| anno_start anno_end anno_text entity_type sentence section | |
| 0 18 Crystal Structures evidence Crystal Structures of Putative Sugar Kinases from Synechococcus Elongatus PCC 7942 and Arabidopsis Thaliana TITLE | |
| 31 44 Sugar Kinases protein_type Crystal Structures of Putative Sugar Kinases from Synechococcus Elongatus PCC 7942 and Arabidopsis Thaliana TITLE | |
| 50 82 Synechococcus Elongatus PCC 7942 species Crystal Structures of Putative Sugar Kinases from Synechococcus Elongatus PCC 7942 and Arabidopsis Thaliana TITLE | |
| 87 107 Arabidopsis Thaliana species Crystal Structures of Putative Sugar Kinases from Synechococcus Elongatus PCC 7942 and Arabidopsis Thaliana TITLE | |
| 18 57 Synechococcus elongatus strain PCC 7942 species The genome of the Synechococcus elongatus strain PCC 7942 encodes a putative sugar kinase (SePSK), which shares 44.9% sequence identity with the xylulose kinase-1 (AtXK-1) from Arabidopsis thaliana. ABSTRACT | |
| 77 89 sugar kinase protein_type The genome of the Synechococcus elongatus strain PCC 7942 encodes a putative sugar kinase (SePSK), which shares 44.9% sequence identity with the xylulose kinase-1 (AtXK-1) from Arabidopsis thaliana. ABSTRACT | |
| 91 96 SePSK protein The genome of the Synechococcus elongatus strain PCC 7942 encodes a putative sugar kinase (SePSK), which shares 44.9% sequence identity with the xylulose kinase-1 (AtXK-1) from Arabidopsis thaliana. ABSTRACT | |
| 145 162 xylulose kinase-1 protein The genome of the Synechococcus elongatus strain PCC 7942 encodes a putative sugar kinase (SePSK), which shares 44.9% sequence identity with the xylulose kinase-1 (AtXK-1) from Arabidopsis thaliana. ABSTRACT | |
| 164 170 AtXK-1 protein The genome of the Synechococcus elongatus strain PCC 7942 encodes a putative sugar kinase (SePSK), which shares 44.9% sequence identity with the xylulose kinase-1 (AtXK-1) from Arabidopsis thaliana. ABSTRACT | |
| 177 197 Arabidopsis thaliana species The genome of the Synechococcus elongatus strain PCC 7942 encodes a putative sugar kinase (SePSK), which shares 44.9% sequence identity with the xylulose kinase-1 (AtXK-1) from Arabidopsis thaliana. ABSTRACT | |
| 0 18 Sequence alignment experimental_method Sequence alignment suggests that both kinases belong to the ribulokinase-like carbohydrate kinases, a sub-family of FGGY family carbohydrate kinases. ABSTRACT | |
| 38 45 kinases protein_type Sequence alignment suggests that both kinases belong to the ribulokinase-like carbohydrate kinases, a sub-family of FGGY family carbohydrate kinases. ABSTRACT | |
| 60 98 ribulokinase-like carbohydrate kinases protein_type Sequence alignment suggests that both kinases belong to the ribulokinase-like carbohydrate kinases, a sub-family of FGGY family carbohydrate kinases. ABSTRACT | |
| 116 148 FGGY family carbohydrate kinases protein_type Sequence alignment suggests that both kinases belong to the ribulokinase-like carbohydrate kinases, a sub-family of FGGY family carbohydrate kinases. ABSTRACT | |
| 8 14 solved experimental_method Here we solved the structures of SePSK and AtXK-1 in both their apo forms and in complex with nucleotide substrates. ABSTRACT | |
| 19 29 structures evidence Here we solved the structures of SePSK and AtXK-1 in both their apo forms and in complex with nucleotide substrates. ABSTRACT | |
| 33 38 SePSK protein Here we solved the structures of SePSK and AtXK-1 in both their apo forms and in complex with nucleotide substrates. ABSTRACT | |
| 43 49 AtXK-1 protein Here we solved the structures of SePSK and AtXK-1 in both their apo forms and in complex with nucleotide substrates. ABSTRACT | |
| 64 67 apo protein_state Here we solved the structures of SePSK and AtXK-1 in both their apo forms and in complex with nucleotide substrates. ABSTRACT | |
| 78 93 in complex with protein_state Here we solved the structures of SePSK and AtXK-1 in both their apo forms and in complex with nucleotide substrates. ABSTRACT | |
| 94 104 nucleotide chemical Here we solved the structures of SePSK and AtXK-1 in both their apo forms and in complex with nucleotide substrates. ABSTRACT | |
| 73 80 kinases protein_type The two kinases exhibit nearly identical overall architecture, with both kinases possessing ATP hydrolysis activity in the absence of substrates. ABSTRACT | |
| 92 95 ATP chemical The two kinases exhibit nearly identical overall architecture, with both kinases possessing ATP hydrolysis activity in the absence of substrates. ABSTRACT | |
| 123 144 absence of substrates protein_state The two kinases exhibit nearly identical overall architecture, with both kinases possessing ATP hydrolysis activity in the absence of substrates. ABSTRACT | |
| 17 33 enzymatic assays experimental_method In addition, our enzymatic assays suggested that SePSK has the capability to phosphorylate D-ribulose. ABSTRACT | |
| 49 54 SePSK protein In addition, our enzymatic assays suggested that SePSK has the capability to phosphorylate D-ribulose. ABSTRACT | |
| 91 101 D-ribulose chemical In addition, our enzymatic assays suggested that SePSK has the capability to phosphorylate D-ribulose. ABSTRACT | |
| 50 55 SePSK protein In order to understand the catalytic mechanism of SePSK, we solved the structure of SePSK in complex with D-ribulose and found two potential substrate binding pockets in SePSK. ABSTRACT | |
| 60 66 solved experimental_method In order to understand the catalytic mechanism of SePSK, we solved the structure of SePSK in complex with D-ribulose and found two potential substrate binding pockets in SePSK. ABSTRACT | |
| 71 80 structure evidence In order to understand the catalytic mechanism of SePSK, we solved the structure of SePSK in complex with D-ribulose and found two potential substrate binding pockets in SePSK. ABSTRACT | |
| 84 89 SePSK protein In order to understand the catalytic mechanism of SePSK, we solved the structure of SePSK in complex with D-ribulose and found two potential substrate binding pockets in SePSK. ABSTRACT | |
| 90 105 in complex with protein_state In order to understand the catalytic mechanism of SePSK, we solved the structure of SePSK in complex with D-ribulose and found two potential substrate binding pockets in SePSK. ABSTRACT | |
