the larger domain of MTases, three helices (αA, αB and αZ) are located at one face of the central β-sheet, while the other three αD, αE and αC sit at the other side. RESULTS | |
| 10 19 conserved protein_state All these conserved structural motifs form a typical α/β Rossmann fold. RESULTS | |
| 53 70 α/β Rossmann fold structure_element All these conserved structural motifs form a typical α/β Rossmann fold. RESULTS | |
| 4 19 catalytic motif structure_element The catalytic motif DPPY lies in a loop connecting αD and β4, and the cofactor AdoMet binds in a neighboring cavity. RESULTS | |
| 20 24 DPPY structure_element The catalytic motif DPPY lies in a loop connecting αD and β4, and the cofactor AdoMet binds in a neighboring cavity. RESULTS | |
| 35 39 loop structure_element The catalytic motif DPPY lies in a loop connecting αD and β4, and the cofactor AdoMet binds in a neighboring cavity. RESULTS | |
| 51 53 αD structure_element The catalytic motif DPPY lies in a loop connecting αD and β4, and the cofactor AdoMet binds in a neighboring cavity. RESULTS | |
| 58 60 β4 structure_element The catalytic motif DPPY lies in a loop connecting αD and β4, and the cofactor AdoMet binds in a neighboring cavity. RESULTS | |
| 79 85 AdoMet chemical The catalytic motif DPPY lies in a loop connecting αD and β4, and the cofactor AdoMet binds in a neighboring cavity. RESULTS | |
| 109 115 cavity site The catalytic motif DPPY lies in a loop connecting αD and β4, and the cofactor AdoMet binds in a neighboring cavity. RESULTS | |
| 4 8 loop structure_element The loop (residues 136-166) located between β7 and αZ corresponds to a highly diverse region in other MTases that is involved in target DNA recognition. RESULTS | |
| 19 26 136-166 residue_range The loop (residues 136-166) located between β7 and αZ corresponds to a highly diverse region in other MTases that is involved in target DNA recognition. RESULTS | |
| 44 46 β7 structure_element The loop (residues 136-166) located between β7 and αZ corresponds to a highly diverse region in other MTases that is involved in target DNA recognition. RESULTS | |
| 51 53 αZ structure_element The loop (residues 136-166) located between β7 and αZ corresponds to a highly diverse region in other MTases that is involved in target DNA recognition. RESULTS | |
| 71 85 highly diverse protein_state The loop (residues 136-166) located between β7 and αZ corresponds to a highly diverse region in other MTases that is involved in target DNA recognition. RESULTS | |
| 102 108 MTases protein_type The loop (residues 136-166) located between β7 and αZ corresponds to a highly diverse region in other MTases that is involved in target DNA recognition. RESULTS | |
| 136 139 DNA chemical The loop (residues 136-166) located between β7 and αZ corresponds to a highly diverse region in other MTases that is involved in target DNA recognition. RESULTS | |
| 4 16 hairpin loop structure_element The hairpin loop (residues 101-133) bridging β6 and β7, which is proposed to bind DNA in the minor groove, displays a similar conformation as those observed in M.MboIIA, M.RsrI and M.pvuII. RESULTS | |
| 27 34 101-133 residue_range The hairpin loop (residues 101-133) bridging β6 and β7, which is proposed to bind DNA in the minor groove, displays a similar conformation as those observed in M.MboIIA, M.RsrI and M.pvuII. RESULTS | |
| 45 47 β6 structure_element The hairpin loop (residues 101-133) bridging β6 and β7, which is proposed to bind DNA in the minor groove, displays a similar conformation as those observed in M.MboIIA, M.RsrI and M.pvuII. RESULTS | |
| 52 54 β7 structure_element The hairpin loop (residues 101-133) bridging β6 and β7, which is proposed to bind DNA in the minor groove, displays a similar conformation as those observed in M.MboIIA, M.RsrI and M.pvuII. RESULTS | |
| 82 85 DNA chemical The hairpin loop (residues 101-133) bridging β6 and β7, which is proposed to bind DNA in the minor groove, displays a similar conformation as those observed in M.MboIIA, M.RsrI and M.pvuII. RESULTS | |
| 93 105 minor groove structure_element The hairpin loop (residues 101-133) bridging β6 and β7, which is proposed to bind DNA in the minor groove, displays a similar conformation as those observed in M.MboIIA, M.RsrI and M.pvuII. RESULTS | |
| 160 168 M.MboIIA protein The hairpin loop (residues 101-133) bridging β6 and β7, which is proposed to bind DNA in the minor groove, displays a similar conformation as those observed in M.MboIIA, M.RsrI and M.pvuII. RESULTS | |
| 170 176 M.RsrI protein The hairpin loop (residues 101-133) bridging β6 and β7, which is proposed to bind DNA in the minor groove, displays a similar conformation as those observed in M.MboIIA, M.RsrI and M.pvuII. RESULTS | |
| 181 188 M.pvuII protein The hairpin loop (residues 101-133) bridging β6 and β7, which is proposed to bind DNA in the minor groove, displays a similar conformation as those observed in M.MboIIA, M.RsrI and M.pvuII. RESULTS | |
| 4 11 missing protein_state The missing loop (residues 33-58) in the structure of M1.HpyAVI corresponds to loop I in M.TaqI, which was also invisible in a structure without DNA. RESULTS | |
| 12 16 loop structure_element The missing loop (residues 33-58) in the structure of M1.HpyAVI corresponds to loop I in M.TaqI, which was also invisible in a structure without DNA. RESULTS | |
| 27 32 33-58 residue_range The missing loop (residues 33-58) in the structure of M1.HpyAVI corresponds to loop I in M.TaqI, which was also invisible in a structure without DNA. RESULTS | |
| 41 50 structure evidence The missing loop (residues 33-58) in the structure of M1.HpyAVI corresponds to loop I in M.TaqI, which was also invisible in a structure without DNA. RESULTS | |
| 54 63 M1.HpyAVI protein The missing loop (residues 33-58) in the structure of M1.HpyAVI corresponds to loop I in M.TaqI, which was also invisible in a structure without DNA. RESULTS | |
| 79 85 loop I structure_element The missing loop (residues 33-58) in the structure of M1.HpyAVI corresponds to loop I in M.TaqI, which was also invisible in a structure without DNA. RESULTS | |
| 89 95 M.TaqI protein The missing loop (residues 33-58) in the structure of M1.HpyAVI corresponds to loop I in M.TaqI, which was also invisible in a structure without DNA. RESULTS | |
| 127 136 structure evidence The missing loop (residues 33-58) in the structure of M1.HpyAVI corresponds to loop I in M.TaqI, which was also invisible in a structure without DNA. RESULTS | |
| 137 148 without DNA protein_state The missing loop (residues 33-58) in the structure of M1.HpyAVI corresponds to loop I in M.TaqI, which was also invisible in a structure without DNA. RESULTS | |
| 5 9 loop structure_element This loop, however, was well ordered in an M.TaqI-DNA complex structure and was shown to play a crucial role in DNA methylation by contacting the flipping adenine and recognizing specific DNA sequence. RESULTS | |
| 24 36 well ordered protein_state This loop, however, was well ordered in an M.TaqI-DNA complex structure and was shown to play a crucial role in DNA methylation by contacting the flipping adenine and recognizing specific DNA sequence. RESULTS | |
| 43 71 M.TaqI-DNA complex structure evidence This loop, however, was well ordered in an M.TaqI-DNA complex structure and was shown to play a crucial role in DNA methylation by contacting the flipping adenine and recognizing specific DNA sequence. RESULTS | |
| 112 127 DNA methylation ptm This loop, however, was well ordered in an M.TaqI-DNA complex structure and was shown to play a crucial role in DNA methylation by contacting the flipping adenine and recognizing specific DNA sequence. RESULTS | |
| 155 162 adenine residue_name This loop, however, was well ordered in an M.TaqI-DNA complex structure and was shown to play a crucial role in DNA methylation by contacting the flipping adenine and recognizing specific DNA sequence. RESULTS | |
| 188 191 DNA chemical This loop, however, was well ordered in an M.TaqI-DNA complex structure and was shown to play a crucial role in DNA methylation by contacting the flipping adenine and recognizing specific DNA sequence. RESULTS | |
| 8 17 structure evidence Overall structure of M1.HpyAVI FIG | |
| 21 30 M1.HpyAVI protein Overall structure of M1.HpyAVI FIG | |
| 3 7 Free protein_state A. Free form B. AdoMet-bound form. FIG | |
| 16 28 AdoMet-bound protein_state A. Free form B. AdoMet-bound form. FIG | |
| 18 27 M1.HpyAVI protein Ribbon diagram of M1.HpyAVI resembles an “AdoMet-dependent MTase fold”, a mixed seven-stranded β-sheet flanked by six α-helices, αA, αB, αZ on one side and αD, αE, αC on the other side, the cofactor AdoMet is bound in a cavity near the conserved enzyme activity motif DPPY. FIG | |
| 42 64 AdoMet-dependent MTase protein_type Ribbon diagram of M1.HpyAVI resembles an “AdoMet-dependent MTase fold”, a mixed seven-stranded β-sheet flanked by six α-helices, αA, αB, αZ on one side and αD, αE, αC on the other side, the cofactor AdoMet is bound in a cavity near the conserved enzyme activity motif DPPY. FIG | |
| 95 102 β-sheet structure_element Ribbon diagram of M1.HpyAVI resembles an “AdoMet-dependent MTase fold”, a mixed seven-stranded β-sheet flanked by six α-helices, αA, αB, αZ on one side and αD, αE, αC on the other side, the cofactor AdoMet is bound in a cavity near the conserved enzyme activity motif DPPY. FIG | |
| 118 127 α-helices structure_element Ribbon diagram of M1.HpyAVI resembles an “AdoMet-dependent MTase fold”, a mixed seven-stranded β-sheet flanked by six α-helices, αA, αB, αZ on one side and αD, αE, αC on the other side, the cofactor AdoMet is bound in a cavity near the conserved enzyme activity motif DPPY. FIG | |
| 129 131 αA structure_element Ribbon diagram of M1.HpyAVI resembles an “AdoMet-dependent MTase fold”, a mixed seven-stranded β-sheet flanked by six α-helices, αA, αB, αZ on one side and αD, αE, αC on the other side, the cofactor AdoMet is bound in a cavity near the conserved enzyme activity motif DPPY. FIG | |
| 133 135 αB structure_element Ribbon diagram of M1.HpyAVI resembles an “AdoMet-dependent MTase fold”, a mixed seven-stranded β-sheet flanked by six α-helices, αA, αB, αZ on one side and αD, αE, αC on the other side, the cofactor AdoMet is bound in a cavity near the conserved enzyme activity motif DPPY. FIG | |
| 137 139 αZ structure_element Ribbon diagram of M1.HpyAVI resembles an “AdoMet-dependent MTase fold”, a mixed seven-stranded β-sheet flanked by six α-helices, αA, αB, αZ on one side and αD, αE, αC on the other side, the cofactor AdoMet is bound in a cavity near the conserved enzyme activity motif DPPY. FIG | |
| 156 158 αD structure_element Ribbon diagram of M1.HpyAVI resembles an “AdoMet-dependent MTase fold”, a mixed seven-stranded β-sheet flanked by six α-helices, αA, αB, αZ on one side and αD, αE, αC on the other side, the cofactor AdoMet is bound in a cavity near the conserved enzyme activity motif DPPY. FIG | |
| 160 162 αE structure_element Ribbon diagram of M1.HpyAVI resembles an “AdoMet-dependent MTase fold”, a mixed seven-stranded β-sheet flanked by six α-helices, αA, αB, αZ on one side and αD, αE, αC on the other side, the cofactor AdoMet is bound in a cavity near the conserved enzyme activity motif DPPY. FIG | |
| 164 166 αC structure_element Ribbon diagram of M1.HpyAVI resembles an “AdoMet-dependent MTase fold”, a mixed seven-stranded β-sheet flanked by six α-helices, αA, αB, αZ on one side and αD, αE, αC on the other side, the cofactor AdoMet is bound in a cavity near the conserved enzyme activity motif DPPY. FIG | |
| 199 205 AdoMet chemical Ribbon diagram of M1.HpyAVI resembles an “AdoMet-dependent MTase fold”, a mixed seven-stranded β-sheet flanked by six α-helices, αA, αB, αZ on one side and αD, αE, αC on the other side, the cofactor AdoMet is bound in a cavity near the conserved enzyme activity motif DPPY. FIG | |
| 209 217 bound in protein_state Ribbon diagram of M1.HpyAVI resembles an “AdoMet-dependent MTase fold”, a mixed seven-stranded β-sheet flanked by six α-helices, αA, αB, αZ on one side and αD, αE, αC on the other side, the cofactor AdoMet is bound in a cavity near the conserved enzyme activity motif DPPY. FIG | |
| 220 226 cavity site Ribbon diagram of M1.HpyAVI resembles an “AdoMet-dependent MTase fold”, a mixed seven-stranded β-sheet flanked by six α-helices, αA, αB, αZ on one side and αD, αE, αC on the other side, the cofactor AdoMet is bound in a cavity near the conserved enzyme activity motif DPPY. FIG | |
| 236 245 conserved protein_state Ribbon diagram of M1.HpyAVI resembles an “AdoMet-dependent MTase fold”, a mixed seven-stranded β-sheet flanked by six α-helices, αA, αB, αZ on one side and αD, αE, αC on the other side, the cofactor AdoMet is bound in a cavity near the conserved enzyme activity motif DPPY. FIG | |
| 268 272 DPPY structure_element Ribbon diagram of M1.HpyAVI resembles an “AdoMet-dependent MTase fold”, a mixed seven-stranded β-sheet flanked by six α-helices, αA, αB, αZ on one side and αD, αE, αC on the other side, the cofactor AdoMet is bound in a cavity near the conserved enzyme activity motif DPPY. FIG | |
| 4 13 α-helices structure_element The α-helices and β-strands are labelled and numbered according to the commonly numbering rule for the known MTases. FIG | |
| 18 27 β-strands structure_element The α-helices and β-strands are labelled and numbered according to the commonly numbering rule for the known MTases. FIG | |
| 109 115 MTases protein_type The α-helices and β-strands are labelled and numbered according to the commonly numbering rule for the known MTases. FIG | |
| 4 10 AdoMet chemical The AdoMet molecule is shown in green. FIG | |
| 0 7 Dimeric oligomeric_state Dimeric state of M1.HpyAVI in crystal and solution RESULTS | |
| 17 26 M1.HpyAVI protein Dimeric state of M1.HpyAVI in crystal and solution RESULTS | |
| 30 37 crystal evidence Dimeric state of M1.HpyAVI in crystal and solution RESULTS | |
| 42 50 solution experimental_method Dimeric state of M1.HpyAVI in crystal and solution RESULTS | |
| 34 44 DNA MTases protein_type Previous studies showed that some DNA MTases, e.g. M.BamHI and M.EcoRI, exist as monomer in solution, in agreement with the fact that a DNA substrate for a typical MTase is hemimethylated and therefore needs only a single methylation event to convert it into a fully methylated state. RESULTS | |
| 51 58 M.BamHI protein Previous studies showed that some DNA MTases, e.g. M.BamHI and M.EcoRI, exist as monomer in solution, in agreement with the fact that a DNA substrate for a typical MTase is hemimethylated and therefore needs only a single methylation event to convert it into a fully methylated state. RESULTS | |
| 63 70 M.EcoRI protein Previous studies showed that some DNA MTases, e.g. M.BamHI and M.EcoRI, exist as monomer in solution, in agreement with the fact that a DNA substrate for a typical MTase is hemimethylated and therefore needs only a single methylation event to convert it into a fully methylated state. RESULTS | |
| 81 88 monomer oligomeric_state Previous studies showed that some DNA MTases, e.g. M.BamHI and M.EcoRI, exist as monomer in solution, in agreement with the fact that a DNA substrate for a typical MTase is hemimethylated and therefore needs only a single methylation event to convert it into a fully methylated state. RESULTS | |
| 136 139 DNA chemical Previous studies showed that some DNA MTases, e.g. M.BamHI and M.EcoRI, exist as monomer in solution, in agreement with the fact that a DNA substrate for a typical MTase is hemimethylated and therefore needs only a single methylation event to convert it into a fully methylated state. RESULTS | |
| 164 169 MTase protein_type Previous studies showed that some DNA MTases, e.g. M.BamHI and M.EcoRI, exist as monomer in solution, in agreement with the fact that a DNA substrate for a typical MTase is hemimethylated and therefore needs only a single methylation event to convert it into a fully methylated state. RESULTS | |
| 173 187 hemimethylated protein_state Previous studies showed that some DNA MTases, e.g. M.BamHI and M.EcoRI, exist as monomer in solution, in agreement with the fact that a DNA substrate for a typical MTase is hemimethylated and therefore needs only a single methylation event to convert it into a fully methylated state. RESULTS | |
| 222 233 methylation ptm Previous studies showed that some DNA MTases, e.g. M.BamHI and M.EcoRI, exist as monomer in solution, in agreement with the fact that a DNA substrate for a typical MTase is hemimethylated and therefore needs only a single methylation event to convert it into a fully methylated state. RESULTS | |
| 261 277 fully methylated protein_state Previous studies showed that some DNA MTases, e.g. M.BamHI and M.EcoRI, exist as monomer in solution, in agreement with the fact that a DNA substrate for a typical MTase is hemimethylated and therefore needs only a single methylation event to convert it into a fully methylated state. RESULTS | |
| 21 28 dimeric oligomeric_state Increasing number of dimeric DNA MTases, however, has been identified from later studies. RESULTS | |
| 29 39 DNA MTases protein_type Increasing number of dimeric DNA MTases, however, has been identified from later studies. RESULTS | |
| 14 21 M.DpnII protein For instance, M.DpnII, M.RsrI, M.KpnI, and M.MboIIA have been found as dimers in solution. RESULTS | |
| 23 29 M.RsrI protein For instance, M.DpnII, M.RsrI, M.KpnI, and M.MboIIA have been found as dimers in solution. RESULTS | |
| 31 37 M.KpnI protein For instance, M.DpnII, M.RsrI, M.KpnI, and M.MboIIA have been found as dimers in solution. RESULTS | |
| 43 51 M.MboIIA protein For instance, M.DpnII, M.RsrI, M.KpnI, and M.MboIIA have been found as dimers in solution. RESULTS | |
| 71 77 dimers oligomeric_state For instance, M.DpnII, M.RsrI, M.KpnI, and M.MboIIA have been found as dimers in solution. RESULTS | |
| 21 27 MTases protein_type In addition, several MTases including M.MboIIA, M.RsrI and TTH0409 form tightly associated dimers in crystal structures. RESULTS | |
| 38 46 M.MboIIA protein In addition, several MTases including M.MboIIA, M.RsrI and TTH0409 form tightly associated dimers in crystal structures. RESULTS | |