| 106 116 D-ribulose chemical In order to understand the catalytic mechanism of SePSK, we solved the structure of SePSK in complex with D-ribulose and found two potential substrate binding pockets in SePSK. ABSTRACT | |
| 141 166 substrate binding pockets site In order to understand the catalytic mechanism of SePSK, we solved the structure of SePSK in complex with D-ribulose and found two potential substrate binding pockets in SePSK. ABSTRACT | |
| 170 175 SePSK protein In order to understand the catalytic mechanism of SePSK, we solved the structure of SePSK in complex with D-ribulose and found two potential substrate binding pockets in SePSK. ABSTRACT | |
| 6 36 mutation and activity analysis experimental_method Using mutation and activity analysis, we further verified the key residues important for its catalytic activity. ABSTRACT | |
| 14 35 structural comparison experimental_method Moreover, our structural comparison with other family members suggests that there are major conformational changes in SePSK upon substrate binding, facilitating the catalytic process. ABSTRACT | |
| 118 123 SePSK protein Moreover, our structural comparison with other family members suggests that there are major conformational changes in SePSK upon substrate binding, facilitating the catalytic process. ABSTRACT | |
| 169 174 SePSK protein Together, these results provide important information for a more detailed understanding of the cofactor and substrate binding mode as well as the catalytic mechanism of SePSK, and possible similarities with its plant homologue AtXK-1. ABSTRACT | |
| 211 216 plant taxonomy_domain Together, these results provide important information for a more detailed understanding of the cofactor and substrate binding mode as well as the catalytic mechanism of SePSK, and possible similarities with its plant homologue AtXK-1. ABSTRACT | |
| 227 233 AtXK-1 protein Together, these results provide important information for a more detailed understanding of the cofactor and substrate binding mode as well as the catalytic mechanism of SePSK, and possible similarities with its plant homologue AtXK-1. ABSTRACT | |
| 0 13 Carbohydrates chemical Carbohydrates are essential cellular compounds involved in the metabolic processes present in all organisms. INTRO | |
| 0 15 Phosphorylation ptm Phosphorylation is one of the various pivotal modifications of carbohydrates, and is catalyzed by specific sugar kinases. INTRO | |
| 63 76 carbohydrates chemical Phosphorylation is one of the various pivotal modifications of carbohydrates, and is catalyzed by specific sugar kinases. INTRO | |
| 107 120 sugar kinases protein_type Phosphorylation is one of the various pivotal modifications of carbohydrates, and is catalyzed by specific sugar kinases. INTRO | |
| 6 13 kinases protein_type These kinases exhibit considerable differences in their folding pattern and substrate specificity. INTRO | |
| 9 26 sequence analysis experimental_method Based on sequence analysis, they can be divided into four families, namely HSP 70_NBD family, FGGY family, Mer_B like family and Parm_like family. INTRO | |
| 75 92 HSP 70_NBD family protein_type Based on sequence analysis, they can be divided into four families, namely HSP 70_NBD family, FGGY family, Mer_B like family and Parm_like family. INTRO | |
| 94 105 FGGY family protein_type Based on sequence analysis, they can be divided into four families, namely HSP 70_NBD family, FGGY family, Mer_B like family and Parm_like family. INTRO | |
| 107 124 Mer_B like family protein_type Based on sequence analysis, they can be divided into four families, namely HSP 70_NBD family, FGGY family, Mer_B like family and Parm_like family. INTRO | |
| 129 145 Parm_like family protein_type Based on sequence analysis, they can be divided into four families, namely HSP 70_NBD family, FGGY family, Mer_B like family and Parm_like family. INTRO | |
| 4 36 FGGY family carbohydrate kinases protein_type The FGGY family carbohydrate kinases contain different types of sugar kinases, all of which possess different catalytic substrates with preferences for short-chained sugar substrates, ranging from triose to heptose. INTRO | |
| 64 77 sugar kinases protein_type The FGGY family carbohydrate kinases contain different types of sugar kinases, all of which possess different catalytic substrates with preferences for short-chained sugar substrates, ranging from triose to heptose. INTRO | |
| 166 171 sugar chemical The FGGY family carbohydrate kinases contain different types of sugar kinases, all of which possess different catalytic substrates with preferences for short-chained sugar substrates, ranging from triose to heptose. INTRO | |
| 197 203 triose chemical The FGGY family carbohydrate kinases contain different types of sugar kinases, all of which possess different catalytic substrates with preferences for short-chained sugar substrates, ranging from triose to heptose. INTRO | |
| 207 214 heptose chemical The FGGY family carbohydrate kinases contain different types of sugar kinases, all of which possess different catalytic substrates with preferences for short-chained sugar substrates, ranging from triose to heptose. INTRO | |
| 6 11 sugar chemical These sugar substrates include L-ribulose, erythritol, L-fuculose, D-glycerol, D-gluconate, L-xylulose, D-ribulose, L-rhamnulose and D-xylulose. INTRO | |
| 31 41 L-ribulose chemical These sugar substrates include L-ribulose, erythritol, L-fuculose, D-glycerol, D-gluconate, L-xylulose, D-ribulose, L-rhamnulose and D-xylulose. INTRO | |
| 43 53 erythritol chemical These sugar substrates include L-ribulose, erythritol, L-fuculose, D-glycerol, D-gluconate, L-xylulose, D-ribulose, L-rhamnulose and D-xylulose. INTRO | |
| 55 65 L-fuculose chemical These sugar substrates include L-ribulose, erythritol, L-fuculose, D-glycerol, D-gluconate, L-xylulose, D-ribulose, L-rhamnulose and D-xylulose. INTRO | |
| 67 77 D-glycerol chemical These sugar substrates include L-ribulose, erythritol, L-fuculose, D-glycerol, D-gluconate, L-xylulose, D-ribulose, L-rhamnulose and D-xylulose. INTRO | |