| 48 54 M.RsrI protein In addition, several MTases including M.MboIIA, M.RsrI and TTH0409 form tightly associated dimers in crystal structures. RESULTS | |
| 59 66 TTH0409 protein In addition, several MTases including M.MboIIA, M.RsrI and TTH0409 form tightly associated dimers in crystal structures. RESULTS | |
| 91 97 dimers oligomeric_state In addition, several MTases including M.MboIIA, M.RsrI and TTH0409 form tightly associated dimers in crystal structures. RESULTS | |
| 101 119 crystal structures evidence In addition, several MTases including M.MboIIA, M.RsrI and TTH0409 form tightly associated dimers in crystal structures. RESULTS | |
| 18 28 DNA MTases protein_type Nonetheless, some DNA MTases such as M.CcrMI and the Bacillus amyloliquefaciens MTase dissociate from dimer into monomer upon DNA-binding. RESULTS | |
| 37 44 M.CcrMI protein Nonetheless, some DNA MTases such as M.CcrMI and the Bacillus amyloliquefaciens MTase dissociate from dimer into monomer upon DNA-binding. RESULTS | |
| 53 79 Bacillus amyloliquefaciens species Nonetheless, some DNA MTases such as M.CcrMI and the Bacillus amyloliquefaciens MTase dissociate from dimer into monomer upon DNA-binding. RESULTS | |
| 80 85 MTase protein_type Nonetheless, some DNA MTases such as M.CcrMI and the Bacillus amyloliquefaciens MTase dissociate from dimer into monomer upon DNA-binding. RESULTS | |
| 102 107 dimer oligomeric_state Nonetheless, some DNA MTases such as M.CcrMI and the Bacillus amyloliquefaciens MTase dissociate from dimer into monomer upon DNA-binding. RESULTS | |
| 113 120 monomer oligomeric_state Nonetheless, some DNA MTases such as M.CcrMI and the Bacillus amyloliquefaciens MTase dissociate from dimer into monomer upon DNA-binding. RESULTS | |
| 126 129 DNA chemical Nonetheless, some DNA MTases such as M.CcrMI and the Bacillus amyloliquefaciens MTase dissociate from dimer into monomer upon DNA-binding. RESULTS | |
| 42 51 conserved protein_state According to the arrangement of the three conserved domains, M1.HpyAVI belongs to the β-subgroup, in which a conserved motif NXXTX9−11AXRXFSXXHX4WX6−9 YXFXLX3RX9−26NPX1−6NVWX29−34A has been identified at the dimerization interface in crystal structures. RESULTS | |
| 61 70 M1.HpyAVI protein According to the arrangement of the three conserved domains, M1.HpyAVI belongs to the β-subgroup, in which a conserved motif NXXTX9−11AXRXFSXXHX4WX6−9 YXFXLX3RX9−26NPX1−6NVWX29−34A has been identified at the dimerization interface in crystal structures. RESULTS | |
| 86 96 β-subgroup protein_type According to the arrangement of the three conserved domains, M1.HpyAVI belongs to the β-subgroup, in which a conserved motif NXXTX9−11AXRXFSXXHX4WX6−9 YXFXLX3RX9−26NPX1−6NVWX29−34A has been identified at the dimerization interface in crystal structures. RESULTS | |
| 109 118 conserved protein_state According to the arrangement of the three conserved domains, M1.HpyAVI belongs to the β-subgroup, in which a conserved motif NXXTX9−11AXRXFSXXHX4WX6−9 YXFXLX3RX9−26NPX1−6NVWX29−34A has been identified at the dimerization interface in crystal structures. RESULTS | |
| 125 180 NXXTX9−11AXRXFSXXHX4WX6−9 YXFXLX3RX9−26NPX1−6NVWX29−34A structure_element According to the arrangement of the three conserved domains, M1.HpyAVI belongs to the β-subgroup, in which a conserved motif NXXTX9−11AXRXFSXXHX4WX6−9 YXFXLX3RX9−26NPX1−6NVWX29−34A has been identified at the dimerization interface in crystal structures. RESULTS | |
| 208 230 dimerization interface site According to the arrangement of the three conserved domains, M1.HpyAVI belongs to the β-subgroup, in which a conserved motif NXXTX9−11AXRXFSXXHX4WX6−9 YXFXLX3RX9−26NPX1−6NVWX29−34A has been identified at the dimerization interface in crystal structures. RESULTS | |
| 234 252 crystal structures evidence According to the arrangement of the three conserved domains, M1.HpyAVI belongs to the β-subgroup, in which a conserved motif NXXTX9−11AXRXFSXXHX4WX6−9 YXFXLX3RX9−26NPX1−6NVWX29−34A has been identified at the dimerization interface in crystal structures. RESULTS | |
| 8 17 conserved protein_state Most of conserved amino acids within that motif are present in the sequence of M1.HpyAVI (Figure 2A), implying dimerization of this protein. RESULTS | |
| 79 88 M1.HpyAVI protein Most of conserved amino acids within that motif are present in the sequence of M1.HpyAVI (Figure 2A), implying dimerization of this protein. RESULTS | |
| 111 123 dimerization oligomeric_state Most of conserved amino acids within that motif are present in the sequence of M1.HpyAVI (Figure 2A), implying dimerization of this protein. RESULTS | |
| 16 21 dimer oligomeric_state In agreement, a dimer of M1.HpyAVI was observed in our crystal structures with the two monomers related by a two-fold axis (Figure 2B and 2C). RESULTS | |
| 25 34 M1.HpyAVI protein In agreement, a dimer of M1.HpyAVI was observed in our crystal structures with the two monomers related by a two-fold axis (Figure 2B and 2C). RESULTS | |
| 55 73 crystal structures evidence In agreement, a dimer of M1.HpyAVI was observed in our crystal structures with the two monomers related by a two-fold axis (Figure 2B and 2C). RESULTS | |
| 87 95 monomers oligomeric_state In agreement, a dimer of M1.HpyAVI was observed in our crystal structures with the two monomers related by a two-fold axis (Figure 2B and 2C). RESULTS | |
| 38 55 dimeric interface site An area of ~1900 Å2 was buried at the dimeric interface, taking up ca 17% of the total area. RESULTS | |
| 4 11 dimeric oligomeric_state The dimeric architecture was greatly stabilized by hydrogen bonds and salt bridges formed among residues R86, D93 and E96. RESULTS | |
| 51 65 hydrogen bonds bond_interaction The dimeric architecture was greatly stabilized by hydrogen bonds and salt bridges formed among residues R86, D93 and E96. RESULTS | |
| 70 82 salt bridges bond_interaction The dimeric architecture was greatly stabilized by hydrogen bonds and salt bridges formed among residues R86, D93 and E96. RESULTS | |
| 105 108 R86 residue_name_number The dimeric architecture was greatly stabilized by hydrogen bonds and salt bridges formed among residues R86, D93 and E96. RESULTS | |
| 110 113 D93 residue_name_number The dimeric architecture was greatly stabilized by hydrogen bonds and salt bridges formed among residues R86, D93 and E96. RESULTS | |
| 118 121 E96 residue_name_number The dimeric architecture was greatly stabilized by hydrogen bonds and salt bridges formed among residues R86, D93 and E96. RESULTS | |
| 31 36 dimer oligomeric_state In addition, comparison of the dimer structure of M1.HpyAVI with some other β-class MTases (M1.MboIIA, M.RsrI and TTHA0409) suggested that the M1.HpyAVI dimer organized in a similar form as others (Figure S3). RESULTS | |
| 37 46 structure evidence In addition, comparison of the dimer structure of M1.HpyAVI with some other β-class MTases (M1.MboIIA, M.RsrI and TTHA0409) suggested that the M1.HpyAVI dimer organized in a similar form as others (Figure S3). RESULTS | |
| 50 59 M1.HpyAVI protein In addition, comparison of the dimer structure of M1.HpyAVI with some other β-class MTases (M1.MboIIA, M.RsrI and TTHA0409) suggested that the M1.HpyAVI dimer organized in a similar form as others (Figure S3). RESULTS | |
| 76 90 β-class MTases protein_type In addition, comparison of the dimer structure of M1.HpyAVI with some other β-class MTases (M1.MboIIA, M.RsrI and TTHA0409) suggested that the M1.HpyAVI dimer organized in a similar form as others (Figure S3). RESULTS | |
| 92 101 M1.MboIIA protein In addition, comparison of the dimer structure of M1.HpyAVI with some other β-class MTases (M1.MboIIA, M.RsrI and TTHA0409) suggested that the M1.HpyAVI dimer organized in a similar form as others (Figure S3). RESULTS | |
| 103 109 M.RsrI protein In addition, comparison of the dimer structure of M1.HpyAVI with some other β-class MTases (M1.MboIIA, M.RsrI and TTHA0409) suggested that the M1.HpyAVI dimer organized in a similar form as others (Figure S3). RESULTS | |
| 114 122 TTHA0409 protein In addition, comparison of the dimer structure of M1.HpyAVI with some other β-class MTases (M1.MboIIA, M.RsrI and TTHA0409) suggested that the M1.HpyAVI dimer organized in a similar form as others (Figure S3). RESULTS | |
| 143 152 M1.HpyAVI protein In addition, comparison of the dimer structure of M1.HpyAVI with some other β-class MTases (M1.MboIIA, M.RsrI and TTHA0409) suggested that the M1.HpyAVI dimer organized in a similar form as others (Figure S3). RESULTS | |
| 153 158 dimer oligomeric_state In addition, comparison of the dimer structure of M1.HpyAVI with some other β-class MTases (M1.MboIIA, M.RsrI and TTHA0409) suggested that the M1.HpyAVI dimer organized in a similar form as others (Figure S3). RESULTS | |
| 0 9 M1.HpyAVI protein M1.HpyAVI exists as dimer in crystal and solution FIG | |
| 20 25 dimer oligomeric_state M1.HpyAVI exists as dimer in crystal and solution FIG | |
| 29 36 crystal evidence M1.HpyAVI exists as dimer in crystal and solution FIG | |
| 5 14 conserved protein_state A. A conserved interface area of β-class MTases is defined in M1.HpyAVI. FIG | |
| 15 29 interface area site A. A conserved interface area of β-class MTases is defined in M1.HpyAVI. FIG | |
| 33 47 β-class MTases protein_type A. A conserved interface area of β-class MTases is defined in M1.HpyAVI. FIG | |
| 62 71 M1.HpyAVI protein A. A conserved interface area of β-class MTases is defined in M1.HpyAVI. FIG | |
| 48 60 Dimerization oligomeric_state Residues that involved are signed in red color; Dimerization of free-form M1.HpyAVI B. and cofactor-bound M1.HpyAVI C. The two monomers are marked in green and blue, AdoMet molecules are marked in magenta. FIG | |
| 64 68 free protein_state Residues that involved are signed in red color; Dimerization of free-form M1.HpyAVI B. and cofactor-bound M1.HpyAVI C. The two monomers are marked in green and blue, AdoMet molecules are marked in magenta. FIG | |
| 74 83 M1.HpyAVI protein Residues that involved are signed in red color; Dimerization of free-form M1.HpyAVI B. and cofactor-bound M1.HpyAVI C. The two monomers are marked in green and blue, AdoMet molecules are marked in magenta. FIG | |
| 91 105 cofactor-bound protein_state Residues that involved are signed in red color; Dimerization of free-form M1.HpyAVI B. and cofactor-bound M1.HpyAVI C. The two monomers are marked in green and blue, AdoMet molecules are marked in magenta. FIG | |
| 106 115 M1.HpyAVI protein Residues that involved are signed in red color; Dimerization of free-form M1.HpyAVI B. and cofactor-bound M1.HpyAVI C. The two monomers are marked in green and blue, AdoMet molecules are marked in magenta. FIG | |
| 127 135 monomers oligomeric_state Residues that involved are signed in red color; Dimerization of free-form M1.HpyAVI B. and cofactor-bound M1.HpyAVI C. The two monomers are marked in green and blue, AdoMet molecules are marked in magenta. FIG | |
| 166 172 AdoMet chemical Residues that involved are signed in red color; Dimerization of free-form M1.HpyAVI B. and cofactor-bound M1.HpyAVI C. The two monomers are marked in green and blue, AdoMet molecules are marked in magenta. FIG | |
| 3 26 Gel-filtration analysis experimental_method D. Gel-filtration analysis revealed that M1.HpyAVI exist as a dimer in solution. FIG | |
| 41 50 M1.HpyAVI protein D. Gel-filtration analysis revealed that M1.HpyAVI exist as a dimer in solution. FIG | |
| 62 67 dimer oligomeric_state D. Gel-filtration analysis revealed that M1.HpyAVI exist as a dimer in solution. FIG | |
| 0 4 FPLC experimental_method FPLC system coupled to a Superdex 75 10/300 column. FIG | |
| 0 16 Elution profiles evidence Elution profiles at 280 nm (blue) and 260 nm (red) are: different concentration (0.05, 0.1, 0.2, 0.5 mg/ml) of M1.HpyAVI protein. FIG | |
| 111 120 M1.HpyAVI protein Elution profiles at 280 nm (blue) and 260 nm (red) are: different concentration (0.05, 0.1, 0.2, 0.5 mg/ml) of M1.HpyAVI protein. FIG | |
| 32 41 M1.HpyAVI protein To probe the oligomeric form of M1.HpyAVI in solution, different concentrations of purified enzyme was loaded onto a Superdex 75 10/300 column. RESULTS | |
| 94 101 dimeric oligomeric_state The protein was eluted at ~10 ml regardless of the protein concentrations, corresponding to a dimeric molecular mass of 54 kDa (Figure 2D). RESULTS | |
| 102 116 molecular mass evidence The protein was eluted at ~10 ml regardless of the protein concentrations, corresponding to a dimeric molecular mass of 54 kDa (Figure 2D). RESULTS | |
| 32 41 M1.HpyAVI protein Our results clearly showed that M1.HpyAVI forms a dimer in both crystal and solution as other β-class MTases, which however disagrees with a previous investigation using dynamic light scattering (DLS) measurement and gel-filtration chromatography, suggesting that M1.HpyAVI is taking a monomeric state in solution. RESULTS | |
| 50 55 dimer oligomeric_state Our results clearly showed that M1.HpyAVI forms a dimer in both crystal and solution as other β-class MTases, which however disagrees with a previous investigation using dynamic light scattering (DLS) measurement and gel-filtration chromatography, suggesting that M1.HpyAVI is taking a monomeric state in solution. RESULTS | |
| 64 71 crystal evidence Our results clearly showed that M1.HpyAVI forms a dimer in both crystal and solution as other β-class MTases, which however disagrees with a previous investigation using dynamic light scattering (DLS) measurement and gel-filtration chromatography, suggesting that M1.HpyAVI is taking a monomeric state in solution. RESULTS | |
| 94 108 β-class MTases protein_type Our results clearly showed that M1.HpyAVI forms a dimer in both crystal and solution as other β-class MTases, which however disagrees with a previous investigation using dynamic light scattering (DLS) measurement and gel-filtration chromatography, suggesting that M1.HpyAVI is taking a monomeric state in solution. RESULTS | |
| 170 194 dynamic light scattering experimental_method Our results clearly showed that M1.HpyAVI forms a dimer in both crystal and solution as other β-class MTases, which however disagrees with a previous investigation using dynamic light scattering (DLS) measurement and gel-filtration chromatography, suggesting that M1.HpyAVI is taking a monomeric state in solution. RESULTS | |
| 196 199 DLS experimental_method Our results clearly showed that M1.HpyAVI forms a dimer in both crystal and solution as other β-class MTases, which however disagrees with a previous investigation using dynamic light scattering (DLS) measurement and gel-filtration chromatography, suggesting that M1.HpyAVI is taking a monomeric state in solution. RESULTS | |
| 217 246 gel-filtration chromatography experimental_method Our results clearly showed that M1.HpyAVI forms a dimer in both crystal and solution as other β-class MTases, which however disagrees with a previous investigation using dynamic light scattering (DLS) measurement and gel-filtration chromatography, suggesting that M1.HpyAVI is taking a monomeric state in solution. RESULTS | |
| 264 273 M1.HpyAVI protein Our results clearly showed that M1.HpyAVI forms a dimer in both crystal and solution as other β-class MTases, which however disagrees with a previous investigation using dynamic light scattering (DLS) measurement and gel-filtration chromatography, suggesting that M1.HpyAVI is taking a monomeric state in solution. RESULTS | |
| 286 295 monomeric oligomeric_state Our results clearly showed that M1.HpyAVI forms a dimer in both crystal and solution as other β-class MTases, which however disagrees with a previous investigation using dynamic light scattering (DLS) measurement and gel-filtration chromatography, suggesting that M1.HpyAVI is taking a monomeric state in solution. RESULTS | |
| 55 63 arginine chemical This variance might be caused by an addition of 100 mM arginine before cell lysis to keep protein solubility and also by later replacement of arginine with 30% glycerol by dialysis. RESULTS | |
| 142 150 arginine chemical This variance might be caused by an addition of 100 mM arginine before cell lysis to keep protein solubility and also by later replacement of arginine with 30% glycerol by dialysis. RESULTS | |
| 160 168 glycerol chemical This variance might be caused by an addition of 100 mM arginine before cell lysis to keep protein solubility and also by later replacement of arginine with 30% glycerol by dialysis. RESULTS | |
| 0 21 Structure comparisons experimental_method Structure comparisons RESULTS | |
| 5 29 β-class N6 adenine MTase protein_type As a β-class N6 adenine MTase, the M1.HpyAVI structure displayed a good similarity with M.MboIIA (PDB ID 1G60) and M.RsrI (PDB ID 1NW7), which are falling into the same subgroup. RESULTS | |
| 35 44 M1.HpyAVI protein As a β-class N6 adenine MTase, the M1.HpyAVI structure displayed a good similarity with M.MboIIA (PDB ID 1G60) and M.RsrI (PDB ID 1NW7), which are falling into the same subgroup. RESULTS | |
| 45 54 structure evidence As a β-class N6 adenine MTase, the M1.HpyAVI structure displayed a good similarity with M.MboIIA (PDB ID 1G60) and M.RsrI (PDB ID 1NW7), which are falling into the same subgroup. RESULTS | |
| 88 96 M.MboIIA protein As a β-class N6 adenine MTase, the M1.HpyAVI structure displayed a good similarity with M.MboIIA (PDB ID 1G60) and M.RsrI (PDB ID 1NW7), which are falling into the same subgroup. RESULTS | |
| 115 121 M.RsrI protein As a β-class N6 adenine MTase, the M1.HpyAVI structure displayed a good similarity with M.MboIIA (PDB ID 1G60) and M.RsrI (PDB ID 1NW7), which are falling into the same subgroup. RESULTS | |
| 0 15 Superimposition experimental_method Superimposition of M1.HpyAVI onto them gave RMSDs of 1.63 Å and 1.9 Å on 168 and 190 Cα atoms, respectively. RESULTS | |
| 19 28 M1.HpyAVI protein Superimposition of M1.HpyAVI onto them gave RMSDs of 1.63 Å and 1.9 Å on 168 and 190 Cα atoms, respectively. RESULTS | |
| 44 49 RMSDs evidence Superimposition of M1.HpyAVI onto them gave RMSDs of 1.63 Å and 1.9 Å on 168 and 190 Cα atoms, respectively. RESULTS | |