| 79 90 D-gluconate chemical These sugar substrates include L-ribulose, erythritol, L-fuculose, D-glycerol, D-gluconate, L-xylulose, D-ribulose, L-rhamnulose and D-xylulose. INTRO | |
| 92 102 L-xylulose chemical These sugar substrates include L-ribulose, erythritol, L-fuculose, D-glycerol, D-gluconate, L-xylulose, D-ribulose, L-rhamnulose and D-xylulose. INTRO | |
| 104 114 D-ribulose chemical These sugar substrates include L-ribulose, erythritol, L-fuculose, D-glycerol, D-gluconate, L-xylulose, D-ribulose, L-rhamnulose and D-xylulose. INTRO | |
| 116 128 L-rhamnulose chemical These sugar substrates include L-ribulose, erythritol, L-fuculose, D-glycerol, D-gluconate, L-xylulose, D-ribulose, L-rhamnulose and D-xylulose. INTRO | |
| 133 143 D-xylulose chemical These sugar substrates include L-ribulose, erythritol, L-fuculose, D-glycerol, D-gluconate, L-xylulose, D-ribulose, L-rhamnulose and D-xylulose. INTRO | |
| 0 10 Structures evidence Structures reported in the Protein Data Bank of the FGGY family carbohydrate kinases exhibit a similar overall architecture containing two protein domains, one of which is responsible for the binding of substrate, while the second is used for binding cofactor ATP. INTRO | |
| 52 84 FGGY family carbohydrate kinases protein_type Structures reported in the Protein Data Bank of the FGGY family carbohydrate kinases exhibit a similar overall architecture containing two protein domains, one of which is responsible for the binding of substrate, while the second is used for binding cofactor ATP. INTRO | |
| 260 263 ATP chemical Structures reported in the Protein Data Bank of the FGGY family carbohydrate kinases exhibit a similar overall architecture containing two protein domains, one of which is responsible for the binding of substrate, while the second is used for binding cofactor ATP. INTRO | |
| 10 25 binding pockets site While the binding pockets for substrates are at the same position, each FGGY family carbohydrate kinases uses different substrate-binding residues, resulting in high substrate specificity. INTRO | |
| 72 104 FGGY family carbohydrate kinases protein_type While the binding pockets for substrates are at the same position, each FGGY family carbohydrate kinases uses different substrate-binding residues, resulting in high substrate specificity. INTRO | |
| 120 146 substrate-binding residues site While the binding pockets for substrates are at the same position, each FGGY family carbohydrate kinases uses different substrate-binding residues, resulting in high substrate specificity. INTRO | |
| 0 15 Synpcc7942_2462 gene Synpcc7942_2462 from the cyanobacteria Synechococcus elongatus PCC 7942 encodes a putative sugar kinase (SePSK), and this kinase contains 426 amino acids. INTRO | |
| 25 38 cyanobacteria taxonomy_domain Synpcc7942_2462 from the cyanobacteria Synechococcus elongatus PCC 7942 encodes a putative sugar kinase (SePSK), and this kinase contains 426 amino acids. INTRO | |
| 39 71 Synechococcus elongatus PCC 7942 species Synpcc7942_2462 from the cyanobacteria Synechococcus elongatus PCC 7942 encodes a putative sugar kinase (SePSK), and this kinase contains 426 amino acids. INTRO | |
| 91 103 sugar kinase protein_type Synpcc7942_2462 from the cyanobacteria Synechococcus elongatus PCC 7942 encodes a putative sugar kinase (SePSK), and this kinase contains 426 amino acids. INTRO | |
| 105 110 SePSK protein Synpcc7942_2462 from the cyanobacteria Synechococcus elongatus PCC 7942 encodes a putative sugar kinase (SePSK), and this kinase contains 426 amino acids. INTRO | |
| 122 128 kinase protein_type Synpcc7942_2462 from the cyanobacteria Synechococcus elongatus PCC 7942 encodes a putative sugar kinase (SePSK), and this kinase contains 426 amino acids. INTRO | |
| 138 141 426 residue_range Synpcc7942_2462 from the cyanobacteria Synechococcus elongatus PCC 7942 encodes a putative sugar kinase (SePSK), and this kinase contains 426 amino acids. INTRO | |
| 4 13 At2g21370 gene The At2g21370 gene product from Arabidopsis thaliana, xylulose kinase-1 (AtXK-1), whose mature form contains 436 amino acids, is located in the chloroplast (ChloroP 1.1 Server). INTRO | |
| 32 52 Arabidopsis thaliana species The At2g21370 gene product from Arabidopsis thaliana, xylulose kinase-1 (AtXK-1), whose mature form contains 436 amino acids, is located in the chloroplast (ChloroP 1.1 Server). INTRO | |
| 54 71 xylulose kinase-1 protein The At2g21370 gene product from Arabidopsis thaliana, xylulose kinase-1 (AtXK-1), whose mature form contains 436 amino acids, is located in the chloroplast (ChloroP 1.1 Server). INTRO | |
| 73 79 AtXK-1 protein The At2g21370 gene product from Arabidopsis thaliana, xylulose kinase-1 (AtXK-1), whose mature form contains 436 amino acids, is located in the chloroplast (ChloroP 1.1 Server). INTRO | |
| 88 99 mature form protein_state The At2g21370 gene product from Arabidopsis thaliana, xylulose kinase-1 (AtXK-1), whose mature form contains 436 amino acids, is located in the chloroplast (ChloroP 1.1 Server). INTRO | |
| 109 112 436 residue_range The At2g21370 gene product from Arabidopsis thaliana, xylulose kinase-1 (AtXK-1), whose mature form contains 436 amino acids, is located in the chloroplast (ChloroP 1.1 Server). INTRO | |
| 0 5 SePSK protein SePSK and AtXK-1 display a sequence identity of 44.9%, and belong to the ribulokinase-like carbohydrate kinases, a sub-family of FGGY family carbohydrate kinases. INTRO | |
| 10 16 AtXK-1 protein SePSK and AtXK-1 display a sequence identity of 44.9%, and belong to the ribulokinase-like carbohydrate kinases, a sub-family of FGGY family carbohydrate kinases. INTRO | |
| 73 111 ribulokinase-like carbohydrate kinases protein_type SePSK and AtXK-1 display a sequence identity of 44.9%, and belong to the ribulokinase-like carbohydrate kinases, a sub-family of FGGY family carbohydrate kinases. INTRO | |
| 129 161 FGGY family carbohydrate kinases protein_type SePSK and AtXK-1 display a sequence identity of 44.9%, and belong to the ribulokinase-like carbohydrate kinases, a sub-family of FGGY family carbohydrate kinases. INTRO | |
| 51 66 phosphorylation ptm Members of this sub-family are responsible for the phosphorylation of sugars similar to L-ribulose and D-ribulose. INTRO | |