| 67 70 TRD structure_element The most striking structural difference was found to locate on the TRD region (residues 133-163 in M1.HpyAVI) (Figure 3A–3C), where the secondary structures vary among these structures. RESULTS | |
| 88 95 133-163 residue_range The most striking structural difference was found to locate on the TRD region (residues 133-163 in M1.HpyAVI) (Figure 3A–3C), where the secondary structures vary among these structures. RESULTS | |
| 99 108 M1.HpyAVI protein The most striking structural difference was found to locate on the TRD region (residues 133-163 in M1.HpyAVI) (Figure 3A–3C), where the secondary structures vary among these structures. RESULTS | |
| 89 98 α-helices structure_element By comparison with the other two enzymes that possess protruding arms containing several α-helices and/or β-strands, the TRD of M1.HpyAVI is much shorter in length (Figure S1), wrapping more closely around the structural core and lacking apparent secondary structures. RESULTS | |
| 106 115 β-strands structure_element By comparison with the other two enzymes that possess protruding arms containing several α-helices and/or β-strands, the TRD of M1.HpyAVI is much shorter in length (Figure S1), wrapping more closely around the structural core and lacking apparent secondary structures. RESULTS | |
| 121 124 TRD structure_element By comparison with the other two enzymes that possess protruding arms containing several α-helices and/or β-strands, the TRD of M1.HpyAVI is much shorter in length (Figure S1), wrapping more closely around the structural core and lacking apparent secondary structures. RESULTS | |
| 128 137 M1.HpyAVI protein By comparison with the other two enzymes that possess protruding arms containing several α-helices and/or β-strands, the TRD of M1.HpyAVI is much shorter in length (Figure S1), wrapping more closely around the structural core and lacking apparent secondary structures. RESULTS | |
| 230 237 lacking protein_state By comparison with the other two enzymes that possess protruding arms containing several α-helices and/or β-strands, the TRD of M1.HpyAVI is much shorter in length (Figure S1), wrapping more closely around the structural core and lacking apparent secondary structures. RESULTS | |
| 31 34 TRD structure_element Given the proposed role of the TRD for DNA interaction at the major groove, some differences of DNA recognition mode can be expected. RESULTS | |
| 39 42 DNA chemical Given the proposed role of the TRD for DNA interaction at the major groove, some differences of DNA recognition mode can be expected. RESULTS | |
| 62 74 major groove structure_element Given the proposed role of the TRD for DNA interaction at the major groove, some differences of DNA recognition mode can be expected. RESULTS | |
| 96 99 DNA chemical Given the proposed role of the TRD for DNA interaction at the major groove, some differences of DNA recognition mode can be expected. RESULTS | |
| 34 49 highly flexible protein_state Another difference locates at the highly flexible loop between β4 and αD (residues 33-58) of M1.HpyAVI, which was invisible in our structures but present in the structures of M.MboIIA and M.RsrI. Sequence alignment revealed that this region of M1.HpyAVI was longer than its counterparts by 13 and 16 amino acids respectively, which likely renders the H. pylori enzyme more flexible. RESULTS | |
| 50 54 loop structure_element Another difference locates at the highly flexible loop between β4 and αD (residues 33-58) of M1.HpyAVI, which was invisible in our structures but present in the structures of M.MboIIA and M.RsrI. Sequence alignment revealed that this region of M1.HpyAVI was longer than its counterparts by 13 and 16 amino acids respectively, which likely renders the H. pylori enzyme more flexible. RESULTS | |
| 63 65 β4 structure_element Another difference locates at the highly flexible loop between β4 and αD (residues 33-58) of M1.HpyAVI, which was invisible in our structures but present in the structures of M.MboIIA and M.RsrI. Sequence alignment revealed that this region of M1.HpyAVI was longer than its counterparts by 13 and 16 amino acids respectively, which likely renders the H. pylori enzyme more flexible. RESULTS | |
| 70 72 αD structure_element Another difference locates at the highly flexible loop between β4 and αD (residues 33-58) of M1.HpyAVI, which was invisible in our structures but present in the structures of M.MboIIA and M.RsrI. Sequence alignment revealed that this region of M1.HpyAVI was longer than its counterparts by 13 and 16 amino acids respectively, which likely renders the H. pylori enzyme more flexible. RESULTS | |
| 83 88 33-58 residue_range Another difference locates at the highly flexible loop between β4 and αD (residues 33-58) of M1.HpyAVI, which was invisible in our structures but present in the structures of M.MboIIA and M.RsrI. Sequence alignment revealed that this region of M1.HpyAVI was longer than its counterparts by 13 and 16 amino acids respectively, which likely renders the H. pylori enzyme more flexible. RESULTS | |
| 93 102 M1.HpyAVI protein Another difference locates at the highly flexible loop between β4 and αD (residues 33-58) of M1.HpyAVI, which was invisible in our structures but present in the structures of M.MboIIA and M.RsrI. Sequence alignment revealed that this region of M1.HpyAVI was longer than its counterparts by 13 and 16 amino acids respectively, which likely renders the H. pylori enzyme more flexible. RESULTS | |
| 131 141 structures evidence Another difference locates at the highly flexible loop between β4 and αD (residues 33-58) of M1.HpyAVI, which was invisible in our structures but present in the structures of M.MboIIA and M.RsrI. Sequence alignment revealed that this region of M1.HpyAVI was longer than its counterparts by 13 and 16 amino acids respectively, which likely renders the H. pylori enzyme more flexible. RESULTS | |
| 161 171 structures evidence Another difference locates at the highly flexible loop between β4 and αD (residues 33-58) of M1.HpyAVI, which was invisible in our structures but present in the structures of M.MboIIA and M.RsrI. Sequence alignment revealed that this region of M1.HpyAVI was longer than its counterparts by 13 and 16 amino acids respectively, which likely renders the H. pylori enzyme more flexible. RESULTS | |
| 175 183 M.MboIIA protein Another difference locates at the highly flexible loop between β4 and αD (residues 33-58) of M1.HpyAVI, which was invisible in our structures but present in the structures of M.MboIIA and M.RsrI. Sequence alignment revealed that this region of M1.HpyAVI was longer than its counterparts by 13 and 16 amino acids respectively, which likely renders the H. pylori enzyme more flexible. RESULTS | |
| 188 194 M.RsrI protein Another difference locates at the highly flexible loop between β4 and αD (residues 33-58) of M1.HpyAVI, which was invisible in our structures but present in the structures of M.MboIIA and M.RsrI. Sequence alignment revealed that this region of M1.HpyAVI was longer than its counterparts by 13 and 16 amino acids respectively, which likely renders the H. pylori enzyme more flexible. RESULTS | |
| 196 214 Sequence alignment experimental_method Another difference locates at the highly flexible loop between β4 and αD (residues 33-58) of M1.HpyAVI, which was invisible in our structures but present in the structures of M.MboIIA and M.RsrI. Sequence alignment revealed that this region of M1.HpyAVI was longer than its counterparts by 13 and 16 amino acids respectively, which likely renders the H. pylori enzyme more flexible. RESULTS | |
| 244 253 M1.HpyAVI protein Another difference locates at the highly flexible loop between β4 and αD (residues 33-58) of M1.HpyAVI, which was invisible in our structures but present in the structures of M.MboIIA and M.RsrI. Sequence alignment revealed that this region of M1.HpyAVI was longer than its counterparts by 13 and 16 amino acids respectively, which likely renders the H. pylori enzyme more flexible. RESULTS | |
| 351 360 H. pylori species Another difference locates at the highly flexible loop between β4 and αD (residues 33-58) of M1.HpyAVI, which was invisible in our structures but present in the structures of M.MboIIA and M.RsrI. Sequence alignment revealed that this region of M1.HpyAVI was longer than its counterparts by 13 and 16 amino acids respectively, which likely renders the H. pylori enzyme more flexible. RESULTS | |
| 373 381 flexible protein_state Another difference locates at the highly flexible loop between β4 and αD (residues 33-58) of M1.HpyAVI, which was invisible in our structures but present in the structures of M.MboIIA and M.RsrI. Sequence alignment revealed that this region of M1.HpyAVI was longer than its counterparts by 13 and 16 amino acids respectively, which likely renders the H. pylori enzyme more flexible. RESULTS | |
| 0 22 Structural comparisons experimental_method Structural comparisons between M1.HpyAVI and other DNA MTases FIG | |
| 31 40 M1.HpyAVI protein Structural comparisons between M1.HpyAVI and other DNA MTases FIG | |
| 51 61 DNA MTases protein_type Structural comparisons between M1.HpyAVI and other DNA MTases FIG | |
| 3 12 M1.HpyAVI protein A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 17 25 M.MboIIA protein A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 30 36 M.RsrI protein A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 41 49 TTHA0409 protein A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 54 58 DpnM protein A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 63 69 M.TaqI protein A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 71 80 M1.HpyAVI protein A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 98 111 long disorder protein_state A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 112 115 TRD structure_element A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 142 156 structure-rich protein_state A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 157 160 TRD structure_element A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 164 172 M.MboIIA protein A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 174 180 M.RsrI protein A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 185 193 TTHA0409 protein A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 208 226 DNA-binding domain structure_element A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 230 234 DpnM protein A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 239 245 M.TaqI protein A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 278 281 TRD structure_element A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 285 294 M1.HpyAVI protein A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 296 304 M.MboIIA protein A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 306 312 M.RsrI protein A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 317 325 TTHA0409 protein A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 356 358 β4 structure_element A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 363 365 αD structure_element A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 369 377 M.MboIIA protein A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 382 388 M.RsrI protein A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 402 420 DNA-binding domain structure_element A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 424 428 DpnM protein A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 448 465 C-terminal domain structure_element A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 469 475 M.TaqI protein A. M1.HpyAVI; B. M.MboIIA; C. M.RsrI; D. TTHA0409; E. DpnM; F. M.TaqI. M1.HpyAVI possesses only a long disorder TRD region, compared with the structure-rich TRD of M.MboIIA, M.RsrI and TTHA0409, or the extra DNA-binding domain of DpnM and M.TaqI. The core structure is in cyan; TRD of M1.HpyAVI, M.MboIIA, M.RsrI and TTHA0409 is in red; The region between β4 and αD of M.MboIIA and M.RsrI is in green; DNA-binding domain of DpnM is in magenta; The C-terminal domain of M.TaqI is in orange. FIG | |
| 0 21 Structural comparison experimental_method Structural comparison between M1.HpyAVI and a putative β-class N4 cytosine MTase named TTHA0409 (PDB ID 2ZIF) showed a good similarity as well, giving an RMSD of 1.73 Å on 164 Cα atoms (Figure 3D). RESULTS | |
| 30 39 M1.HpyAVI protein Structural comparison between M1.HpyAVI and a putative β-class N4 cytosine MTase named TTHA0409 (PDB ID 2ZIF) showed a good similarity as well, giving an RMSD of 1.73 Å on 164 Cα atoms (Figure 3D). RESULTS | |
| 55 80 β-class N4 cytosine MTase protein_type Structural comparison between M1.HpyAVI and a putative β-class N4 cytosine MTase named TTHA0409 (PDB ID 2ZIF) showed a good similarity as well, giving an RMSD of 1.73 Å on 164 Cα atoms (Figure 3D). RESULTS | |
| 87 95 TTHA0409 protein Structural comparison between M1.HpyAVI and a putative β-class N4 cytosine MTase named TTHA0409 (PDB ID 2ZIF) showed a good similarity as well, giving an RMSD of 1.73 Å on 164 Cα atoms (Figure 3D). RESULTS | |
| 154 158 RMSD evidence Structural comparison between M1.HpyAVI and a putative β-class N4 cytosine MTase named TTHA0409 (PDB ID 2ZIF) showed a good similarity as well, giving an RMSD of 1.73 Å on 164 Cα atoms (Figure 3D). RESULTS | |
| 81 84 TRD structure_element Exactly like the above comparison, the most significant difference exists in the TRD, where the structures vary in terms of length and presence of α-helices (Figure S1). RESULTS | |
| 96 106 structures evidence Exactly like the above comparison, the most significant difference exists in the TRD, where the structures vary in terms of length and presence of α-helices (Figure S1). RESULTS | |
| 147 156 α-helices structure_element Exactly like the above comparison, the most significant difference exists in the TRD, where the structures vary in terms of length and presence of α-helices (Figure S1). RESULTS | |
| 0 9 M1.HpyAVI protein M1.HpyAVI displayed a considerable structural dissimilarity in comparison with N6-adenine MTases from other subgroups including the α-class DpnM (PDB ID 2DPM) and the γ-class M.TaqI (PDB ID 2ADM). RESULTS | |
| 79 96 N6-adenine MTases protein_type M1.HpyAVI displayed a considerable structural dissimilarity in comparison with N6-adenine MTases from other subgroups including the α-class DpnM (PDB ID 2DPM) and the γ-class M.TaqI (PDB ID 2ADM). RESULTS | |
| 132 139 α-class protein_type M1.HpyAVI displayed a considerable structural dissimilarity in comparison with N6-adenine MTases from other subgroups including the α-class DpnM (PDB ID 2DPM) and the γ-class M.TaqI (PDB ID 2ADM). RESULTS | |
| 140 144 DpnM protein M1.HpyAVI displayed a considerable structural dissimilarity in comparison with N6-adenine MTases from other subgroups including the α-class DpnM (PDB ID 2DPM) and the γ-class M.TaqI (PDB ID 2ADM). RESULTS | |
| 167 174 γ-class protein_type M1.HpyAVI displayed a considerable structural dissimilarity in comparison with N6-adenine MTases from other subgroups including the α-class DpnM (PDB ID 2DPM) and the γ-class M.TaqI (PDB ID 2ADM). RESULTS | |
| 175 181 M.TaqI protein M1.HpyAVI displayed a considerable structural dissimilarity in comparison with N6-adenine MTases from other subgroups including the α-class DpnM (PDB ID 2DPM) and the γ-class M.TaqI (PDB ID 2ADM). RESULTS | |
| 22 27 RMSDs evidence Both comparisons gave RMSDs above 3.0 Å (Figure 3E and 3F). RESULTS | |
| 18 22 lack protein_state These two enzymes lack a counterpart loop present in the TRD of M1.HpyAVI, but instead rely on an extra domain for DNA binding and sequence recognition. RESULTS | |
| 25 41 counterpart loop structure_element These two enzymes lack a counterpart loop present in the TRD of M1.HpyAVI, but instead rely on an extra domain for DNA binding and sequence recognition. RESULTS | |
| 57 60 TRD structure_element These two enzymes lack a counterpart loop present in the TRD of M1.HpyAVI, but instead rely on an extra domain for DNA binding and sequence recognition. RESULTS | |
| 64 73 M1.HpyAVI protein These two enzymes lack a counterpart loop present in the TRD of M1.HpyAVI, but instead rely on an extra domain for DNA binding and sequence recognition. RESULTS | |
| 115 118 DNA chemical These two enzymes lack a counterpart loop present in the TRD of M1.HpyAVI, but instead rely on an extra domain for DNA binding and sequence recognition. RESULTS | |
| 14 23 M1.HpyAVI protein Collectively, M1.HpyAVI possesses a long disordered TRD, which is in sharp contrast to the secondary structure-rich TRD in other β-class N6 adenine or N4 cytosine MTases or the extra DNA binding domain present in DNA MTases from other subgroups. RESULTS | |
| 36 51 long disordered protein_state Collectively, M1.HpyAVI possesses a long disordered TRD, which is in sharp contrast to the secondary structure-rich TRD in other β-class N6 adenine or N4 cytosine MTases or the extra DNA binding domain present in DNA MTases from other subgroups. RESULTS | |
| 52 55 TRD structure_element Collectively, M1.HpyAVI possesses a long disordered TRD, which is in sharp contrast to the secondary structure-rich TRD in other β-class N6 adenine or N4 cytosine MTases or the extra DNA binding domain present in DNA MTases from other subgroups. RESULTS | |
| 91 115 secondary structure-rich protein_state Collectively, M1.HpyAVI possesses a long disordered TRD, which is in sharp contrast to the secondary structure-rich TRD in other β-class N6 adenine or N4 cytosine MTases or the extra DNA binding domain present in DNA MTases from other subgroups. RESULTS | |
| 116 119 TRD structure_element Collectively, M1.HpyAVI possesses a long disordered TRD, which is in sharp contrast to the secondary structure-rich TRD in other β-class N6 adenine or N4 cytosine MTases or the extra DNA binding domain present in DNA MTases from other subgroups. RESULTS | |
| 129 169 β-class N6 adenine or N4 cytosine MTases protein_type Collectively, M1.HpyAVI possesses a long disordered TRD, which is in sharp contrast to the secondary structure-rich TRD in other β-class N6 adenine or N4 cytosine MTases or the extra DNA binding domain present in DNA MTases from other subgroups. RESULTS | |
| 213 223 DNA MTases protein_type Collectively, M1.HpyAVI possesses a long disordered TRD, which is in sharp contrast to the secondary structure-rich TRD in other β-class N6 adenine or N4 cytosine MTases or the extra DNA binding domain present in DNA MTases from other subgroups. RESULTS | |
| 98 107 H. pylori species This striking difference may be a significant determinant of the wider substrate spectrum of this H. pylori enzyme. RESULTS | |
| 0 21 AdoMet-binding pocket site AdoMet-binding pocket RESULTS | |
| 4 27 cofactor binding pocket site The cofactor binding pocket of M1.HpyAVI is surrounded by residues 7-9, 29-31, 165-167, 216-218 and 221 (Figure 4A), which are conserved among most of DNA MTases. RESULTS | |
| 31 40 M1.HpyAVI protein The cofactor binding pocket of M1.HpyAVI is surrounded by residues 7-9, 29-31, 165-167, 216-218 and 221 (Figure 4A), which are conserved among most of DNA MTases. RESULTS | |
| 67 70 7-9 residue_range The cofactor binding pocket of M1.HpyAVI is surrounded by residues 7-9, 29-31, 165-167, 216-218 and 221 (Figure 4A), which are conserved among most of DNA MTases. RESULTS | |
| 72 77 29-31 residue_range The cofactor binding pocket of M1.HpyAVI is surrounded by residues 7-9, 29-31, 165-167, 216-218 and 221 (Figure 4A), which are conserved among most of DNA MTases. RESULTS | |
| 79 86 165-167 residue_range The cofactor binding pocket of M1.HpyAVI is surrounded by residues 7-9, 29-31, 165-167, 216-218 and 221 (Figure 4A), which are conserved among most of DNA MTases. RESULTS | |
| 88 95 216-218 residue_range The cofactor binding pocket of M1.HpyAVI is surrounded by residues 7-9, 29-31, 165-167, 216-218 and 221 (Figure 4A), which are conserved among most of DNA MTases. RESULTS | |
| 100 103 221 residue_number The cofactor binding pocket of M1.HpyAVI is surrounded by residues 7-9, 29-31, 165-167, 216-218 and 221 (Figure 4A), which are conserved among most of DNA MTases. RESULTS | |
| 127 136 conserved protein_state The cofactor binding pocket of M1.HpyAVI is surrounded by residues 7-9, 29-31, 165-167, 216-218 and 221 (Figure 4A), which are conserved among most of DNA MTases. RESULTS | |
| 151 161 DNA MTases protein_type The cofactor binding pocket of M1.HpyAVI is surrounded by residues 7-9, 29-31, 165-167, 216-218 and 221 (Figure 4A), which are conserved among most of DNA MTases. RESULTS | |
| 2 15 hydrogen bond bond_interaction A hydrogen bond between D29 in the catalytic motif DPPY and the amino group of bound AdoMet is preserved as other MTase structures. RESULTS | |
| 24 27 D29 residue_name_number A hydrogen bond between D29 in the catalytic motif DPPY and the amino group of bound AdoMet is preserved as other MTase structures. RESULTS | |
| 35 50 catalytic motif structure_element A hydrogen bond between D29 in the catalytic motif DPPY and the amino group of bound AdoMet is preserved as other MTase structures. RESULTS | |
| 51 55 DPPY structure_element A hydrogen bond between D29 in the catalytic motif DPPY and the amino group of bound AdoMet is preserved as other MTase structures. RESULTS | |
| 79 84 bound protein_state A hydrogen bond between D29 in the catalytic motif DPPY and the amino group of bound AdoMet is preserved as other MTase structures. RESULTS | |
| 85 91 AdoMet chemical A hydrogen bond between D29 in the catalytic motif DPPY and the amino group of bound AdoMet is preserved as other MTase structures. RESULTS | |
| 114 119 MTase protein_type A hydrogen bond between D29 in the catalytic motif DPPY and the amino group of bound AdoMet is preserved as other MTase structures. RESULTS | |
| 120 130 structures evidence A hydrogen bond between D29 in the catalytic motif DPPY and the amino group of bound AdoMet is preserved as other MTase structures. RESULTS | |
| 9 11 D8 residue_name_number Residues D8 and A9 from hydrogen-bonds with N6 and N1 of the purine ring, respectively, and E216 also locates at hydrogen bonding distance with O2′ and O3′ of the ribose. RESULTS | |
| 16 18 A9 residue_name_number Residues D8 and A9 from hydrogen-bonds with N6 and N1 of the purine ring, respectively, and E216 also locates at hydrogen bonding distance with O2′ and O3′ of the ribose. RESULTS | |
| 24 38 hydrogen-bonds bond_interaction Residues D8 and A9 from hydrogen-bonds with N6 and N1 of the purine ring, respectively, and E216 also locates at hydrogen bonding distance with O2′ and O3′ of the ribose. RESULTS | |
| 61 67 purine chemical Residues D8 and A9 from hydrogen-bonds with N6 and N1 of the purine ring, respectively, and E216 also locates at hydrogen bonding distance with O2′ and O3′ of the ribose. RESULTS | |
| 92 96 E216 residue_name_number Residues D8 and A9 from hydrogen-bonds with N6 and N1 of the purine ring, respectively, and E216 also locates at hydrogen bonding distance with O2′ and O3′ of the ribose. RESULTS | |
| 113 129 hydrogen bonding bond_interaction Residues D8 and A9 from hydrogen-bonds with N6 and N1 of the purine ring, respectively, and E216 also locates at hydrogen bonding distance with O2′ and O3′ of the ribose. RESULTS | |
| 163 169 ribose chemical Residues D8 and A9 from hydrogen-bonds with N6 and N1 of the purine ring, respectively, and E216 also locates at hydrogen bonding distance with O2′ and O3′ of the ribose. RESULTS | |
| 13 17 H168 residue_name_number In addition, H168, T200 and S198 contact the terminal carboxyl of AdoMet. RESULTS | |
| 19 23 T200 residue_name_number In addition, H168, T200 and S198 contact the terminal carboxyl of AdoMet. RESULTS | |
| 28 32 S198 residue_name_number In addition, H168, T200 and S198 contact the terminal carboxyl of AdoMet. RESULTS | |
| 66 72 AdoMet chemical In addition, H168, T200 and S198 contact the terminal carboxyl of AdoMet. RESULTS | |
| 0 13 Superposition experimental_method Superposition of M1.HpyAVI with the five structures shown in Figure 3 reveals that the orientation of cofactor is rather conserved except for M.TaqI (Figure 4B). RESULTS | |
| 17 26 M1.HpyAVI protein Superposition of M1.HpyAVI with the five structures shown in Figure 3 reveals that the orientation of cofactor is rather conserved except for M.TaqI (Figure 4B). RESULTS | |
| 41 51 structures evidence Superposition of M1.HpyAVI with the five structures shown in Figure 3 reveals that the orientation of cofactor is rather conserved except for M.TaqI (Figure 4B). RESULTS | |
| 114 130 rather conserved protein_state Superposition of M1.HpyAVI with the five structures shown in Figure 3 reveals that the orientation of cofactor is rather conserved except for M.TaqI (Figure 4B). RESULTS | |
| 142 148 M.TaqI protein Superposition of M1.HpyAVI with the five structures shown in Figure 3 reveals that the orientation of cofactor is rather conserved except for M.TaqI (Figure 4B). RESULTS | |
| 34 39 bound protein_state The different conformation of the bound cofactor observed in M.TaqI might be attributable to the absence of corresponding residues of the conserved AdoMet-binding motif FXGXG in that structure. RESULTS | |
| 61 67 M.TaqI protein The different conformation of the bound cofactor observed in M.TaqI might be attributable to the absence of corresponding residues of the conserved AdoMet-binding motif FXGXG in that structure. RESULTS | |
| 97 107 absence of protein_state The different conformation of the bound cofactor observed in M.TaqI might be attributable to the absence of corresponding residues of the conserved AdoMet-binding motif FXGXG in that structure. RESULTS | |
| 138 147 conserved protein_state The different conformation of the bound cofactor observed in M.TaqI might be attributable to the absence of corresponding residues of the conserved AdoMet-binding motif FXGXG in that structure. RESULTS | |
| 148 154 AdoMet chemical The different conformation of the bound cofactor observed in M.TaqI might be attributable to the absence of corresponding residues of the conserved AdoMet-binding motif FXGXG in that structure. RESULTS | |
| 169 174 FXGXG structure_element The different conformation of the bound cofactor observed in M.TaqI might be attributable to the absence of corresponding residues of the conserved AdoMet-binding motif FXGXG in that structure. RESULTS | |
| 183 192 structure evidence The different conformation of the bound cofactor observed in M.TaqI might be attributable to the absence of corresponding residues of the conserved AdoMet-binding motif FXGXG in that structure. RESULTS | |
| 0 35 Structural and biochemical analyses experimental_method Structural and biochemical analyses define two conserved residues D29 and E216 to be the key sites for AdoMet binding FIG | |
| 47 56 conserved protein_state Structural and biochemical analyses define two conserved residues D29 and E216 to be the key sites for AdoMet binding FIG | |
| 66 69 D29 residue_name_number Structural and biochemical analyses define two conserved residues D29 and E216 to be the key sites for AdoMet binding FIG | |
| 74 78 E216 residue_name_number Structural and biochemical analyses define two conserved residues D29 and E216 to be the key sites for AdoMet binding FIG | |
| 103 109 AdoMet chemical Structural and biochemical analyses define two conserved residues D29 and E216 to be the key sites for AdoMet binding FIG | |
| 7 30 cofactor-binding cavity site A. The cofactor-binding cavity of M1.HpyAVI. FIG | |
| 34 43 M1.HpyAVI protein A. The cofactor-binding cavity of M1.HpyAVI. FIG | |
| 35 49 hydrogen bonds bond_interaction Residues (yellow) that form direct hydrogen bonds with AdoMet (green) are indicated, distance of the hydrogen bond is marked. FIG | |
| 55 61 AdoMet chemical Residues (yellow) that form direct hydrogen bonds with AdoMet (green) are indicated, distance of the hydrogen bond is marked. FIG | |
| 101 114 hydrogen bond bond_interaction Residues (yellow) that form direct hydrogen bonds with AdoMet (green) are indicated, distance of the hydrogen bond is marked. FIG | |
| 3 16 Superposition experimental_method B. Superposition of AdoMet in the structures of M1.HpyAVI (green), DpnM (yellow) and M.TaqI (orange). FIG | |
| 20 26 AdoMet chemical B. Superposition of AdoMet in the structures of M1.HpyAVI (green), DpnM (yellow) and M.TaqI (orange). FIG | |
| 34 44 structures evidence B. Superposition of AdoMet in the structures of M1.HpyAVI (green), DpnM (yellow) and M.TaqI (orange). FIG | |
| 48 57 M1.HpyAVI protein B. Superposition of AdoMet in the structures of M1.HpyAVI (green), DpnM (yellow) and M.TaqI (orange). FIG | |
| 67 71 DpnM protein B. Superposition of AdoMet in the structures of M1.HpyAVI (green), DpnM (yellow) and M.TaqI (orange). FIG | |
| 85 91 M.TaqI protein B. Superposition of AdoMet in the structures of M1.HpyAVI (green), DpnM (yellow) and M.TaqI (orange). FIG | |
| 4 10 AdoMet chemical The AdoMet terminal carboxyl of M.TaqI reveals different orientations. FIG | |
| 32 38 M.TaqI protein The AdoMet terminal carboxyl of M.TaqI reveals different orientations. FIG | |
| 3 28 Cofactor binding affinity evidence C. Cofactor binding affinity of wt-/mutants M1.HpyAVI proteins analyzed by microscale thermophoresis (MST). FIG | |
| 32 34 wt protein_state C. Cofactor binding affinity of wt-/mutants M1.HpyAVI proteins analyzed by microscale thermophoresis (MST). FIG | |
| 36 43 mutants protein_state C. Cofactor binding affinity of wt-/mutants M1.HpyAVI proteins analyzed by microscale thermophoresis (MST). FIG | |
| 44 53 M1.HpyAVI protein C. Cofactor binding affinity of wt-/mutants M1.HpyAVI proteins analyzed by microscale thermophoresis (MST). FIG | |
| 75 100 microscale thermophoresis experimental_method C. Cofactor binding affinity of wt-/mutants M1.HpyAVI proteins analyzed by microscale thermophoresis (MST). FIG | |
| 102 105 MST experimental_method C. Cofactor binding affinity of wt-/mutants M1.HpyAVI proteins analyzed by microscale thermophoresis (MST). FIG | |
| 4 20 binding affinity evidence The binding affinity was determined between fluorescently labelled M1.HpyAVI protein and unlabeled AdoMet. FIG | |
| 67 76 M1.HpyAVI protein The binding affinity was determined between fluorescently labelled M1.HpyAVI protein and unlabeled AdoMet. FIG | |
| 89 98 unlabeled protein_state The binding affinity was determined between fluorescently labelled M1.HpyAVI protein and unlabeled AdoMet. FIG | |
| 99 105 AdoMet chemical The binding affinity was determined between fluorescently labelled M1.HpyAVI protein and unlabeled AdoMet. FIG | |
| 0 6 AdoMet chemical AdoMet (15 nM to 1 mM) was titrated into a fixed concentration of M1.HpyAVI wt/mutant proteins (800 nM). FIG | |
| 27 35 titrated experimental_method AdoMet (15 nM to 1 mM) was titrated into a fixed concentration of M1.HpyAVI wt/mutant proteins (800 nM). FIG | |
| 66 75 M1.HpyAVI protein AdoMet (15 nM to 1 mM) was titrated into a fixed concentration of M1.HpyAVI wt/mutant proteins (800 nM). FIG | |
| 76 78 wt protein_state AdoMet (15 nM to 1 mM) was titrated into a fixed concentration of M1.HpyAVI wt/mutant proteins (800 nM). FIG | |
| 79 85 mutant protein_state AdoMet (15 nM to 1 mM) was titrated into a fixed concentration of M1.HpyAVI wt/mutant proteins (800 nM). FIG | |
| 4 25 dissociation constant evidence The dissociation constant (KD) is yielded according to the law of mass action from the isotherm derived of the raw data: M1.HpyAVI-wt: 41 ± 6 μM; M1.HpyAVI-D8A :212 ± 11 μM; M1.HpyAVI-D29A : 0 μM; M1.HpyAVI-H168A : 471 ± 51 μM; M1.HpyAVI-S198A : 242 ± 32 μM; M1.HpyAVI-T200A : 252 ± 28 μM; M1.HpyAVI-E216A : 0 μM. Standard for three replicates is indicated. FIG | |
| 27 29 KD evidence The dissociation constant (KD) is yielded according to the law of mass action from the isotherm derived of the raw data: M1.HpyAVI-wt: 41 ± 6 μM; M1.HpyAVI-D8A :212 ± 11 μM; M1.HpyAVI-D29A : 0 μM; M1.HpyAVI-H168A : 471 ± 51 μM; M1.HpyAVI-S198A : 242 ± 32 μM; M1.HpyAVI-T200A : 252 ± 28 μM; M1.HpyAVI-E216A : 0 μM. Standard for three replicates is indicated. FIG | |
| 87 95 isotherm evidence The dissociation constant (KD) is yielded according to the law of mass action from the isotherm derived of the raw data: M1.HpyAVI-wt: 41 ± 6 μM; M1.HpyAVI-D8A :212 ± 11 μM; M1.HpyAVI-D29A : 0 μM; M1.HpyAVI-H168A : 471 ± 51 μM; M1.HpyAVI-S198A : 242 ± 32 μM; M1.HpyAVI-T200A : 252 ± 28 μM; M1.HpyAVI-E216A : 0 μM. Standard for three replicates is indicated. FIG | |
| 121 130 M1.HpyAVI protein The dissociation constant (KD) is yielded according to the law of mass action from the isotherm derived of the raw data: M1.HpyAVI-wt: 41 ± 6 μM; M1.HpyAVI-D8A :212 ± 11 μM; M1.HpyAVI-D29A : 0 μM; M1.HpyAVI-H168A : 471 ± 51 μM; M1.HpyAVI-S198A : 242 ± 32 μM; M1.HpyAVI-T200A : 252 ± 28 μM; M1.HpyAVI-E216A : 0 μM. Standard for three replicates is indicated. FIG | |
| 131 133 wt protein_state The dissociation constant (KD) is yielded according to the law of mass action from the isotherm derived of the raw data: M1.HpyAVI-wt: 41 ± 6 μM; M1.HpyAVI-D8A :212 ± 11 μM; M1.HpyAVI-D29A : 0 μM; M1.HpyAVI-H168A : 471 ± 51 μM; M1.HpyAVI-S198A : 242 ± 32 μM; M1.HpyAVI-T200A : 252 ± 28 μM; M1.HpyAVI-E216A : 0 μM. Standard for three replicates is indicated. FIG | |
| 146 159 M1.HpyAVI-D8A mutant The dissociation constant (KD) is yielded according to the law of mass action from the isotherm derived of the raw data: M1.HpyAVI-wt: 41 ± 6 μM; M1.HpyAVI-D8A :212 ± 11 μM; M1.HpyAVI-D29A : 0 μM; M1.HpyAVI-H168A : 471 ± 51 μM; M1.HpyAVI-S198A : 242 ± 32 μM; M1.HpyAVI-T200A : 252 ± 28 μM; M1.HpyAVI-E216A : 0 μM. Standard for three replicates is indicated. FIG | |
| 174 188 M1.HpyAVI-D29A mutant The dissociation constant (KD) is yielded according to the law of mass action from the isotherm derived of the raw data: M1.HpyAVI-wt: 41 ± 6 μM; M1.HpyAVI-D8A :212 ± 11 μM; M1.HpyAVI-D29A : 0 μM; M1.HpyAVI-H168A : 471 ± 51 μM; M1.HpyAVI-S198A : 242 ± 32 μM; M1.HpyAVI-T200A : 252 ± 28 μM; M1.HpyAVI-E216A : 0 μM. Standard for three replicates is indicated. FIG | |
| 197 212 M1.HpyAVI-H168A mutant The dissociation constant (KD) is yielded according to the law of mass action from the isotherm derived of the raw data: M1.HpyAVI-wt: 41 ± 6 μM; M1.HpyAVI-D8A :212 ± 11 μM; M1.HpyAVI-D29A : 0 μM; M1.HpyAVI-H168A : 471 ± 51 μM; M1.HpyAVI-S198A : 242 ± 32 μM; M1.HpyAVI-T200A : 252 ± 28 μM; M1.HpyAVI-E216A : 0 μM. Standard for three replicates is indicated. FIG | |
| 228 243 M1.HpyAVI-S198A mutant The dissociation constant (KD) is yielded according to the law of mass action from the isotherm derived of the raw data: M1.HpyAVI-wt: 41 ± 6 μM; M1.HpyAVI-D8A :212 ± 11 μM; M1.HpyAVI-D29A : 0 μM; M1.HpyAVI-H168A : 471 ± 51 μM; M1.HpyAVI-S198A : 242 ± 32 μM; M1.HpyAVI-T200A : 252 ± 28 μM; M1.HpyAVI-E216A : 0 μM. Standard for three replicates is indicated. FIG | |
| 259 274 M1.HpyAVI-T200A mutant The dissociation constant (KD) is yielded according to the law of mass action from the isotherm derived of the raw data: M1.HpyAVI-wt: 41 ± 6 μM; M1.HpyAVI-D8A :212 ± 11 μM; M1.HpyAVI-D29A : 0 μM; M1.HpyAVI-H168A : 471 ± 51 μM; M1.HpyAVI-S198A : 242 ± 32 μM; M1.HpyAVI-T200A : 252 ± 28 μM; M1.HpyAVI-E216A : 0 μM. Standard for three replicates is indicated. FIG | |
| 290 305 M1.HpyAVI-E216A mutant The dissociation constant (KD) is yielded according to the law of mass action from the isotherm derived of the raw data: M1.HpyAVI-wt: 41 ± 6 μM; M1.HpyAVI-D8A :212 ± 11 μM; M1.HpyAVI-D29A : 0 μM; M1.HpyAVI-H168A : 471 ± 51 μM; M1.HpyAVI-S198A : 242 ± 32 μM; M1.HpyAVI-T200A : 252 ± 28 μM; M1.HpyAVI-E216A : 0 μM. Standard for three replicates is indicated. FIG | |
| 3 24 DNA methyltransferase protein_type D. DNA methyltransferase activity of wide type protein and the mutants is quantified using radioactive assay. FIG | |
| 37 46 wide type protein_state D. DNA methyltransferase activity of wide type protein and the mutants is quantified using radioactive assay. FIG | |
| 63 70 mutants protein_state D. DNA methyltransferase activity of wide type protein and the mutants is quantified using radioactive assay. FIG | |
| 91 108 radioactive assay experimental_method D. DNA methyltransferase activity of wide type protein and the mutants is quantified using radioactive assay. FIG | |