| 70 76 sugars chemical Members of this sub-family are responsible for the phosphorylation of sugars similar to L-ribulose and D-ribulose. INTRO | |
| 88 98 L-ribulose chemical Members of this sub-family are responsible for the phosphorylation of sugars similar to L-ribulose and D-ribulose. INTRO | |
| 103 113 D-ribulose chemical Members of this sub-family are responsible for the phosphorylation of sugars similar to L-ribulose and D-ribulose. INTRO | |
| 46 84 ribulokinase-like carbohydrate kinases protein_type The sequence and the substrate specificity of ribulokinase-like carbohydrate kinases are different, but they share the common folding feature with two domains. INTRO | |
| 0 8 Domain I structure_element Domain I exhibits a ribonuclease H-like folding pattern, and is responsible for the substrate binding, while domain II possesses an actin-like ATPase domain that binds cofactor ATP. INTRO | |
| 20 55 ribonuclease H-like folding pattern structure_element Domain I exhibits a ribonuclease H-like folding pattern, and is responsible for the substrate binding, while domain II possesses an actin-like ATPase domain that binds cofactor ATP. INTRO | |
| 109 118 domain II structure_element Domain I exhibits a ribonuclease H-like folding pattern, and is responsible for the substrate binding, while domain II possesses an actin-like ATPase domain that binds cofactor ATP. INTRO | |
| 132 156 actin-like ATPase domain structure_element Domain I exhibits a ribonuclease H-like folding pattern, and is responsible for the substrate binding, while domain II possesses an actin-like ATPase domain that binds cofactor ATP. INTRO | |
| 177 180 ATP chemical Domain I exhibits a ribonuclease H-like folding pattern, and is responsible for the substrate binding, while domain II possesses an actin-like ATPase domain that binds cofactor ATP. INTRO | |
| 13 29 xylulose kinases protein_type Two possible xylulose kinases (xylulose kinase-1: XK-1 and xylulose kinase-2: XK-2) from Arabidopsis thaliana were previously proposed. INTRO | |
| 31 48 xylulose kinase-1 protein Two possible xylulose kinases (xylulose kinase-1: XK-1 and xylulose kinase-2: XK-2) from Arabidopsis thaliana were previously proposed. INTRO | |
| 50 54 XK-1 protein Two possible xylulose kinases (xylulose kinase-1: XK-1 and xylulose kinase-2: XK-2) from Arabidopsis thaliana were previously proposed. INTRO | |
| 59 76 xylulose kinase-2 protein Two possible xylulose kinases (xylulose kinase-1: XK-1 and xylulose kinase-2: XK-2) from Arabidopsis thaliana were previously proposed. INTRO | |
| 78 82 XK-2 protein Two possible xylulose kinases (xylulose kinase-1: XK-1 and xylulose kinase-2: XK-2) from Arabidopsis thaliana were previously proposed. INTRO | |
| 89 109 Arabidopsis thaliana species Two possible xylulose kinases (xylulose kinase-1: XK-1 and xylulose kinase-2: XK-2) from Arabidopsis thaliana were previously proposed. INTRO | |
| 18 22 XK-2 protein It was shown that XK-2 (At5g49650) located in the cytosol is indeed xylulose kinase. INTRO | |
| 24 33 At5g49650 gene It was shown that XK-2 (At5g49650) located in the cytosol is indeed xylulose kinase. INTRO | |
| 68 83 xylulose kinase protein_type It was shown that XK-2 (At5g49650) located in the cytosol is indeed xylulose kinase. INTRO | |
| 25 29 XK-1 protein However, the function of XK-1 (At2g21370) inside the chloroplast stroma has remained unknown. INTRO | |
| 31 40 At2g21370 gene However, the function of XK-1 (At2g21370) inside the chloroplast stroma has remained unknown. INTRO | |
| 0 5 SePSK protein SePSK from Synechococcus elongatus strain PCC 7942 is the homolog of AtXK-1, though its physiological function and substrates remain unclear. INTRO | |
| 11 50 Synechococcus elongatus strain PCC 7942 species SePSK from Synechococcus elongatus strain PCC 7942 is the homolog of AtXK-1, though its physiological function and substrates remain unclear. INTRO | |
| 69 75 AtXK-1 protein SePSK from Synechococcus elongatus strain PCC 7942 is the homolog of AtXK-1, though its physiological function and substrates remain unclear. INTRO | |
| 104 122 crystal structures evidence In order to obtain functional and structural information about these two proteins, here we reported the crystal structures of SePSK and AtXK-1. INTRO | |
| 126 131 SePSK protein In order to obtain functional and structural information about these two proteins, here we reported the crystal structures of SePSK and AtXK-1. INTRO | |
| 136 142 AtXK-1 protein In order to obtain functional and structural information about these two proteins, here we reported the crystal structures of SePSK and AtXK-1. INTRO | |
| 63 68 SePSK protein Our findings provide new details of the catalytic mechanism of SePSK and lay the foundation for future studies into its homologs in eukaryotes. INTRO | |
| 132 142 eukaryotes taxonomy_domain Our findings provide new details of the catalytic mechanism of SePSK and lay the foundation for future studies into its homologs in eukaryotes. INTRO | |
| 8 18 structures evidence Overall structures of apo-SePSK and apo-AtXK-1 RESULTS | |
| 22 25 apo protein_state Overall structures of apo-SePSK and apo-AtXK-1 RESULTS | |
| 26 31 SePSK protein Overall structures of apo-SePSK and apo-AtXK-1 RESULTS | |
| 36 39 apo protein_state Overall structures of apo-SePSK and apo-AtXK-1 RESULTS | |
| 40 46 AtXK-1 protein Overall structures of apo-SePSK and apo-AtXK-1 RESULTS | |
| 25 30 SePSK protein The attempt to solve the SePSK structure by molecular replacement method failed with ribulokinase from Bacillus halodurans (PDB code: 3QDK, 15.7% sequence identity) as an initial model. RESULTS | |
| 31 40 structure evidence The attempt to solve the SePSK structure by molecular replacement method failed with ribulokinase from Bacillus halodurans (PDB code: 3QDK, 15.7% sequence identity) as an initial model. RESULTS | |
| 44 72 molecular replacement method experimental_method The attempt to solve the SePSK structure by molecular replacement method failed with ribulokinase from Bacillus halodurans (PDB code: 3QDK, 15.7% sequence identity) as an initial model. RESULTS | |