| 0 11 [3H]-methyl chemical [3H]-methyl transferred to duplex DNA containing 5′-GAGG-3′ was quantified by Beckman LS6500 for 10 min, experiments were repeated for three times and data were corrected by subtraction of the background. FIG | |
| 34 37 DNA chemical [3H]-methyl transferred to duplex DNA containing 5′-GAGG-3′ was quantified by Beckman LS6500 for 10 min, experiments were repeated for three times and data were corrected by subtraction of the background. FIG | |
| 49 59 5′-GAGG-3′ chemical [3H]-methyl transferred to duplex DNA containing 5′-GAGG-3′ was quantified by Beckman LS6500 for 10 min, experiments were repeated for three times and data were corrected by subtraction of the background. FIG | |
| 3 16 Superposition experimental_method E. Superposition of M1.HpyAVI (green) with M.MboIIA (cyan) and M.RsrI (magenta). FIG | |
| 20 29 M1.HpyAVI protein E. Superposition of M1.HpyAVI (green) with M.MboIIA (cyan) and M.RsrI (magenta). FIG | |
| 43 51 M.MboIIA protein E. Superposition of M1.HpyAVI (green) with M.MboIIA (cyan) and M.RsrI (magenta). FIG | |
| 63 69 M.RsrI protein E. Superposition of M1.HpyAVI (green) with M.MboIIA (cyan) and M.RsrI (magenta). FIG | |
| 9 12 D29 residue_name_number Residues D29 and E216 are conserved through all the DNA MTases mentioned in Figure 3 (not shown in Figure 4). FIG | |
| 17 21 E216 residue_name_number Residues D29 and E216 are conserved through all the DNA MTases mentioned in Figure 3 (not shown in Figure 4). FIG | |
| 26 35 conserved protein_state Residues D29 and E216 are conserved through all the DNA MTases mentioned in Figure 3 (not shown in Figure 4). FIG | |
| 52 62 DNA MTases protein_type Residues D29 and E216 are conserved through all the DNA MTases mentioned in Figure 3 (not shown in Figure 4). FIG | |
| 72 86 single mutants experimental_method To confirm the key residues for ligand binding, we prepared a series of single mutants by replacing D8, D29, H168, S198, T200, E216 with alanine and investigated their ligand binding affinity using microscale thermophoresis (MST) assay. RESULTS | |
| 90 99 replacing experimental_method To confirm the key residues for ligand binding, we prepared a series of single mutants by replacing D8, D29, H168, S198, T200, E216 with alanine and investigated their ligand binding affinity using microscale thermophoresis (MST) assay. RESULTS | |
| 100 102 D8 residue_name_number To confirm the key residues for ligand binding, we prepared a series of single mutants by replacing D8, D29, H168, S198, T200, E216 with alanine and investigated their ligand binding affinity using microscale thermophoresis (MST) assay. RESULTS | |
| 104 107 D29 residue_name_number To confirm the key residues for ligand binding, we prepared a series of single mutants by replacing D8, D29, H168, S198, T200, E216 with alanine and investigated their ligand binding affinity using microscale thermophoresis (MST) assay. RESULTS | |
| 109 113 H168 residue_name_number To confirm the key residues for ligand binding, we prepared a series of single mutants by replacing D8, D29, H168, S198, T200, E216 with alanine and investigated their ligand binding affinity using microscale thermophoresis (MST) assay. RESULTS | |
| 115 119 S198 residue_name_number To confirm the key residues for ligand binding, we prepared a series of single mutants by replacing D8, D29, H168, S198, T200, E216 with alanine and investigated their ligand binding affinity using microscale thermophoresis (MST) assay. RESULTS | |
| 121 125 T200 residue_name_number To confirm the key residues for ligand binding, we prepared a series of single mutants by replacing D8, D29, H168, S198, T200, E216 with alanine and investigated their ligand binding affinity using microscale thermophoresis (MST) assay. RESULTS | |
| 127 131 E216 residue_name_number To confirm the key residues for ligand binding, we prepared a series of single mutants by replacing D8, D29, H168, S198, T200, E216 with alanine and investigated their ligand binding affinity using microscale thermophoresis (MST) assay. RESULTS | |
| 137 144 alanine residue_name To confirm the key residues for ligand binding, we prepared a series of single mutants by replacing D8, D29, H168, S198, T200, E216 with alanine and investigated their ligand binding affinity using microscale thermophoresis (MST) assay. RESULTS | |
| 168 191 ligand binding affinity evidence To confirm the key residues for ligand binding, we prepared a series of single mutants by replacing D8, D29, H168, S198, T200, E216 with alanine and investigated their ligand binding affinity using microscale thermophoresis (MST) assay. RESULTS | |
| 198 223 microscale thermophoresis experimental_method To confirm the key residues for ligand binding, we prepared a series of single mutants by replacing D8, D29, H168, S198, T200, E216 with alanine and investigated their ligand binding affinity using microscale thermophoresis (MST) assay. RESULTS | |
| 225 228 MST experimental_method To confirm the key residues for ligand binding, we prepared a series of single mutants by replacing D8, D29, H168, S198, T200, E216 with alanine and investigated their ligand binding affinity using microscale thermophoresis (MST) assay. RESULTS | |
| 42 51 wild type protein_state As shown in Figure 4C, by contrast to the wild type enzyme, most mutants displayed variable reduction of KD value, among them the D29A and E216A mutants displayed no protein-AdoMet affinity at all. RESULTS | |
| 65 72 mutants protein_state As shown in Figure 4C, by contrast to the wild type enzyme, most mutants displayed variable reduction of KD value, among them the D29A and E216A mutants displayed no protein-AdoMet affinity at all. RESULTS | |
| 105 107 KD evidence As shown in Figure 4C, by contrast to the wild type enzyme, most mutants displayed variable reduction of KD value, among them the D29A and E216A mutants displayed no protein-AdoMet affinity at all. RESULTS | |
| 130 134 D29A mutant As shown in Figure 4C, by contrast to the wild type enzyme, most mutants displayed variable reduction of KD value, among them the D29A and E216A mutants displayed no protein-AdoMet affinity at all. RESULTS | |
| 139 144 E216A mutant As shown in Figure 4C, by contrast to the wild type enzyme, most mutants displayed variable reduction of KD value, among them the D29A and E216A mutants displayed no protein-AdoMet affinity at all. RESULTS | |
| 145 152 mutants protein_state As shown in Figure 4C, by contrast to the wild type enzyme, most mutants displayed variable reduction of KD value, among them the D29A and E216A mutants displayed no protein-AdoMet affinity at all. RESULTS | |
| 166 189 protein-AdoMet affinity evidence As shown in Figure 4C, by contrast to the wild type enzyme, most mutants displayed variable reduction of KD value, among them the D29A and E216A mutants displayed no protein-AdoMet affinity at all. RESULTS | |
| 31 45 hydrogen bonds bond_interaction The results suggested that the hydrogen bonds formed by D29 and E216 with AdoMet were most crucial interactions for cofactor binding. RESULTS | |
| 56 59 D29 residue_name_number The results suggested that the hydrogen bonds formed by D29 and E216 with AdoMet were most crucial interactions for cofactor binding. RESULTS | |
| 64 68 E216 residue_name_number The results suggested that the hydrogen bonds formed by D29 and E216 with AdoMet were most crucial interactions for cofactor binding. RESULTS | |
| 74 80 AdoMet chemical The results suggested that the hydrogen bonds formed by D29 and E216 with AdoMet were most crucial interactions for cofactor binding. RESULTS | |
| 0 8 Mutation experimental_method Mutation of the two residues may directly prevent the methyl transfer reaction of M1.HpyAVI. RESULTS | |
| 54 60 methyl chemical Mutation of the two residues may directly prevent the methyl transfer reaction of M1.HpyAVI. RESULTS | |
| 82 91 M1.HpyAVI protein Mutation of the two residues may directly prevent the methyl transfer reaction of M1.HpyAVI. RESULTS | |
| 18 21 D29 residue_name_number The importance of D29 is preserved because it belongs to the catalytic active site DPPY, but the residue E216 has not been fully investigated even being a conserved amino acid throughout MTases (Figure 4E). RESULTS | |
| 61 82 catalytic active site site The importance of D29 is preserved because it belongs to the catalytic active site DPPY, but the residue E216 has not been fully investigated even being a conserved amino acid throughout MTases (Figure 4E). RESULTS | |
| 83 87 DPPY structure_element The importance of D29 is preserved because it belongs to the catalytic active site DPPY, but the residue E216 has not been fully investigated even being a conserved amino acid throughout MTases (Figure 4E). RESULTS | |
| 105 109 E216 residue_name_number The importance of D29 is preserved because it belongs to the catalytic active site DPPY, but the residue E216 has not been fully investigated even being a conserved amino acid throughout MTases (Figure 4E). RESULTS | |
| 155 164 conserved protein_state The importance of D29 is preserved because it belongs to the catalytic active site DPPY, but the residue E216 has not been fully investigated even being a conserved amino acid throughout MTases (Figure 4E). RESULTS | |
| 165 175 amino acid chemical The importance of D29 is preserved because it belongs to the catalytic active site DPPY, but the residue E216 has not been fully investigated even being a conserved amino acid throughout MTases (Figure 4E). RESULTS | |
| 187 193 MTases protein_type The importance of D29 is preserved because it belongs to the catalytic active site DPPY, but the residue E216 has not been fully investigated even being a conserved amino acid throughout MTases (Figure 4E). RESULTS | |
| 0 4 E216 residue_name_number E216 is the last residue of β2, which contacts the two hydroxyls of the ribose of AdoMet. RESULTS | |
| 28 30 β2 structure_element E216 is the last residue of β2, which contacts the two hydroxyls of the ribose of AdoMet. RESULTS | |
| 72 78 ribose chemical E216 is the last residue of β2, which contacts the two hydroxyls of the ribose of AdoMet. RESULTS | |
| 82 88 AdoMet chemical E216 is the last residue of β2, which contacts the two hydroxyls of the ribose of AdoMet. RESULTS | |
| 0 11 Replacement experimental_method Replacement of this residue by alanine completely abolishes the key hydrogen bonds for AdoMet-binding, and very likely blocks the methyl transfer reaction. RESULTS | |
| 31 38 alanine residue_name Replacement of this residue by alanine completely abolishes the key hydrogen bonds for AdoMet-binding, and very likely blocks the methyl transfer reaction. RESULTS | |
| 68 82 hydrogen bonds bond_interaction Replacement of this residue by alanine completely abolishes the key hydrogen bonds for AdoMet-binding, and very likely blocks the methyl transfer reaction. RESULTS | |
| 87 93 AdoMet chemical Replacement of this residue by alanine completely abolishes the key hydrogen bonds for AdoMet-binding, and very likely blocks the methyl transfer reaction. RESULTS | |
| 130 136 methyl chemical Replacement of this residue by alanine completely abolishes the key hydrogen bonds for AdoMet-binding, and very likely blocks the methyl transfer reaction. RESULTS | |
| 24 53 [3H]AdoMet radiological assay experimental_method To confirm this notion, [3H]AdoMet radiological assay was applied to quantify the methyl transfer activity of the mutants. RESULTS | |
| 82 88 methyl chemical To confirm this notion, [3H]AdoMet radiological assay was applied to quantify the methyl transfer activity of the mutants. RESULTS | |
| 114 121 mutants protein_state To confirm this notion, [3H]AdoMet radiological assay was applied to quantify the methyl transfer activity of the mutants. RESULTS | |
| 37 55 radiological assay experimental_method As shown in Figure 4D, the result of radiological assay agreed well with the MST measurement. RESULTS | |
| 77 80 MST experimental_method As shown in Figure 4D, the result of radiological assay agreed well with the MST measurement. RESULTS | |
| 4 8 D29A mutant The D29A and E216A mutants showed little or no methyl transfer activity, while other mutants exhibited reduced methyltransferase activity. RESULTS | |
| 13 18 E216A mutant The D29A and E216A mutants showed little or no methyl transfer activity, while other mutants exhibited reduced methyltransferase activity. RESULTS | |
| 19 26 mutants protein_state The D29A and E216A mutants showed little or no methyl transfer activity, while other mutants exhibited reduced methyltransferase activity. RESULTS | |
| 47 53 methyl chemical The D29A and E216A mutants showed little or no methyl transfer activity, while other mutants exhibited reduced methyltransferase activity. RESULTS | |
| 85 92 mutants protein_state The D29A and E216A mutants showed little or no methyl transfer activity, while other mutants exhibited reduced methyltransferase activity. RESULTS | |
| 111 128 methyltransferase protein_type The D29A and E216A mutants showed little or no methyl transfer activity, while other mutants exhibited reduced methyltransferase activity. RESULTS | |
| 25 30 FXGXG structure_element As mentioned previously, FXGXG is a conserved AdoMet-binding motif of DNA MTases. RESULTS | |
| 36 45 conserved protein_state As mentioned previously, FXGXG is a conserved AdoMet-binding motif of DNA MTases. RESULTS | |
| 46 52 AdoMet chemical As mentioned previously, FXGXG is a conserved AdoMet-binding motif of DNA MTases. RESULTS | |
| 70 80 DNA MTases protein_type As mentioned previously, FXGXG is a conserved AdoMet-binding motif of DNA MTases. RESULTS | |
| 13 20 mutants protein_state We also made mutants of “FMGSG” to alanine for every amino acid, and found that the F195A mutant was insoluble probably due to decreasing the local hydrophobicity upon this mutation. RESULTS | |
| 25 30 FMGSG structure_element We also made mutants of “FMGSG” to alanine for every amino acid, and found that the F195A mutant was insoluble probably due to decreasing the local hydrophobicity upon this mutation. RESULTS | |
| 35 42 alanine residue_name We also made mutants of “FMGSG” to alanine for every amino acid, and found that the F195A mutant was insoluble probably due to decreasing the local hydrophobicity upon this mutation. RESULTS | |
| 53 63 amino acid chemical We also made mutants of “FMGSG” to alanine for every amino acid, and found that the F195A mutant was insoluble probably due to decreasing the local hydrophobicity upon this mutation. RESULTS | |
| 84 89 F195A mutant We also made mutants of “FMGSG” to alanine for every amino acid, and found that the F195A mutant was insoluble probably due to decreasing the local hydrophobicity upon this mutation. RESULTS | |
| 90 96 mutant protein_state We also made mutants of “FMGSG” to alanine for every amino acid, and found that the F195A mutant was insoluble probably due to decreasing the local hydrophobicity upon this mutation. RESULTS | |
| 33 56 ligand binding affinity evidence We subsequently investigated the ligand binding affinity and methyl transfer reaction of the other mutants using MST and a radiological assay. RESULTS | |
| 61 67 methyl chemical We subsequently investigated the ligand binding affinity and methyl transfer reaction of the other mutants using MST and a radiological assay. RESULTS | |
| 99 106 mutants protein_state We subsequently investigated the ligand binding affinity and methyl transfer reaction of the other mutants using MST and a radiological assay. RESULTS | |
| 113 116 MST experimental_method We subsequently investigated the ligand binding affinity and methyl transfer reaction of the other mutants using MST and a radiological assay. RESULTS | |
| 123 141 radiological assay experimental_method We subsequently investigated the ligand binding affinity and methyl transfer reaction of the other mutants using MST and a radiological assay. RESULTS | |
| 14 18 G197 residue_name_number We found that G197 played a crucial role in AdoMet-binding, while mutagenesis of M196 and G199 did not influence cofactor binding and catalytic activity (Figure S2A and B). RESULTS | |
| 44 50 AdoMet chemical We found that G197 played a crucial role in AdoMet-binding, while mutagenesis of M196 and G199 did not influence cofactor binding and catalytic activity (Figure S2A and B). RESULTS | |
| 66 77 mutagenesis experimental_method We found that G197 played a crucial role in AdoMet-binding, while mutagenesis of M196 and G199 did not influence cofactor binding and catalytic activity (Figure S2A and B). RESULTS | |
| 81 85 M196 residue_name_number We found that G197 played a crucial role in AdoMet-binding, while mutagenesis of M196 and G199 did not influence cofactor binding and catalytic activity (Figure S2A and B). RESULTS | |
| 90 94 G199 residue_name_number We found that G197 played a crucial role in AdoMet-binding, while mutagenesis of M196 and G199 did not influence cofactor binding and catalytic activity (Figure S2A and B). RESULTS | |
| 0 4 G197 residue_name_number G197 is a conserved residue throughout the DNA MTases, and replacing by alanine at this site likely change the local conformation of cofactor-binding pocket. RESULTS | |
| 10 19 conserved protein_state G197 is a conserved residue throughout the DNA MTases, and replacing by alanine at this site likely change the local conformation of cofactor-binding pocket. RESULTS | |
| 43 53 DNA MTases protein_type G197 is a conserved residue throughout the DNA MTases, and replacing by alanine at this site likely change the local conformation of cofactor-binding pocket. RESULTS | |
| 59 68 replacing experimental_method G197 is a conserved residue throughout the DNA MTases, and replacing by alanine at this site likely change the local conformation of cofactor-binding pocket. RESULTS | |
| 72 79 alanine residue_name G197 is a conserved residue throughout the DNA MTases, and replacing by alanine at this site likely change the local conformation of cofactor-binding pocket. RESULTS | |
| 133 156 cofactor-binding pocket site G197 is a conserved residue throughout the DNA MTases, and replacing by alanine at this site likely change the local conformation of cofactor-binding pocket. RESULTS | |
| 0 11 Mutagenesis experimental_method Mutagenesis on this glycine residue in M.EcoKI or M.EcoP15I also abolished the AdoMet-binding activity. RESULTS | |
| 20 27 glycine residue_name Mutagenesis on this glycine residue in M.EcoKI or M.EcoP15I also abolished the AdoMet-binding activity. RESULTS | |
| 39 46 M.EcoKI protein Mutagenesis on this glycine residue in M.EcoKI or M.EcoP15I also abolished the AdoMet-binding activity. RESULTS | |
| 50 59 M.EcoP15I protein Mutagenesis on this glycine residue in M.EcoKI or M.EcoP15I also abolished the AdoMet-binding activity. RESULTS | |
| 79 85 AdoMet chemical Mutagenesis on this glycine residue in M.EcoKI or M.EcoP15I also abolished the AdoMet-binding activity. RESULTS | |
| 9 25 mutational study experimental_method Although mutational study could not tell the role of F195 in ligand binding due to the insolubility of the F195A mutant, structural analysis suggested the importance of this residue in AdoMet-binding. RESULTS | |
| 53 57 F195 residue_name_number Although mutational study could not tell the role of F195 in ligand binding due to the insolubility of the F195A mutant, structural analysis suggested the importance of this residue in AdoMet-binding. RESULTS | |
| 107 112 F195A mutant Although mutational study could not tell the role of F195 in ligand binding due to the insolubility of the F195A mutant, structural analysis suggested the importance of this residue in AdoMet-binding. RESULTS | |
| 113 119 mutant protein_state Although mutational study could not tell the role of F195 in ligand binding due to the insolubility of the F195A mutant, structural analysis suggested the importance of this residue in AdoMet-binding. RESULTS | |
| 121 140 structural analysis experimental_method Although mutational study could not tell the role of F195 in ligand binding due to the insolubility of the F195A mutant, structural analysis suggested the importance of this residue in AdoMet-binding. RESULTS | |
| 185 191 AdoMet chemical Although mutational study could not tell the role of F195 in ligand binding due to the insolubility of the F195A mutant, structural analysis suggested the importance of this residue in AdoMet-binding. RESULTS | |
| 19 23 F195 residue_name_number The phenyl ring of F195 forms a perpendicular π-stacking interaction with the purine ring of AdoMet, which stabilizes the orientation of AdoMet bound in the pocket of M1.HpyAVI (Figure S2C). RESULTS | |
| 46 68 π-stacking interaction bond_interaction The phenyl ring of F195 forms a perpendicular π-stacking interaction with the purine ring of AdoMet, which stabilizes the orientation of AdoMet bound in the pocket of M1.HpyAVI (Figure S2C). RESULTS | |
| 93 99 AdoMet chemical The phenyl ring of F195 forms a perpendicular π-stacking interaction with the purine ring of AdoMet, which stabilizes the orientation of AdoMet bound in the pocket of M1.HpyAVI (Figure S2C). RESULTS | |
| 137 143 AdoMet chemical The phenyl ring of F195 forms a perpendicular π-stacking interaction with the purine ring of AdoMet, which stabilizes the orientation of AdoMet bound in the pocket of M1.HpyAVI (Figure S2C). RESULTS | |
| 144 152 bound in protein_state The phenyl ring of F195 forms a perpendicular π-stacking interaction with the purine ring of AdoMet, which stabilizes the orientation of AdoMet bound in the pocket of M1.HpyAVI (Figure S2C). RESULTS | |
| 157 163 pocket site The phenyl ring of F195 forms a perpendicular π-stacking interaction with the purine ring of AdoMet, which stabilizes the orientation of AdoMet bound in the pocket of M1.HpyAVI (Figure S2C). RESULTS | |
| 167 176 M1.HpyAVI protein The phenyl ring of F195 forms a perpendicular π-stacking interaction with the purine ring of AdoMet, which stabilizes the orientation of AdoMet bound in the pocket of M1.HpyAVI (Figure S2C). RESULTS | |
| 24 35 mutagenesis experimental_method In a separate scenario, mutagenesis of this residue in M.EcoRV has been proven to play an important role in AdoMet binding. RESULTS | |
| 55 62 M.EcoRV protein In a separate scenario, mutagenesis of this residue in M.EcoRV has been proven to play an important role in AdoMet binding. RESULTS | |
| 108 114 AdoMet chemical In a separate scenario, mutagenesis of this residue in M.EcoRV has been proven to play an important role in AdoMet binding. RESULTS | |
| 10 27 DNA-binding sites site Potential DNA-binding sites RESULTS | |
| 13 31 DNA binding region site The putative DNA binding region of M1.HpyAVI involves the hairpin loop (residue 101-133), the TRD (residues 136-166), and a highly flexible loop (residues 33-58). RESULTS | |
| 35 44 M1.HpyAVI protein The putative DNA binding region of M1.HpyAVI involves the hairpin loop (residue 101-133), the TRD (residues 136-166), and a highly flexible loop (residues 33-58). RESULTS | |
| 58 70 hairpin loop structure_element The putative DNA binding region of M1.HpyAVI involves the hairpin loop (residue 101-133), the TRD (residues 136-166), and a highly flexible loop (residues 33-58). RESULTS | |
| 80 87 101-133 residue_range The putative DNA binding region of M1.HpyAVI involves the hairpin loop (residue 101-133), the TRD (residues 136-166), and a highly flexible loop (residues 33-58). RESULTS | |
| 94 97 TRD structure_element The putative DNA binding region of M1.HpyAVI involves the hairpin loop (residue 101-133), the TRD (residues 136-166), and a highly flexible loop (residues 33-58). RESULTS | |
| 108 115 136-166 residue_range The putative DNA binding region of M1.HpyAVI involves the hairpin loop (residue 101-133), the TRD (residues 136-166), and a highly flexible loop (residues 33-58). RESULTS | |
| 124 139 highly flexible protein_state The putative DNA binding region of M1.HpyAVI involves the hairpin loop (residue 101-133), the TRD (residues 136-166), and a highly flexible loop (residues 33-58). RESULTS | |
| 140 144 loop structure_element The putative DNA binding region of M1.HpyAVI involves the hairpin loop (residue 101-133), the TRD (residues 136-166), and a highly flexible loop (residues 33-58). RESULTS | |
| 155 160 33-58 residue_range The putative DNA binding region of M1.HpyAVI involves the hairpin loop (residue 101-133), the TRD (residues 136-166), and a highly flexible loop (residues 33-58). RESULTS | |
| 4 16 hairpin loop structure_element The hairpin loop between β6 and β7 strands that carries a conserved HRRY sequence signature in the middle is proposed to insert into the minor groove of the bound DNA. RESULTS | |
| 25 27 β6 structure_element The hairpin loop between β6 and β7 strands that carries a conserved HRRY sequence signature in the middle is proposed to insert into the minor groove of the bound DNA. RESULTS | |
| 32 34 β7 structure_element The hairpin loop between β6 and β7 strands that carries a conserved HRRY sequence signature in the middle is proposed to insert into the minor groove of the bound DNA. RESULTS | |
| 58 67 conserved protein_state The hairpin loop between β6 and β7 strands that carries a conserved HRRY sequence signature in the middle is proposed to insert into the minor groove of the bound DNA. RESULTS | |
| 68 72 HRRY structure_element The hairpin loop between β6 and β7 strands that carries a conserved HRRY sequence signature in the middle is proposed to insert into the minor groove of the bound DNA. RESULTS | |
| 137 149 minor groove structure_element The hairpin loop between β6 and β7 strands that carries a conserved HRRY sequence signature in the middle is proposed to insert into the minor groove of the bound DNA. RESULTS | |
| 157 162 bound protein_state The hairpin loop between β6 and β7 strands that carries a conserved HRRY sequence signature in the middle is proposed to insert into the minor groove of the bound DNA. RESULTS | |
| 163 166 DNA chemical The hairpin loop between β6 and β7 strands that carries a conserved HRRY sequence signature in the middle is proposed to insert into the minor groove of the bound DNA. RESULTS | |
| 23 26 TRD structure_element As aforementioned, the TRD of M1.HpyAVI shows striking difference from the other DNA MTases, and the relaxed specificity of substrate recognition may be at least partially attributable to the disordered TRD. RESULTS | |
| 30 39 M1.HpyAVI protein As aforementioned, the TRD of M1.HpyAVI shows striking difference from the other DNA MTases, and the relaxed specificity of substrate recognition may be at least partially attributable to the disordered TRD. RESULTS | |
| 81 91 DNA MTases protein_type As aforementioned, the TRD of M1.HpyAVI shows striking difference from the other DNA MTases, and the relaxed specificity of substrate recognition may be at least partially attributable to the disordered TRD. RESULTS | |
| 192 202 disordered protein_state As aforementioned, the TRD of M1.HpyAVI shows striking difference from the other DNA MTases, and the relaxed specificity of substrate recognition may be at least partially attributable to the disordered TRD. RESULTS | |
| 203 206 TRD structure_element As aforementioned, the TRD of M1.HpyAVI shows striking difference from the other DNA MTases, and the relaxed specificity of substrate recognition may be at least partially attributable to the disordered TRD. RESULTS | |
| 17 32 highly flexible protein_state In addition, the highly flexible loop immediately following the DPPY motif in M1.HpyAVI was poorly defined in electron density, exactly like the corresponding loops in the AdoMet-bound structures of M.PvuII, DpnM or M.TaqI that were invisible either. RESULTS | |
| 33 37 loop structure_element In addition, the highly flexible loop immediately following the DPPY motif in M1.HpyAVI was poorly defined in electron density, exactly like the corresponding loops in the AdoMet-bound structures of M.PvuII, DpnM or M.TaqI that were invisible either. RESULTS | |
| 64 68 DPPY structure_element In addition, the highly flexible loop immediately following the DPPY motif in M1.HpyAVI was poorly defined in electron density, exactly like the corresponding loops in the AdoMet-bound structures of M.PvuII, DpnM or M.TaqI that were invisible either. RESULTS | |
| 78 87 M1.HpyAVI protein In addition, the highly flexible loop immediately following the DPPY motif in M1.HpyAVI was poorly defined in electron density, exactly like the corresponding loops in the AdoMet-bound structures of M.PvuII, DpnM or M.TaqI that were invisible either. RESULTS | |
| 110 126 electron density evidence In addition, the highly flexible loop immediately following the DPPY motif in M1.HpyAVI was poorly defined in electron density, exactly like the corresponding loops in the AdoMet-bound structures of M.PvuII, DpnM or M.TaqI that were invisible either. RESULTS | |
| 159 164 loops structure_element In addition, the highly flexible loop immediately following the DPPY motif in M1.HpyAVI was poorly defined in electron density, exactly like the corresponding loops in the AdoMet-bound structures of M.PvuII, DpnM or M.TaqI that were invisible either. RESULTS | |
| 172 184 AdoMet-bound protein_state In addition, the highly flexible loop immediately following the DPPY motif in M1.HpyAVI was poorly defined in electron density, exactly like the corresponding loops in the AdoMet-bound structures of M.PvuII, DpnM or M.TaqI that were invisible either. RESULTS | |
| 185 195 structures evidence In addition, the highly flexible loop immediately following the DPPY motif in M1.HpyAVI was poorly defined in electron density, exactly like the corresponding loops in the AdoMet-bound structures of M.PvuII, DpnM or M.TaqI that were invisible either. RESULTS | |
| 199 206 M.PvuII protein In addition, the highly flexible loop immediately following the DPPY motif in M1.HpyAVI was poorly defined in electron density, exactly like the corresponding loops in the AdoMet-bound structures of M.PvuII, DpnM or M.TaqI that were invisible either. RESULTS | |
| 208 212 DpnM protein In addition, the highly flexible loop immediately following the DPPY motif in M1.HpyAVI was poorly defined in electron density, exactly like the corresponding loops in the AdoMet-bound structures of M.PvuII, DpnM or M.TaqI that were invisible either. RESULTS | |
| 216 222 M.TaqI protein In addition, the highly flexible loop immediately following the DPPY motif in M1.HpyAVI was poorly defined in electron density, exactly like the corresponding loops in the AdoMet-bound structures of M.PvuII, DpnM or M.TaqI that were invisible either. RESULTS | |
| 5 9 loop structure_element This loop, however, was largely stabilized upon DNA binding, as observed in the protein-DNA complex structures of M.TaqI (PDB ID 2IBS), M.HhaI (PDB ID 1MHT) and M.HaeIII (PDB ID 1DCT). RESULTS | |
| 48 51 DNA chemical This loop, however, was largely stabilized upon DNA binding, as observed in the protein-DNA complex structures of M.TaqI (PDB ID 2IBS), M.HhaI (PDB ID 1MHT) and M.HaeIII (PDB ID 1DCT). RESULTS | |
| 80 110 protein-DNA complex structures evidence This loop, however, was largely stabilized upon DNA binding, as observed in the protein-DNA complex structures of M.TaqI (PDB ID 2IBS), M.HhaI (PDB ID 1MHT) and M.HaeIII (PDB ID 1DCT). RESULTS | |
| 114 120 M.TaqI protein This loop, however, was largely stabilized upon DNA binding, as observed in the protein-DNA complex structures of M.TaqI (PDB ID 2IBS), M.HhaI (PDB ID 1MHT) and M.HaeIII (PDB ID 1DCT). RESULTS | |
| 136 142 M.HhaI protein This loop, however, was largely stabilized upon DNA binding, as observed in the protein-DNA complex structures of M.TaqI (PDB ID 2IBS), M.HhaI (PDB ID 1MHT) and M.HaeIII (PDB ID 1DCT). RESULTS | |
| 161 169 M.HaeIII protein This loop, however, was largely stabilized upon DNA binding, as observed in the protein-DNA complex structures of M.TaqI (PDB ID 2IBS), M.HhaI (PDB ID 1MHT) and M.HaeIII (PDB ID 1DCT). RESULTS | |
| 4 16 well-ordered protein_state The well-ordered loop in those structures directly contacts the flipping adenine and forms hydrogen bond with neighboring bases. RESULTS | |
| 17 21 loop structure_element The well-ordered loop in those structures directly contacts the flipping adenine and forms hydrogen bond with neighboring bases. RESULTS | |
| 31 41 structures evidence The well-ordered loop in those structures directly contacts the flipping adenine and forms hydrogen bond with neighboring bases. RESULTS | |
| 73 80 adenine residue_name The well-ordered loop in those structures directly contacts the flipping adenine and forms hydrogen bond with neighboring bases. RESULTS | |
| 91 104 hydrogen bond bond_interaction The well-ordered loop in those structures directly contacts the flipping adenine and forms hydrogen bond with neighboring bases. RESULTS | |
| 50 54 loop structure_element These observations implied that the corresponding loop in other MTases, e.g. M1.HpyAVI, is likely responsible for reducing sequence recognition specificity and thus plays crucial roles in catalysis. RESULTS | |
| 64 70 MTases protein_type These observations implied that the corresponding loop in other MTases, e.g. M1.HpyAVI, is likely responsible for reducing sequence recognition specificity and thus plays crucial roles in catalysis. RESULTS | |
| 77 86 M1.HpyAVI protein These observations implied that the corresponding loop in other MTases, e.g. M1.HpyAVI, is likely responsible for reducing sequence recognition specificity and thus plays crucial roles in catalysis. RESULTS | |
| 33 42 M1.HpyAVI protein Previous research suggested that M1.HpyAVI from strain 26695 was the first N6 adenine MTase that can methylate the adenine of 5′-GAGG-3′/5′-GGAG-3′ or both two adenines of 5′-GAAG-3′, compared with the homologs from other strains that can methylate only one adenine of 5′-GAGG-3′. To answer why M1.HpyAVI displayed a wider specificity for DNA recognition, we randomly choose fifty of M1.HpyAVI sequences from hundreds of H. pylori strains for multiple sequence alignment. RESULTS | |
| 75 91 N6 adenine MTase protein_type Previous research suggested that M1.HpyAVI from strain 26695 was the first N6 adenine MTase that can methylate the adenine of 5′-GAGG-3′/5′-GGAG-3′ or both two adenines of 5′-GAAG-3′, compared with the homologs from other strains that can methylate only one adenine of 5′-GAGG-3′. To answer why M1.HpyAVI displayed a wider specificity for DNA recognition, we randomly choose fifty of M1.HpyAVI sequences from hundreds of H. pylori strains for multiple sequence alignment. RESULTS | |
| 115 122 adenine residue_name Previous research suggested that M1.HpyAVI from strain 26695 was the first N6 adenine MTase that can methylate the adenine of 5′-GAGG-3′/5′-GGAG-3′ or both two adenines of 5′-GAAG-3′, compared with the homologs from other strains that can methylate only one adenine of 5′-GAGG-3′. To answer why M1.HpyAVI displayed a wider specificity for DNA recognition, we randomly choose fifty of M1.HpyAVI sequences from hundreds of H. pylori strains for multiple sequence alignment. RESULTS | |
| 126 136 5′-GAGG-3′ chemical Previous research suggested that M1.HpyAVI from strain 26695 was the first N6 adenine MTase that can methylate the adenine of 5′-GAGG-3′/5′-GGAG-3′ or both two adenines of 5′-GAAG-3′, compared with the homologs from other strains that can methylate only one adenine of 5′-GAGG-3′. To answer why M1.HpyAVI displayed a wider specificity for DNA recognition, we randomly choose fifty of M1.HpyAVI sequences from hundreds of H. pylori strains for multiple sequence alignment. RESULTS | |
| 137 147 5′-GGAG-3′ chemical Previous research suggested that M1.HpyAVI from strain 26695 was the first N6 adenine MTase that can methylate the adenine of 5′-GAGG-3′/5′-GGAG-3′ or both two adenines of 5′-GAAG-3′, compared with the homologs from other strains that can methylate only one adenine of 5′-GAGG-3′. To answer why M1.HpyAVI displayed a wider specificity for DNA recognition, we randomly choose fifty of M1.HpyAVI sequences from hundreds of H. pylori strains for multiple sequence alignment. RESULTS | |