| 85 97 ribulokinase protein The attempt to solve the SePSK structure by molecular replacement method failed with ribulokinase from Bacillus halodurans (PDB code: 3QDK, 15.7% sequence identity) as an initial model. RESULTS | |
| 103 122 Bacillus halodurans species The attempt to solve the SePSK structure by molecular replacement method failed with ribulokinase from Bacillus halodurans (PDB code: 3QDK, 15.7% sequence identity) as an initial model. RESULTS | |
| 18 76 single isomorphous replacement anomalous scattering method experimental_method We therefore used single isomorphous replacement anomalous scattering method (SIRAS) for successful solution of the apo-SePSK structure at a resolution of 2.3 Γ . Subsequently, the apo-SePSK structure was used as molecular replacement model to solve all other structures identified in this study. RESULTS | |
| 78 83 SIRAS experimental_method We therefore used single isomorphous replacement anomalous scattering method (SIRAS) for successful solution of the apo-SePSK structure at a resolution of 2.3 Γ . Subsequently, the apo-SePSK structure was used as molecular replacement model to solve all other structures identified in this study. RESULTS | |
| 116 119 apo protein_state We therefore used single isomorphous replacement anomalous scattering method (SIRAS) for successful solution of the apo-SePSK structure at a resolution of 2.3 Γ . Subsequently, the apo-SePSK structure was used as molecular replacement model to solve all other structures identified in this study. RESULTS | |
| 120 125 SePSK protein We therefore used single isomorphous replacement anomalous scattering method (SIRAS) for successful solution of the apo-SePSK structure at a resolution of 2.3 Γ . Subsequently, the apo-SePSK structure was used as molecular replacement model to solve all other structures identified in this study. RESULTS | |
| 126 135 structure evidence We therefore used single isomorphous replacement anomalous scattering method (SIRAS) for successful solution of the apo-SePSK structure at a resolution of 2.3 Γ . Subsequently, the apo-SePSK structure was used as molecular replacement model to solve all other structures identified in this study. RESULTS | |
| 180 183 apo protein_state We therefore used single isomorphous replacement anomalous scattering method (SIRAS) for successful solution of the apo-SePSK structure at a resolution of 2.3 Γ . Subsequently, the apo-SePSK structure was used as molecular replacement model to solve all other structures identified in this study. RESULTS | |
| 184 189 SePSK protein We therefore used single isomorphous replacement anomalous scattering method (SIRAS) for successful solution of the apo-SePSK structure at a resolution of 2.3 Γ . Subsequently, the apo-SePSK structure was used as molecular replacement model to solve all other structures identified in this study. RESULTS | |
| 190 199 structure evidence We therefore used single isomorphous replacement anomalous scattering method (SIRAS) for successful solution of the apo-SePSK structure at a resolution of 2.3 Γ . Subsequently, the apo-SePSK structure was used as molecular replacement model to solve all other structures identified in this study. RESULTS | |
| 212 239 molecular replacement model experimental_method We therefore used single isomorphous replacement anomalous scattering method (SIRAS) for successful solution of the apo-SePSK structure at a resolution of 2.3 Γ . Subsequently, the apo-SePSK structure was used as molecular replacement model to solve all other structures identified in this study. RESULTS | |
| 259 269 structures evidence We therefore used single isomorphous replacement anomalous scattering method (SIRAS) for successful solution of the apo-SePSK structure at a resolution of 2.3 Γ . Subsequently, the apo-SePSK structure was used as molecular replacement model to solve all other structures identified in this study. RESULTS | |
| 4 23 structural analysis experimental_method Our structural analysis showed that apo-SePSK consists of one SePSK protein molecule in an asymmetric unit. RESULTS | |
| 36 39 apo protein_state Our structural analysis showed that apo-SePSK consists of one SePSK protein molecule in an asymmetric unit. RESULTS | |
| 40 45 SePSK protein Our structural analysis showed that apo-SePSK consists of one SePSK protein molecule in an asymmetric unit. RESULTS | |
| 62 67 SePSK protein Our structural analysis showed that apo-SePSK consists of one SePSK protein molecule in an asymmetric unit. RESULTS | |
| 41 45 Val2 residue_name_number The amino-acid residues were traced from Val2 to His419, except for the Met1 residue and the seven residues at the C-termini. RESULTS | |
| 49 55 His419 residue_name_number The amino-acid residues were traced from Val2 to His419, except for the Met1 residue and the seven residues at the C-termini. RESULTS | |
| 72 76 Met1 residue_name_number The amino-acid residues were traced from Val2 to His419, except for the Met1 residue and the seven residues at the C-termini. RESULTS | |
| 0 3 Apo protein_state Apo-SePSK contains two domains referred to further on as domain I and domain II (Fig 1A). RESULTS | |
| 4 9 SePSK protein Apo-SePSK contains two domains referred to further on as domain I and domain II (Fig 1A). RESULTS | |
| 57 65 domain I structure_element Apo-SePSK contains two domains referred to further on as domain I and domain II (Fig 1A). RESULTS | |
| 70 79 domain II structure_element Apo-SePSK contains two domains referred to further on as domain I and domain II (Fig 1A). RESULTS | |
| 0 8 Domain I structure_element Domain I consists of non-contiguous portions of the polypeptide chains (aa. RESULTS | |
| 0 5 2β228 residue_range 2β228 and aa. RESULTS | |
| 0 7 402β419 residue_range 402β419), exhibiting 11 Ξ±-helices and 11 Ξ²-sheets. RESULTS | |
| 24 33 Ξ±-helices structure_element 402β419), exhibiting 11 Ξ±-helices and 11 Ξ²-sheets. RESULTS | |
| 41 49 Ξ²-sheets structure_element 402β419), exhibiting 11 Ξ±-helices and 11 Ξ²-sheets. RESULTS | |
| 37 39 Ξ±4 structure_element Among all these structural elements, Ξ±4/Ξ±5/Ξ±11/Ξ±18, Ξ²3/Ξ²2/Ξ²1/Ξ²6/Ξ²19/Ξ²20/Ξ²17 and Ξ±21/Ξ±32 form three patches, referred to as A1, B1 and A2, exhibiting the core region. RESULTS | |