| 160 168 adenines residue_name Previous research suggested that M1.HpyAVI from strain 26695 was the first N6 adenine MTase that can methylate the adenine of 5′-GAGG-3′/5′-GGAG-3′ or both two adenines of 5′-GAAG-3′, compared with the homologs from other strains that can methylate only one adenine of 5′-GAGG-3′. To answer why M1.HpyAVI displayed a wider specificity for DNA recognition, we randomly choose fifty of M1.HpyAVI sequences from hundreds of H. pylori strains for multiple sequence alignment. RESULTS | |
| 172 182 5′-GAAG-3′ chemical Previous research suggested that M1.HpyAVI from strain 26695 was the first N6 adenine MTase that can methylate the adenine of 5′-GAGG-3′/5′-GGAG-3′ or both two adenines of 5′-GAAG-3′, compared with the homologs from other strains that can methylate only one adenine of 5′-GAGG-3′. To answer why M1.HpyAVI displayed a wider specificity for DNA recognition, we randomly choose fifty of M1.HpyAVI sequences from hundreds of H. pylori strains for multiple sequence alignment. RESULTS | |
| 258 265 adenine residue_name Previous research suggested that M1.HpyAVI from strain 26695 was the first N6 adenine MTase that can methylate the adenine of 5′-GAGG-3′/5′-GGAG-3′ or both two adenines of 5′-GAAG-3′, compared with the homologs from other strains that can methylate only one adenine of 5′-GAGG-3′. To answer why M1.HpyAVI displayed a wider specificity for DNA recognition, we randomly choose fifty of M1.HpyAVI sequences from hundreds of H. pylori strains for multiple sequence alignment. RESULTS | |
| 269 279 5′-GAGG-3′ chemical Previous research suggested that M1.HpyAVI from strain 26695 was the first N6 adenine MTase that can methylate the adenine of 5′-GAGG-3′/5′-GGAG-3′ or both two adenines of 5′-GAAG-3′, compared with the homologs from other strains that can methylate only one adenine of 5′-GAGG-3′. To answer why M1.HpyAVI displayed a wider specificity for DNA recognition, we randomly choose fifty of M1.HpyAVI sequences from hundreds of H. pylori strains for multiple sequence alignment. RESULTS | |
| 295 304 M1.HpyAVI protein Previous research suggested that M1.HpyAVI from strain 26695 was the first N6 adenine MTase that can methylate the adenine of 5′-GAGG-3′/5′-GGAG-3′ or both two adenines of 5′-GAAG-3′, compared with the homologs from other strains that can methylate only one adenine of 5′-GAGG-3′. To answer why M1.HpyAVI displayed a wider specificity for DNA recognition, we randomly choose fifty of M1.HpyAVI sequences from hundreds of H. pylori strains for multiple sequence alignment. RESULTS | |
| 339 342 DNA chemical Previous research suggested that M1.HpyAVI from strain 26695 was the first N6 adenine MTase that can methylate the adenine of 5′-GAGG-3′/5′-GGAG-3′ or both two adenines of 5′-GAAG-3′, compared with the homologs from other strains that can methylate only one adenine of 5′-GAGG-3′. To answer why M1.HpyAVI displayed a wider specificity for DNA recognition, we randomly choose fifty of M1.HpyAVI sequences from hundreds of H. pylori strains for multiple sequence alignment. RESULTS | |
| 384 393 M1.HpyAVI protein Previous research suggested that M1.HpyAVI from strain 26695 was the first N6 adenine MTase that can methylate the adenine of 5′-GAGG-3′/5′-GGAG-3′ or both two adenines of 5′-GAAG-3′, compared with the homologs from other strains that can methylate only one adenine of 5′-GAGG-3′. To answer why M1.HpyAVI displayed a wider specificity for DNA recognition, we randomly choose fifty of M1.HpyAVI sequences from hundreds of H. pylori strains for multiple sequence alignment. RESULTS | |
| 421 430 H. pylori species Previous research suggested that M1.HpyAVI from strain 26695 was the first N6 adenine MTase that can methylate the adenine of 5′-GAGG-3′/5′-GGAG-3′ or both two adenines of 5′-GAAG-3′, compared with the homologs from other strains that can methylate only one adenine of 5′-GAGG-3′. To answer why M1.HpyAVI displayed a wider specificity for DNA recognition, we randomly choose fifty of M1.HpyAVI sequences from hundreds of H. pylori strains for multiple sequence alignment. RESULTS | |
| 443 470 multiple sequence alignment experimental_method Previous research suggested that M1.HpyAVI from strain 26695 was the first N6 adenine MTase that can methylate the adenine of 5′-GAGG-3′/5′-GGAG-3′ or both two adenines of 5′-GAAG-3′, compared with the homologs from other strains that can methylate only one adenine of 5′-GAGG-3′. To answer why M1.HpyAVI displayed a wider specificity for DNA recognition, we randomly choose fifty of M1.HpyAVI sequences from hundreds of H. pylori strains for multiple sequence alignment. RESULTS | |
| 9 28 sequence comparison experimental_method Based on sequence comparison and structural analysis, four residues including P41, N111, K165 and T166 were selected and replaced by serine, threonine, threonine and valine, respectively (Figure 5A). RESULTS | |
| 33 52 structural analysis experimental_method Based on sequence comparison and structural analysis, four residues including P41, N111, K165 and T166 were selected and replaced by serine, threonine, threonine and valine, respectively (Figure 5A). RESULTS | |
| 78 81 P41 residue_name_number Based on sequence comparison and structural analysis, four residues including P41, N111, K165 and T166 were selected and replaced by serine, threonine, threonine and valine, respectively (Figure 5A). RESULTS | |
| 83 87 N111 residue_name_number Based on sequence comparison and structural analysis, four residues including P41, N111, K165 and T166 were selected and replaced by serine, threonine, threonine and valine, respectively (Figure 5A). RESULTS | |
| 89 93 K165 residue_name_number Based on sequence comparison and structural analysis, four residues including P41, N111, K165 and T166 were selected and replaced by serine, threonine, threonine and valine, respectively (Figure 5A). RESULTS | |
| 98 102 T166 residue_name_number Based on sequence comparison and structural analysis, four residues including P41, N111, K165 and T166 were selected and replaced by serine, threonine, threonine and valine, respectively (Figure 5A). RESULTS | |
| 121 129 replaced experimental_method Based on sequence comparison and structural analysis, four residues including P41, N111, K165 and T166 were selected and replaced by serine, threonine, threonine and valine, respectively (Figure 5A). RESULTS | |
| 133 139 serine residue_name Based on sequence comparison and structural analysis, four residues including P41, N111, K165 and T166 were selected and replaced by serine, threonine, threonine and valine, respectively (Figure 5A). RESULTS | |
| 141 150 threonine residue_name Based on sequence comparison and structural analysis, four residues including P41, N111, K165 and T166 were selected and replaced by serine, threonine, threonine and valine, respectively (Figure 5A). RESULTS | |
| 152 161 threonine residue_name Based on sequence comparison and structural analysis, four residues including P41, N111, K165 and T166 were selected and replaced by serine, threonine, threonine and valine, respectively (Figure 5A). RESULTS | |
| 166 172 valine residue_name Based on sequence comparison and structural analysis, four residues including P41, N111, K165 and T166 were selected and replaced by serine, threonine, threonine and valine, respectively (Figure 5A). RESULTS | |
| 8 37 [3H]AdoMet radiological assay experimental_method Then, a [3H]AdoMet radiological assay was applied to quantify the methyl transfer activity of the wide type protein and the mutants. RESULTS | |
| 66 72 methyl chemical Then, a [3H]AdoMet radiological assay was applied to quantify the methyl transfer activity of the wide type protein and the mutants. RESULTS | |
| 98 107 wide type protein_state Then, a [3H]AdoMet radiological assay was applied to quantify the methyl transfer activity of the wide type protein and the mutants. RESULTS | |
| 124 131 mutants protein_state Then, a [3H]AdoMet radiological assay was applied to quantify the methyl transfer activity of the wide type protein and the mutants. RESULTS | |
| 41 44 DNA chemical As shown in Figure 5, when the substrate DNA contains 5′-GAGG-3′ or 5′-GAAG-3′, all the mutants showed no apparent difference of methyl transfer activity compared to the wt-M1.HpyAVI; but when the recognition sequence was 5′-GGAG-3′, the methyl transfer activity of the P41S mutant was significantly reduced compared to the wild type M1.HpyAVI. RESULTS | |
| 54 64 5′-GAGG-3′ chemical As shown in Figure 5, when the substrate DNA contains 5′-GAGG-3′ or 5′-GAAG-3′, all the mutants showed no apparent difference of methyl transfer activity compared to the wt-M1.HpyAVI; but when the recognition sequence was 5′-GGAG-3′, the methyl transfer activity of the P41S mutant was significantly reduced compared to the wild type M1.HpyAVI. RESULTS | |
| 68 79 5′-GAAG-3′, chemical As shown in Figure 5, when the substrate DNA contains 5′-GAGG-3′ or 5′-GAAG-3′, all the mutants showed no apparent difference of methyl transfer activity compared to the wt-M1.HpyAVI; but when the recognition sequence was 5′-GGAG-3′, the methyl transfer activity of the P41S mutant was significantly reduced compared to the wild type M1.HpyAVI. RESULTS | |
| 88 95 mutants protein_state As shown in Figure 5, when the substrate DNA contains 5′-GAGG-3′ or 5′-GAAG-3′, all the mutants showed no apparent difference of methyl transfer activity compared to the wt-M1.HpyAVI; but when the recognition sequence was 5′-GGAG-3′, the methyl transfer activity of the P41S mutant was significantly reduced compared to the wild type M1.HpyAVI. RESULTS | |
| 129 135 methyl chemical As shown in Figure 5, when the substrate DNA contains 5′-GAGG-3′ or 5′-GAAG-3′, all the mutants showed no apparent difference of methyl transfer activity compared to the wt-M1.HpyAVI; but when the recognition sequence was 5′-GGAG-3′, the methyl transfer activity of the P41S mutant was significantly reduced compared to the wild type M1.HpyAVI. RESULTS | |
| 170 172 wt protein_state As shown in Figure 5, when the substrate DNA contains 5′-GAGG-3′ or 5′-GAAG-3′, all the mutants showed no apparent difference of methyl transfer activity compared to the wt-M1.HpyAVI; but when the recognition sequence was 5′-GGAG-3′, the methyl transfer activity of the P41S mutant was significantly reduced compared to the wild type M1.HpyAVI. RESULTS | |
| 173 182 M1.HpyAVI protein As shown in Figure 5, when the substrate DNA contains 5′-GAGG-3′ or 5′-GAAG-3′, all the mutants showed no apparent difference of methyl transfer activity compared to the wt-M1.HpyAVI; but when the recognition sequence was 5′-GGAG-3′, the methyl transfer activity of the P41S mutant was significantly reduced compared to the wild type M1.HpyAVI. RESULTS | |
| 222 233 5′-GGAG-3′, chemical As shown in Figure 5, when the substrate DNA contains 5′-GAGG-3′ or 5′-GAAG-3′, all the mutants showed no apparent difference of methyl transfer activity compared to the wt-M1.HpyAVI; but when the recognition sequence was 5′-GGAG-3′, the methyl transfer activity of the P41S mutant was significantly reduced compared to the wild type M1.HpyAVI. RESULTS | |
| 238 244 methyl chemical As shown in Figure 5, when the substrate DNA contains 5′-GAGG-3′ or 5′-GAAG-3′, all the mutants showed no apparent difference of methyl transfer activity compared to the wt-M1.HpyAVI; but when the recognition sequence was 5′-GGAG-3′, the methyl transfer activity of the P41S mutant was significantly reduced compared to the wild type M1.HpyAVI. RESULTS | |
| 270 274 P41S mutant As shown in Figure 5, when the substrate DNA contains 5′-GAGG-3′ or 5′-GAAG-3′, all the mutants showed no apparent difference of methyl transfer activity compared to the wt-M1.HpyAVI; but when the recognition sequence was 5′-GGAG-3′, the methyl transfer activity of the P41S mutant was significantly reduced compared to the wild type M1.HpyAVI. RESULTS | |
| 275 281 mutant protein_state As shown in Figure 5, when the substrate DNA contains 5′-GAGG-3′ or 5′-GAAG-3′, all the mutants showed no apparent difference of methyl transfer activity compared to the wt-M1.HpyAVI; but when the recognition sequence was 5′-GGAG-3′, the methyl transfer activity of the P41S mutant was significantly reduced compared to the wild type M1.HpyAVI. RESULTS | |
| 324 333 wild type protein_state As shown in Figure 5, when the substrate DNA contains 5′-GAGG-3′ or 5′-GAAG-3′, all the mutants showed no apparent difference of methyl transfer activity compared to the wt-M1.HpyAVI; but when the recognition sequence was 5′-GGAG-3′, the methyl transfer activity of the P41S mutant was significantly reduced compared to the wild type M1.HpyAVI. RESULTS | |
| 334 343 M1.HpyAVI protein As shown in Figure 5, when the substrate DNA contains 5′-GAGG-3′ or 5′-GAAG-3′, all the mutants showed no apparent difference of methyl transfer activity compared to the wt-M1.HpyAVI; but when the recognition sequence was 5′-GGAG-3′, the methyl transfer activity of the P41S mutant was significantly reduced compared to the wild type M1.HpyAVI. RESULTS | |
| 0 18 Sequence alignment experimental_method Sequence alignment, structural analysis and radioactive methyl transfer activity define the key residue for wider substrate specificity of M1.HpyAVI FIG | |
| 20 39 structural analysis experimental_method Sequence alignment, structural analysis and radioactive methyl transfer activity define the key residue for wider substrate specificity of M1.HpyAVI FIG | |
| 44 80 radioactive methyl transfer activity experimental_method Sequence alignment, structural analysis and radioactive methyl transfer activity define the key residue for wider substrate specificity of M1.HpyAVI FIG | |
| 139 148 M1.HpyAVI protein Sequence alignment, structural analysis and radioactive methyl transfer activity define the key residue for wider substrate specificity of M1.HpyAVI FIG | |
| 3 21 Sequence alignment experimental_method A. Sequence alignment of M1.HpyAVI from 50 H. pylori strains including 26695 revealed several variant residues. FIG | |
| 25 34 M1.HpyAVI protein A. Sequence alignment of M1.HpyAVI from 50 H. pylori strains including 26695 revealed several variant residues. FIG | |
| 43 52 H. pylori species A. Sequence alignment of M1.HpyAVI from 50 H. pylori strains including 26695 revealed several variant residues. FIG | |
| 9 12 P41 residue_name_number Residues P41, N111, K165 and T166 of M1.HpyAVI from strain 26695 were chosen based on structural analysis and sequence alignment (shown in red arrow). FIG | |
| 14 18 N111 residue_name_number Residues P41, N111, K165 and T166 of M1.HpyAVI from strain 26695 were chosen based on structural analysis and sequence alignment (shown in red arrow). FIG | |
| 20 24 K165 residue_name_number Residues P41, N111, K165 and T166 of M1.HpyAVI from strain 26695 were chosen based on structural analysis and sequence alignment (shown in red arrow). FIG | |
| 29 33 T166 residue_name_number Residues P41, N111, K165 and T166 of M1.HpyAVI from strain 26695 were chosen based on structural analysis and sequence alignment (shown in red arrow). FIG | |
| 37 46 M1.HpyAVI protein Residues P41, N111, K165 and T166 of M1.HpyAVI from strain 26695 were chosen based on structural analysis and sequence alignment (shown in red arrow). FIG | |
| 59 64 26695 species Residues P41, N111, K165 and T166 of M1.HpyAVI from strain 26695 were chosen based on structural analysis and sequence alignment (shown in red arrow). FIG | |
| 86 105 structural analysis experimental_method Residues P41, N111, K165 and T166 of M1.HpyAVI from strain 26695 were chosen based on structural analysis and sequence alignment (shown in red arrow). FIG | |
| 110 128 sequence alignment experimental_method Residues P41, N111, K165 and T166 of M1.HpyAVI from strain 26695 were chosen based on structural analysis and sequence alignment (shown in red arrow). FIG | |
| 42 49 WebLogo experimental_method Amino-acid conservation is depicted using WebLogo (Crooks et al, 2004). FIG | |
| 11 17 Methyl chemical B., C., D. Methyl transfer reactions were performed using wt-M1.HpyAVI, M1.HpyAVI-P41S, M1.HpyAVI-N111T, and M1.HpyAVI-K165R T166V, respectively. FIG | |
| 58 60 wt protein_state B., C., D. Methyl transfer reactions were performed using wt-M1.HpyAVI, M1.HpyAVI-P41S, M1.HpyAVI-N111T, and M1.HpyAVI-K165R T166V, respectively. FIG | |
| 61 70 M1.HpyAVI protein B., C., D. Methyl transfer reactions were performed using wt-M1.HpyAVI, M1.HpyAVI-P41S, M1.HpyAVI-N111T, and M1.HpyAVI-K165R T166V, respectively. FIG | |
| 72 86 M1.HpyAVI-P41S mutant B., C., D. Methyl transfer reactions were performed using wt-M1.HpyAVI, M1.HpyAVI-P41S, M1.HpyAVI-N111T, and M1.HpyAVI-K165R T166V, respectively. FIG | |
| 88 103 M1.HpyAVI-N111T mutant B., C., D. Methyl transfer reactions were performed using wt-M1.HpyAVI, M1.HpyAVI-P41S, M1.HpyAVI-N111T, and M1.HpyAVI-K165R T166V, respectively. FIG | |
| 109 130 M1.HpyAVI-K165R T166V mutant B., C., D. Methyl transfer reactions were performed using wt-M1.HpyAVI, M1.HpyAVI-P41S, M1.HpyAVI-N111T, and M1.HpyAVI-K165R T166V, respectively. FIG | |
| 43 46 DNA chemical Radioactivity incorporated into the duplex DNA containing 5′-GAGG-3′, 5′-GAAG-3′ or 5′-GGAG-3′ was quantified by Beckman LS6500 for 10 min. FIG | |
| 58 68 5′-GAGG-3′ chemical Radioactivity incorporated into the duplex DNA containing 5′-GAGG-3′, 5′-GAAG-3′ or 5′-GGAG-3′ was quantified by Beckman LS6500 for 10 min. FIG | |
| 70 80 5′-GAAG-3′ chemical Radioactivity incorporated into the duplex DNA containing 5′-GAGG-3′, 5′-GAAG-3′ or 5′-GGAG-3′ was quantified by Beckman LS6500 for 10 min. FIG | |
| 84 94 5′-GGAG-3′ chemical Radioactivity incorporated into the duplex DNA containing 5′-GAGG-3′, 5′-GAAG-3′ or 5′-GGAG-3′ was quantified by Beckman LS6500 for 10 min. FIG | |
| 33 36 P41 residue_name_number Our experimental data identified P41 as a key residue determining the recognition of GGAG of M1.HpyAVI. RESULTS | |
| 85 89 GGAG structure_element Our experimental data identified P41 as a key residue determining the recognition of GGAG of M1.HpyAVI. RESULTS | |
| 93 102 M1.HpyAVI protein Our experimental data identified P41 as a key residue determining the recognition of GGAG of M1.HpyAVI. RESULTS | |