| 40 42 Ξ±5 structure_element Among all these structural elements, Ξ±4/Ξ±5/Ξ±11/Ξ±18, Ξ²3/Ξ²2/Ξ²1/Ξ²6/Ξ²19/Ξ²20/Ξ²17 and Ξ±21/Ξ±32 form three patches, referred to as A1, B1 and A2, exhibiting the core region. RESULTS | |
| 43 46 Ξ±11 structure_element Among all these structural elements, Ξ±4/Ξ±5/Ξ±11/Ξ±18, Ξ²3/Ξ²2/Ξ²1/Ξ²6/Ξ²19/Ξ²20/Ξ²17 and Ξ±21/Ξ±32 form three patches, referred to as A1, B1 and A2, exhibiting the core region. RESULTS | |
| 47 50 Ξ±18 structure_element Among all these structural elements, Ξ±4/Ξ±5/Ξ±11/Ξ±18, Ξ²3/Ξ²2/Ξ²1/Ξ²6/Ξ²19/Ξ²20/Ξ²17 and Ξ±21/Ξ±32 form three patches, referred to as A1, B1 and A2, exhibiting the core region. RESULTS | |
| 52 54 Ξ²3 structure_element Among all these structural elements, Ξ±4/Ξ±5/Ξ±11/Ξ±18, Ξ²3/Ξ²2/Ξ²1/Ξ²6/Ξ²19/Ξ²20/Ξ²17 and Ξ±21/Ξ±32 form three patches, referred to as A1, B1 and A2, exhibiting the core region. RESULTS | |
| 55 57 Ξ²2 structure_element Among all these structural elements, Ξ±4/Ξ±5/Ξ±11/Ξ±18, Ξ²3/Ξ²2/Ξ²1/Ξ²6/Ξ²19/Ξ²20/Ξ²17 and Ξ±21/Ξ±32 form three patches, referred to as A1, B1 and A2, exhibiting the core region. RESULTS | |
| 58 60 Ξ²1 structure_element Among all these structural elements, Ξ±4/Ξ±5/Ξ±11/Ξ±18, Ξ²3/Ξ²2/Ξ²1/Ξ²6/Ξ²19/Ξ²20/Ξ²17 and Ξ±21/Ξ±32 form three patches, referred to as A1, B1 and A2, exhibiting the core region. RESULTS | |
| 61 63 Ξ²6 structure_element Among all these structural elements, Ξ±4/Ξ±5/Ξ±11/Ξ±18, Ξ²3/Ξ²2/Ξ²1/Ξ²6/Ξ²19/Ξ²20/Ξ²17 and Ξ±21/Ξ±32 form three patches, referred to as A1, B1 and A2, exhibiting the core region. RESULTS | |
| 64 67 Ξ²19 structure_element Among all these structural elements, Ξ±4/Ξ±5/Ξ±11/Ξ±18, Ξ²3/Ξ²2/Ξ²1/Ξ²6/Ξ²19/Ξ²20/Ξ²17 and Ξ±21/Ξ±32 form three patches, referred to as A1, B1 and A2, exhibiting the core region. RESULTS | |
| 68 71 Ξ²20 structure_element Among all these structural elements, Ξ±4/Ξ±5/Ξ±11/Ξ±18, Ξ²3/Ξ²2/Ξ²1/Ξ²6/Ξ²19/Ξ²20/Ξ²17 and Ξ±21/Ξ±32 form three patches, referred to as A1, B1 and A2, exhibiting the core region. RESULTS | |
| 72 75 Ξ²17 structure_element Among all these structural elements, Ξ±4/Ξ±5/Ξ±11/Ξ±18, Ξ²3/Ξ²2/Ξ²1/Ξ²6/Ξ²19/Ξ²20/Ξ²17 and Ξ±21/Ξ±32 form three patches, referred to as A1, B1 and A2, exhibiting the core region. RESULTS | |
| 80 83 Ξ±21 structure_element Among all these structural elements, Ξ±4/Ξ±5/Ξ±11/Ξ±18, Ξ²3/Ξ²2/Ξ²1/Ξ²6/Ξ²19/Ξ²20/Ξ²17 and Ξ±21/Ξ±32 form three patches, referred to as A1, B1 and A2, exhibiting the core region. RESULTS | |
| 84 87 Ξ±32 structure_element Among all these structural elements, Ξ±4/Ξ±5/Ξ±11/Ξ±18, Ξ²3/Ξ²2/Ξ²1/Ξ²6/Ξ²19/Ξ²20/Ξ²17 and Ξ±21/Ξ±32 form three patches, referred to as A1, B1 and A2, exhibiting the core region. RESULTS | |
| 123 125 A1 structure_element Among all these structural elements, Ξ±4/Ξ±5/Ξ±11/Ξ±18, Ξ²3/Ξ²2/Ξ²1/Ξ²6/Ξ²19/Ξ²20/Ξ²17 and Ξ±21/Ξ±32 form three patches, referred to as A1, B1 and A2, exhibiting the core region. RESULTS | |
| 127 129 B1 structure_element Among all these structural elements, Ξ±4/Ξ±5/Ξ±11/Ξ±18, Ξ²3/Ξ²2/Ξ²1/Ξ²6/Ξ²19/Ξ²20/Ξ²17 and Ξ±21/Ξ±32 form three patches, referred to as A1, B1 and A2, exhibiting the core region. RESULTS | |
| 134 136 A2 structure_element Among all these structural elements, Ξ±4/Ξ±5/Ξ±11/Ξ±18, Ξ²3/Ξ²2/Ξ²1/Ξ²6/Ξ²19/Ξ²20/Ξ²17 and Ξ±21/Ξ±32 form three patches, referred to as A1, B1 and A2, exhibiting the core region. RESULTS | |
| 153 164 core region structure_element Among all these structural elements, Ξ±4/Ξ±5/Ξ±11/Ξ±18, Ξ²3/Ξ²2/Ξ²1/Ξ²6/Ξ²19/Ξ²20/Ξ²17 and Ξ±21/Ξ±32 form three patches, referred to as A1, B1 and A2, exhibiting the core region. RESULTS | |
| 18 26 Ξ²-sheets structure_element In addition, four Ξ²-sheets (Ξ²7, Ξ²10, Ξ²12 and Ξ²16) and five Ξ±-helices (Ξ±8, Ξ±9, Ξ±13, Ξ±14 and Ξ±15) flank the left side of the core region. RESULTS | |
| 28 30 Ξ²7 structure_element In addition, four Ξ²-sheets (Ξ²7, Ξ²10, Ξ²12 and Ξ²16) and five Ξ±-helices (Ξ±8, Ξ±9, Ξ±13, Ξ±14 and Ξ±15) flank the left side of the core region. RESULTS | |
| 32 35 Ξ²10 structure_element In addition, four Ξ²-sheets (Ξ²7, Ξ²10, Ξ²12 and Ξ²16) and five Ξ±-helices (Ξ±8, Ξ±9, Ξ±13, Ξ±14 and Ξ±15) flank the left side of the core region. RESULTS | |
| 37 40 Ξ²12 structure_element In addition, four Ξ²-sheets (Ξ²7, Ξ²10, Ξ²12 and Ξ²16) and five Ξ±-helices (Ξ±8, Ξ±9, Ξ±13, Ξ±14 and Ξ±15) flank the left side of the core region. RESULTS | |
| 45 48 Ξ²16 structure_element In addition, four Ξ²-sheets (Ξ²7, Ξ²10, Ξ²12 and Ξ²16) and five Ξ±-helices (Ξ±8, Ξ±9, Ξ±13, Ξ±14 and Ξ±15) flank the left side of the core region. RESULTS | |
| 59 68 Ξ±-helices structure_element In addition, four Ξ²-sheets (Ξ²7, Ξ²10, Ξ²12 and Ξ²16) and five Ξ±-helices (Ξ±8, Ξ±9, Ξ±13, Ξ±14 and Ξ±15) flank the left side of the core region. RESULTS | |
| 70 72 Ξ±8 structure_element In addition, four Ξ²-sheets (Ξ²7, Ξ²10, Ξ²12 and Ξ²16) and five Ξ±-helices (Ξ±8, Ξ±9, Ξ±13, Ξ±14 and Ξ±15) flank the left side of the core region. RESULTS | |
| 74 76 Ξ±9 structure_element In addition, four Ξ²-sheets (Ξ²7, Ξ²10, Ξ²12 and Ξ²16) and five Ξ±-helices (Ξ±8, Ξ±9, Ξ±13, Ξ±14 and Ξ±15) flank the left side of the core region. RESULTS | |
| 78 81 Ξ±13 structure_element In addition, four Ξ²-sheets (Ξ²7, Ξ²10, Ξ²12 and Ξ²16) and five Ξ±-helices (Ξ±8, Ξ±9, Ξ±13, Ξ±14 and Ξ±15) flank the left side of the core region. RESULTS | |
| 83 86 Ξ±14 structure_element In addition, four Ξ²-sheets (Ξ²7, Ξ²10, Ξ²12 and Ξ²16) and five Ξ±-helices (Ξ±8, Ξ±9, Ξ±13, Ξ±14 and Ξ±15) flank the left side of the core region. RESULTS | |
| 91 94 Ξ±15 structure_element In addition, four Ξ²-sheets (Ξ²7, Ξ²10, Ξ²12 and Ξ²16) and five Ξ±-helices (Ξ±8, Ξ±9, Ξ±13, Ξ±14 and Ξ±15) flank the left side of the core region. RESULTS | |
| 123 134 core region structure_element In addition, four Ξ²-sheets (Ξ²7, Ξ²10, Ξ²12 and Ξ²16) and five Ξ±-helices (Ξ±8, Ξ±9, Ξ±13, Ξ±14 and Ξ±15) flank the left side of the core region. RESULTS | |
| 0 9 Domain II structure_element Domain II is comprised of aa. RESULTS | |
| 0 7 229β401 residue_range 229β401 and classified into B2 (Ξ²31/Ξ²29/Ξ²22/Ξ²23/Ξ²25/Ξ²24) and A3 (Ξ±26/Ξ±27/Ξ±28/Ξ±30) (Fig 1A and S1 Fig). RESULTS | |
| 28 30 B2 structure_element 229β401 and classified into B2 (Ξ²31/Ξ²29/Ξ²22/Ξ²23/Ξ²25/Ξ²24) and A3 (Ξ±26/Ξ±27/Ξ±28/Ξ±30) (Fig 1A and S1 Fig). RESULTS | |
| 32 35 Ξ²31 structure_element 229β401 and classified into B2 (Ξ²31/Ξ²29/Ξ²22/Ξ²23/Ξ²25/Ξ²24) and A3 (Ξ±26/Ξ±27/Ξ±28/Ξ±30) (Fig 1A and S1 Fig). RESULTS | |
| 36 39 Ξ²29 structure_element 229β401 and classified into B2 (Ξ²31/Ξ²29/Ξ²22/Ξ²23/Ξ²25/Ξ²24) and A3 (Ξ±26/Ξ±27/Ξ±28/Ξ±30) (Fig 1A and S1 Fig). RESULTS | |
| 40 43 Ξ²22 structure_element 229β401 and classified into B2 (Ξ²31/Ξ²29/Ξ²22/Ξ²23/Ξ²25/Ξ²24) and A3 (Ξ±26/Ξ±27/Ξ±28/Ξ±30) (Fig 1A and S1 Fig). RESULTS | |
| 44 47 Ξ²23 structure_element 229β401 and classified into B2 (Ξ²31/Ξ²29/Ξ²22/Ξ²23/Ξ²25/Ξ²24) and A3 (Ξ±26/Ξ±27/Ξ±28/Ξ±30) (Fig 1A and S1 Fig). RESULTS | |
| 48 51 Ξ²25 structure_element 229β401 and classified into B2 (Ξ²31/Ξ²29/Ξ²22/Ξ²23/Ξ²25/Ξ²24) and A3 (Ξ±26/Ξ±27/Ξ±28/Ξ±30) (Fig 1A and S1 Fig). RESULTS | |
| 52 55 Ξ²24 structure_element 229β401 and classified into B2 (Ξ²31/Ξ²29/Ξ²22/Ξ²23/Ξ²25/Ξ²24) and A3 (Ξ±26/Ξ±27/Ξ±28/Ξ±30) (Fig 1A and S1 Fig). RESULTS | |
| 61 63 A3 structure_element 229β401 and classified into B2 (Ξ²31/Ξ²29/Ξ²22/Ξ²23/Ξ²25/Ξ²24) and A3 (Ξ±26/Ξ±27/Ξ±28/Ξ±30) (Fig 1A and S1 Fig). RESULTS | |
| 65 68 Ξ±26 structure_element 229β401 and classified into B2 (Ξ²31/Ξ²29/Ξ²22/Ξ²23/Ξ²25/Ξ²24) and A3 (Ξ±26/Ξ±27/Ξ±28/Ξ±30) (Fig 1A and S1 Fig). RESULTS | |
| 69 72 Ξ±27 structure_element 229β401 and classified into B2 (Ξ²31/Ξ²29/Ξ²22/Ξ²23/Ξ²25/Ξ²24) and A3 (Ξ±26/Ξ±27/Ξ±28/Ξ±30) (Fig 1A and S1 Fig). RESULTS | |
| 73 76 Ξ±28 structure_element 229β401 and classified into B2 (Ξ²31/Ξ²29/Ξ²22/Ξ²23/Ξ²25/Ξ²24) and A3 (Ξ±26/Ξ±27/Ξ±28/Ξ±30) (Fig 1A and S1 Fig). RESULTS | |
| 77 80 Ξ±30 structure_element 229β401 and classified into B2 (Ξ²31/Ξ²29/Ξ²22/Ξ²23/Ξ²25/Ξ²24) and A3 (Ξ±26/Ξ±27/Ξ±28/Ξ±30) (Fig 1A and S1 Fig). RESULTS | |
| 7 12 SePSK protein In the SePSK structure, B1 and B2 are sandwiched by A1, A2 and A3, and the whole structure shows the A1/B1/A2/B2/A3 (Ξ±/Ξ²/Ξ±/Ξ²/Ξ±) folding pattern, which is in common with other members of FGGY family carbohydrate kinases (S2 Fig). RESULTS | |
| 13 22 structure evidence In the SePSK structure, B1 and B2 are sandwiched by A1, A2 and A3, and the whole structure shows the A1/B1/A2/B2/A3 (Ξ±/Ξ²/Ξ±/Ξ²/Ξ±) folding pattern, which is in common with other members of FGGY family carbohydrate kinases (S2 Fig). RESULTS | |
| 24 26 B1 structure_element In the SePSK structure, B1 and B2 are sandwiched by A1, A2 and A3, and the whole structure shows the A1/B1/A2/B2/A3 (Ξ±/Ξ²/Ξ±/Ξ²/Ξ±) folding pattern, which is in common with other members of FGGY family carbohydrate kinases (S2 Fig). RESULTS | |
| 31 33 B2 structure_element In the SePSK structure, B1 and B2 are sandwiched by A1, A2 and A3, and the whole structure shows the A1/B1/A2/B2/A3 (Ξ±/Ξ²/Ξ±/Ξ²/Ξ±) folding pattern, which is in common with other members of FGGY family carbohydrate kinases (S2 Fig). RESULTS | |
| 52 54 A1 structure_element In the SePSK structure, B1 and B2 are sandwiched by A1, A2 and A3, and the whole structure shows the A1/B1/A2/B2/A3 (Ξ±/Ξ²/Ξ±/Ξ²/Ξ±) folding pattern, which is in common with other members of FGGY family carbohydrate kinases (S2 Fig). RESULTS | |
| 56 58 A2 structure_element In the SePSK structure, B1 and B2 are sandwiched by A1, A2 and A3, and the whole structure shows the A1/B1/A2/B2/A3 (Ξ±/Ξ²/Ξ±/Ξ²/Ξ±) folding pattern, which is in common with other members of FGGY family carbohydrate kinases (S2 Fig). RESULTS | |
| 63 65 A3 structure_element In the SePSK structure, B1 and B2 are sandwiched by A1, A2 and A3, and the whole structure shows the A1/B1/A2/B2/A3 (Ξ±/Ξ²/Ξ±/Ξ²/Ξ±) folding pattern, which is in common with other members of FGGY family carbohydrate kinases (S2 Fig). RESULTS | |
| 81 90 structure evidence In the SePSK structure, B1 and B2 are sandwiched by A1, A2 and A3, and the whole structure shows the A1/B1/A2/B2/A3 (Ξ±/Ξ²/Ξ±/Ξ²/Ξ±) folding pattern, which is in common with other members of FGGY family carbohydrate kinases (S2 Fig). RESULTS | |
| 101 103 A1 structure_element In the SePSK structure, B1 and B2 are sandwiched by A1, A2 and A3, and the whole structure shows the A1/B1/A2/B2/A3 (Ξ±/Ξ²/Ξ±/Ξ²/Ξ±) folding pattern, which is in common with other members of FGGY family carbohydrate kinases (S2 Fig). RESULTS | |
| 104 106 B1 structure_element In the SePSK structure, B1 and B2 are sandwiched by A1, A2 and A3, and the whole structure shows the A1/B1/A2/B2/A3 (Ξ±/Ξ²/Ξ±/Ξ²/Ξ±) folding pattern, which is in common with other members of FGGY family carbohydrate kinases (S2 Fig). RESULTS | |
| 107 109 A2 structure_element In the SePSK structure, B1 and B2 are sandwiched by A1, A2 and A3, and the whole structure shows the A1/B1/A2/B2/A3 (Ξ±/Ξ²/Ξ±/Ξ²/Ξ±) folding pattern, which is in common with other members of FGGY family carbohydrate kinases (S2 Fig). RESULTS | |
| 110 112 B2 structure_element In the SePSK structure, B1 and B2 are sandwiched by A1, A2 and A3, and the whole structure shows the A1/B1/A2/B2/A3 (Ξ±/Ξ²/Ξ±/Ξ²/Ξ±) folding pattern, which is in common with other members of FGGY family carbohydrate kinases (S2 Fig). RESULTS | |
| 113 115 A3 structure_element In the SePSK structure, B1 and B2 are sandwiched by A1, A2 and A3, and the whole structure shows the A1/B1/A2/B2/A3 (Ξ±/Ξ²/Ξ±/Ξ²/Ξ±) folding pattern, which is in common with other members of FGGY family carbohydrate kinases (S2 Fig). RESULTS | |
| 117 118 Ξ± structure_element In the SePSK structure, B1 and B2 are sandwiched by A1, A2 and A3, and the whole structure shows the A1/B1/A2/B2/A3 (Ξ±/Ξ²/Ξ±/Ξ²/Ξ±) folding pattern, which is in common with other members of FGGY family carbohydrate kinases (S2 Fig). RESULTS | |
| 119 120 Ξ² structure_element In the SePSK structure, B1 and B2 are sandwiched by A1, A2 and A3, and the whole structure shows the A1/B1/A2/B2/A3 (Ξ±/Ξ²/Ξ±/Ξ²/Ξ±) folding pattern, which is in common with other members of FGGY family carbohydrate kinases (S2 Fig). RESULTS | |
| 121 122 Ξ± structure_element In the SePSK structure, B1 and B2 are sandwiched by A1, A2 and A3, and the whole structure shows the A1/B1/A2/B2/A3 (Ξ±/Ξ²/Ξ±/Ξ²/Ξ±) folding pattern, which is in common with other members of FGGY family carbohydrate kinases (S2 Fig). RESULTS | |