| 31 46 highly flexible protein_state This amino acid locates in the highly flexible loop between residues 33 and 58, which is involved in DNA binding and substrate recognition as shown above. RESULTS | |
| 47 51 loop structure_element This amino acid locates in the highly flexible loop between residues 33 and 58, which is involved in DNA binding and substrate recognition as shown above. RESULTS | |
| 69 78 33 and 58 residue_range This amino acid locates in the highly flexible loop between residues 33 and 58, which is involved in DNA binding and substrate recognition as shown above. RESULTS | |
| 101 104 DNA chemical This amino acid locates in the highly flexible loop between residues 33 and 58, which is involved in DNA binding and substrate recognition as shown above. RESULTS | |
| 0 11 Replacement experimental_method Replacement by serine at this position definitely changes the local conformation and hydrophobicity, and probably some structural properties of the whole loop, which may in turn result in reduced specificity for sequence recognition of the enzyme from strain 26695. RESULTS | |
| 15 21 serine residue_name Replacement by serine at this position definitely changes the local conformation and hydrophobicity, and probably some structural properties of the whole loop, which may in turn result in reduced specificity for sequence recognition of the enzyme from strain 26695. RESULTS | |
| 154 158 loop structure_element Replacement by serine at this position definitely changes the local conformation and hydrophobicity, and probably some structural properties of the whole loop, which may in turn result in reduced specificity for sequence recognition of the enzyme from strain 26695. RESULTS | |
| 259 264 26695 species Replacement by serine at this position definitely changes the local conformation and hydrophobicity, and probably some structural properties of the whole loop, which may in turn result in reduced specificity for sequence recognition of the enzyme from strain 26695. RESULTS | |
| 13 22 DNA-bound protein_state Although the DNA-bound structure of previous investigation on a γ-class N6-adenine MTase revealed that the target adenine was rotated out of DNA helix, details of the methyl transfer process were still unclear. DISCUSS | |
| 23 32 structure evidence Although the DNA-bound structure of previous investigation on a γ-class N6-adenine MTase revealed that the target adenine was rotated out of DNA helix, details of the methyl transfer process were still unclear. DISCUSS | |
| 64 88 γ-class N6-adenine MTase protein_type Although the DNA-bound structure of previous investigation on a γ-class N6-adenine MTase revealed that the target adenine was rotated out of DNA helix, details of the methyl transfer process were still unclear. DISCUSS | |
| 114 121 adenine residue_name Although the DNA-bound structure of previous investigation on a γ-class N6-adenine MTase revealed that the target adenine was rotated out of DNA helix, details of the methyl transfer process were still unclear. DISCUSS | |
| 141 144 DNA chemical Although the DNA-bound structure of previous investigation on a γ-class N6-adenine MTase revealed that the target adenine was rotated out of DNA helix, details of the methyl transfer process were still unclear. DISCUSS | |
| 167 173 methyl chemical Although the DNA-bound structure of previous investigation on a γ-class N6-adenine MTase revealed that the target adenine was rotated out of DNA helix, details of the methyl transfer process were still unclear. DISCUSS | |
| 56 72 N6-methyladenine ptm Additionally, recent studies reported the importance of N6-methyladenine in some eukaryotic species, but until now there has not been any N6-adenine MTases being identified in eukaryotes. DISCUSS | |
| 81 91 eukaryotic taxonomy_domain Additionally, recent studies reported the importance of N6-methyladenine in some eukaryotic species, but until now there has not been any N6-adenine MTases being identified in eukaryotes. DISCUSS | |
| 138 155 N6-adenine MTases protein_type Additionally, recent studies reported the importance of N6-methyladenine in some eukaryotic species, but until now there has not been any N6-adenine MTases being identified in eukaryotes. DISCUSS | |
| 176 186 eukaryotes taxonomy_domain Additionally, recent studies reported the importance of N6-methyladenine in some eukaryotic species, but until now there has not been any N6-adenine MTases being identified in eukaryotes. DISCUSS | |
| 0 43 Biochemical and structural characterization experimental_method Biochemical and structural characterization of M1.HpyAVI provides a new model for uncovering the methyl transfer mechanism and for investigating the N6-methyladenine in eukaryotes. DISCUSS | |
| 47 56 M1.HpyAVI protein Biochemical and structural characterization of M1.HpyAVI provides a new model for uncovering the methyl transfer mechanism and for investigating the N6-methyladenine in eukaryotes. DISCUSS | |
| 97 103 methyl chemical Biochemical and structural characterization of M1.HpyAVI provides a new model for uncovering the methyl transfer mechanism and for investigating the N6-methyladenine in eukaryotes. DISCUSS | |
| 149 165 N6-methyladenine ptm Biochemical and structural characterization of M1.HpyAVI provides a new model for uncovering the methyl transfer mechanism and for investigating the N6-methyladenine in eukaryotes. DISCUSS | |
| 169 179 eukaryotes taxonomy_domain Biochemical and structural characterization of M1.HpyAVI provides a new model for uncovering the methyl transfer mechanism and for investigating the N6-methyladenine in eukaryotes. DISCUSS | |
| 20 30 DNA MTases protein_type Oligomeric state of DNA MTases was long accepted as monomer, but our study indicated here that M1.HpyAVI exists as a dimer both in crystal and solution. DISCUSS | |
| 52 59 monomer oligomeric_state Oligomeric state of DNA MTases was long accepted as monomer, but our study indicated here that M1.HpyAVI exists as a dimer both in crystal and solution. DISCUSS | |
| 95 104 M1.HpyAVI protein Oligomeric state of DNA MTases was long accepted as monomer, but our study indicated here that M1.HpyAVI exists as a dimer both in crystal and solution. DISCUSS | |
| 117 122 dimer oligomeric_state Oligomeric state of DNA MTases was long accepted as monomer, but our study indicated here that M1.HpyAVI exists as a dimer both in crystal and solution. DISCUSS | |
| 131 138 crystal evidence Oligomeric state of DNA MTases was long accepted as monomer, but our study indicated here that M1.HpyAVI exists as a dimer both in crystal and solution. DISCUSS | |
| 26 54 β-class DNA exocyclic MTases protein_type Interestingly, some other β-class DNA exocyclic MTases showed similar oligomeric state in crystal and in solution, indicating that dimer may be the functional state shared by a subgroup of DNA MTases. DISCUSS | |
| 90 97 crystal evidence Interestingly, some other β-class DNA exocyclic MTases showed similar oligomeric state in crystal and in solution, indicating that dimer may be the functional state shared by a subgroup of DNA MTases. DISCUSS | |
| 131 136 dimer oligomeric_state Interestingly, some other β-class DNA exocyclic MTases showed similar oligomeric state in crystal and in solution, indicating that dimer may be the functional state shared by a subgroup of DNA MTases. DISCUSS | |
| 189 199 DNA MTases protein_type Interestingly, some other β-class DNA exocyclic MTases showed similar oligomeric state in crystal and in solution, indicating that dimer may be the functional state shared by a subgroup of DNA MTases. DISCUSS | |
| 4 19 highly flexible protein_state The highly flexible region (residues 33-58) and TRD (residues 133-163) of M1.HpyAVI are supposed to interact with DNA at minor and major grooves, respectively. DISCUSS | |
| 37 42 33-58 residue_range The highly flexible region (residues 33-58) and TRD (residues 133-163) of M1.HpyAVI are supposed to interact with DNA at minor and major grooves, respectively. DISCUSS | |
| 48 51 TRD structure_element The highly flexible region (residues 33-58) and TRD (residues 133-163) of M1.HpyAVI are supposed to interact with DNA at minor and major grooves, respectively. DISCUSS | |
| 62 69 133-163 residue_range The highly flexible region (residues 33-58) and TRD (residues 133-163) of M1.HpyAVI are supposed to interact with DNA at minor and major grooves, respectively. DISCUSS | |
| 74 83 M1.HpyAVI protein The highly flexible region (residues 33-58) and TRD (residues 133-163) of M1.HpyAVI are supposed to interact with DNA at minor and major grooves, respectively. DISCUSS | |
| 114 117 DNA chemical The highly flexible region (residues 33-58) and TRD (residues 133-163) of M1.HpyAVI are supposed to interact with DNA at minor and major grooves, respectively. DISCUSS | |
| 121 144 minor and major grooves structure_element The highly flexible region (residues 33-58) and TRD (residues 133-163) of M1.HpyAVI are supposed to interact with DNA at minor and major grooves, respectively. DISCUSS | |
| 12 15 P41 residue_name_number And residue P41 might be a key residue partially determining the substrate spectrum of M1.HpyAVI. DISCUSS | |
| 87 96 M1.HpyAVI protein And residue P41 might be a key residue partially determining the substrate spectrum of M1.HpyAVI. DISCUSS | |
| 4 11 missing protein_state The missing loop between residues 33 and 58 may need DNA binding so as to form a stable conformation, which is similar to the condition of M.TaqI. Crystallization of M1.HpyAVI-DNA complex warrants future investigations, with the purpose of revealing the mechanism behind the wider substrate specificity of this enzyme. DISCUSS | |
| 12 16 loop structure_element The missing loop between residues 33 and 58 may need DNA binding so as to form a stable conformation, which is similar to the condition of M.TaqI. Crystallization of M1.HpyAVI-DNA complex warrants future investigations, with the purpose of revealing the mechanism behind the wider substrate specificity of this enzyme. DISCUSS | |
| 34 43 33 and 58 residue_range The missing loop between residues 33 and 58 may need DNA binding so as to form a stable conformation, which is similar to the condition of M.TaqI. Crystallization of M1.HpyAVI-DNA complex warrants future investigations, with the purpose of revealing the mechanism behind the wider substrate specificity of this enzyme. DISCUSS | |
| 53 56 DNA chemical The missing loop between residues 33 and 58 may need DNA binding so as to form a stable conformation, which is similar to the condition of M.TaqI. Crystallization of M1.HpyAVI-DNA complex warrants future investigations, with the purpose of revealing the mechanism behind the wider substrate specificity of this enzyme. DISCUSS | |
| 81 87 stable protein_state The missing loop between residues 33 and 58 may need DNA binding so as to form a stable conformation, which is similar to the condition of M.TaqI. Crystallization of M1.HpyAVI-DNA complex warrants future investigations, with the purpose of revealing the mechanism behind the wider substrate specificity of this enzyme. DISCUSS | |
| 139 145 M.TaqI protein The missing loop between residues 33 and 58 may need DNA binding so as to form a stable conformation, which is similar to the condition of M.TaqI. Crystallization of M1.HpyAVI-DNA complex warrants future investigations, with the purpose of revealing the mechanism behind the wider substrate specificity of this enzyme. DISCUSS | |
| 147 162 Crystallization experimental_method The missing loop between residues 33 and 58 may need DNA binding so as to form a stable conformation, which is similar to the condition of M.TaqI. Crystallization of M1.HpyAVI-DNA complex warrants future investigations, with the purpose of revealing the mechanism behind the wider substrate specificity of this enzyme. DISCUSS | |
| 166 179 M1.HpyAVI-DNA complex_assembly The missing loop between residues 33 and 58 may need DNA binding so as to form a stable conformation, which is similar to the condition of M.TaqI. Crystallization of M1.HpyAVI-DNA complex warrants future investigations, with the purpose of revealing the mechanism behind the wider substrate specificity of this enzyme. DISCUSS | |
| 0 15 DNA methylation ptm DNA methylation plays an important role in bacterial pathogenicity. DISCUSS | |
| 43 52 bacterial taxonomy_domain DNA methylation plays an important role in bacterial pathogenicity. DISCUSS | |
| 0 23 DNA adenine methylation ptm DNA adenine methylation was known to regulate the expression of some virulence genes in bacteria including H.pylori. DISCUSS | |
| 88 96 bacteria taxonomy_domain DNA adenine methylation was known to regulate the expression of some virulence genes in bacteria including H.pylori. DISCUSS | |
| 107 115 H.pylori species DNA adenine methylation was known to regulate the expression of some virulence genes in bacteria including H.pylori. DISCUSS | |
| 14 37 DNA adenine methylation ptm Inhibitors of DNA adenine methylation may have a broad antimicrobial action by targeting DNA adenine methyltransferase. DISCUSS | |
| 89 118 DNA adenine methyltransferase protein_type Inhibitors of DNA adenine methylation may have a broad antimicrobial action by targeting DNA adenine methyltransferase. DISCUSS | |
| 41 56 DNA methylation ptm As an important biological modification, DNA methylation directly influences bacterial survival. DISCUSS | |
| 77 86 bacterial taxonomy_domain As an important biological modification, DNA methylation directly influences bacterial survival. DISCUSS | |
| 0 11 Knockout of experimental_method Knockout of M1.HpyAVI largely prevents the growth of H. pylori. DISCUSS | |
| 12 21 M1.HpyAVI protein Knockout of M1.HpyAVI largely prevents the growth of H. pylori. DISCUSS | |
| 53 62 H. pylori species Knockout of M1.HpyAVI largely prevents the growth of H. pylori. DISCUSS | |
| 13 22 H. pylori species Importantly, H. pylori is involved in 90% of all gastric malignancies. DISCUSS | |
| 83 91 H.pylori species Appropriate antibiotic regimens could successfully cure gastric diseases caused by H.pylori infection. DISCUSS | |
| 24 33 H. pylori species However, eradication of H. pylori infection remains a big challenge for the significantly increasing prevalence of its resistance to antibiotics. DISCUSS | |
| 39 53 adenine MTases protein_type The development of new drugs targeting adenine MTases such as M1.HpyAVI offers a new opportunity for inhibition of H. pylori infection. DISCUSS | |
| 62 71 M1.HpyAVI protein The development of new drugs targeting adenine MTases such as M1.HpyAVI offers a new opportunity for inhibition of H. pylori infection. DISCUSS | |
| 115 124 H. pylori species The development of new drugs targeting adenine MTases such as M1.HpyAVI offers a new opportunity for inhibition of H. pylori infection. DISCUSS | |
| 61 64 D29 residue_name_number Residues that play crucial roles for catalytic activity like D29 or E216 may influence the H.pylori survival. DISCUSS | |
| 68 72 E216 residue_name_number Residues that play crucial roles for catalytic activity like D29 or E216 may influence the H.pylori survival. DISCUSS | |
| 91 99 H.pylori species Residues that play crucial roles for catalytic activity like D29 or E216 may influence the H.pylori survival. DISCUSS | |
| 32 48 highly conserved protein_state Small molecules targeting these highly conserved residues are likely to emerge less drug resistance. DISCUSS | |
| 16 25 structure evidence In summary, the structure of M1.HpyAVI is featured with a disordered TRD and a key residue P41that located in the putative DNA binding region that may associate with the wider substrate specificity. DISCUSS | |
| 29 38 M1.HpyAVI protein In summary, the structure of M1.HpyAVI is featured with a disordered TRD and a key residue P41that located in the putative DNA binding region that may associate with the wider substrate specificity. DISCUSS | |
| 58 68 disordered protein_state In summary, the structure of M1.HpyAVI is featured with a disordered TRD and a key residue P41that located in the putative DNA binding region that may associate with the wider substrate specificity. DISCUSS | |
| 69 72 TRD structure_element In summary, the structure of M1.HpyAVI is featured with a disordered TRD and a key residue P41that located in the putative DNA binding region that may associate with the wider substrate specificity. DISCUSS | |
| 91 94 P41 residue_name_number In summary, the structure of M1.HpyAVI is featured with a disordered TRD and a key residue P41that located in the putative DNA binding region that may associate with the wider substrate specificity. DISCUSS | |
| 123 141 DNA binding region site In summary, the structure of M1.HpyAVI is featured with a disordered TRD and a key residue P41that located in the putative DNA binding region that may associate with the wider substrate specificity. DISCUSS | |
| 9 12 D29 residue_name_number Residues D29 and E216 were identified to play a crucial role in cofactor binding. DISCUSS | |
| 17 21 E216 residue_name_number Residues D29 and E216 were identified to play a crucial role in cofactor binding. DISCUSS | |
| 13 30 crystal structure evidence As the first crystal structure of N6-adenine MTase in H.pylori, this model may shed light on design of new antibiotics to interfere the growth and pathogenesis of H.pylori in human. DISCUSS | |
| 34 50 N6-adenine MTase protein_type As the first crystal structure of N6-adenine MTase in H.pylori, this model may shed light on design of new antibiotics to interfere the growth and pathogenesis of H.pylori in human. DISCUSS | |
| 54 62 H.pylori species As the first crystal structure of N6-adenine MTase in H.pylori, this model may shed light on design of new antibiotics to interfere the growth and pathogenesis of H.pylori in human. DISCUSS | |
| 163 171 H.pylori species As the first crystal structure of N6-adenine MTase in H.pylori, this model may shed light on design of new antibiotics to interfere the growth and pathogenesis of H.pylori in human. DISCUSS | |
| 175 180 human species As the first crystal structure of N6-adenine MTase in H.pylori, this model may shed light on design of new antibiotics to interfere the growth and pathogenesis of H.pylori in human. DISCUSS | |