| 123 124 Ξ² structure_element In the SePSK structure, B1 and B2 are sandwiched by A1, A2 and A3, and the whole structure shows the A1/B1/A2/B2/A3 (Ξ±/Ξ²/Ξ±/Ξ²/Ξ±) folding pattern, which is in common with other members of FGGY family carbohydrate kinases (S2 Fig). RESULTS | |
| 125 126 Ξ± structure_element In the SePSK structure, B1 and B2 are sandwiched by A1, A2 and A3, and the whole structure shows the A1/B1/A2/B2/A3 (Ξ±/Ξ²/Ξ±/Ξ²/Ξ±) folding pattern, which is in common with other members of FGGY family carbohydrate kinases (S2 Fig). RESULTS | |
| 186 218 FGGY family carbohydrate kinases protein_type In the SePSK structure, B1 and B2 are sandwiched by A1, A2 and A3, and the whole structure shows the A1/B1/A2/B2/A3 (Ξ±/Ξ²/Ξ±/Ξ²/Ξ±) folding pattern, which is in common with other members of FGGY family carbohydrate kinases (S2 Fig). RESULTS | |
| 23 28 SePSK protein The overall folding of SePSK resembles a clip, with A2 of domain I acting as a hinge region. RESULTS | |
| 52 54 A2 structure_element The overall folding of SePSK resembles a clip, with A2 of domain I acting as a hinge region. RESULTS | |
| 58 66 domain I structure_element The overall folding of SePSK resembles a clip, with A2 of domain I acting as a hinge region. RESULTS | |
| 79 91 hinge region structure_element The overall folding of SePSK resembles a clip, with A2 of domain I acting as a hinge region. RESULTS | |
| 8 18 structures evidence Overall structures of SePSK and AtXK-1. FIG | |
| 22 27 SePSK protein Overall structures of SePSK and AtXK-1. FIG | |
| 32 38 AtXK-1 protein Overall structures of SePSK and AtXK-1. FIG | |
| 22 31 structure evidence (A) Three-dimensional structure of apo-SePSK. FIG | |
| 35 38 apo protein_state (A) Three-dimensional structure of apo-SePSK. FIG | |
| 39 44 SePSK protein (A) Three-dimensional structure of apo-SePSK. FIG | |
| 49 56 Ξ±-helix structure_element The secondary structural elements are indicated (Ξ±-helix: cyan, Ξ²-sheet: yellow). FIG | |
| 64 71 Ξ²-sheet structure_element The secondary structural elements are indicated (Ξ±-helix: cyan, Ξ²-sheet: yellow). FIG | |
| 22 31 structure evidence (B) Three-dimensional structure of apo-AtXK-1. FIG | |
| 35 38 apo protein_state (B) Three-dimensional structure of apo-AtXK-1. FIG | |
| 39 45 AtXK-1 protein (B) Three-dimensional structure of apo-AtXK-1. FIG | |
| 49 56 Ξ±-helix structure_element The secondary structural elements are indicated (Ξ±-helix: green, Ξ²-sheet: wheat). FIG | |
| 65 72 Ξ²-sheet structure_element The secondary structural elements are indicated (Ξ±-helix: green, Ξ²-sheet: wheat). FIG | |
| 0 3 Apo protein_state Apo-AtXK-1 exhibits a folding pattern similar to that of SePSK in line with their high sequence identity (Fig 1B and S1 Fig). RESULTS | |
| 4 10 AtXK-1 protein Apo-AtXK-1 exhibits a folding pattern similar to that of SePSK in line with their high sequence identity (Fig 1B and S1 Fig). RESULTS | |
| 57 62 SePSK protein Apo-AtXK-1 exhibits a folding pattern similar to that of SePSK in line with their high sequence identity (Fig 1B and S1 Fig). RESULTS | |
| 9 22 superposition experimental_method However, superposition of structures of AtXK-1 and SePSK shows some differences, especially at the loop regions. RESULTS | |
| 26 36 structures evidence However, superposition of structures of AtXK-1 and SePSK shows some differences, especially at the loop regions. RESULTS | |
| 40 46 AtXK-1 protein However, superposition of structures of AtXK-1 and SePSK shows some differences, especially at the loop regions. RESULTS | |
| 51 56 SePSK protein However, superposition of structures of AtXK-1 and SePSK shows some differences, especially at the loop regions. RESULTS | |
| 99 111 loop regions structure_element However, superposition of structures of AtXK-1 and SePSK shows some differences, especially at the loop regions. RESULTS | |
| 42 47 loop3 structure_element A considerable difference is found in the loop3 linking Ξ²3 and Ξ±4, which is stretched out in the AtXK-1 structure, while in the SePSK structure, it is bent back towards the inner part. RESULTS | |
| 56 58 Ξ²3 structure_element A considerable difference is found in the loop3 linking Ξ²3 and Ξ±4, which is stretched out in the AtXK-1 structure, while in the SePSK structure, it is bent back towards the inner part. RESULTS | |
| 63 65 Ξ±4 structure_element A considerable difference is found in the loop3 linking Ξ²3 and Ξ±4, which is stretched out in the AtXK-1 structure, while in the SePSK structure, it is bent back towards the inner part. RESULTS | |
| 97 103 AtXK-1 protein A considerable difference is found in the loop3 linking Ξ²3 and Ξ±4, which is stretched out in the AtXK-1 structure, while in the SePSK structure, it is bent back towards the inner part. RESULTS | |
| 104 113 structure evidence A considerable difference is found in the loop3 linking Ξ²3 and Ξ±4, which is stretched out in the AtXK-1 structure, while in the SePSK structure, it is bent back towards the inner part. RESULTS | |
| 128 133 SePSK protein A considerable difference is found in the loop3 linking Ξ²3 and Ξ±4, which is stretched out in the AtXK-1 structure, while in the SePSK structure, it is bent back towards the inner part. RESULTS | |
| 134 143 structure evidence A considerable difference is found in the loop3 linking Ξ²3 and Ξ±4, which is stretched out in the AtXK-1 structure, while in the SePSK structure, it is bent back towards the inner part. RESULTS | |
| 45 55 structures evidence The corresponding residues between these two structures (SePSK-Lys35 and AtXK-1-Lys48) have a distance of 15.4 Γ (S3 Fig). RESULTS | |
| 57 62 SePSK protein The corresponding residues between these two structures (SePSK-Lys35 and AtXK-1-Lys48) have a distance of 15.4 Γ (S3 Fig). RESULTS | |
| 63 68 Lys35 residue_name_number The corresponding residues between these two structures (SePSK-Lys35 and AtXK-1-Lys48) have a distance of 15.4 Γ (S3 Fig). RESULTS | |
| 73 79 AtXK-1 protein The corresponding residues between these two structures (SePSK-Lys35 and AtXK-1-Lys48) have a distance of 15.4 Γ (S3 Fig). RESULTS | |
| 80 85 Lys48 residue_name_number The corresponding residues between these two structures (SePSK-Lys35 and AtXK-1-Lys48) have a distance of 15.4 Γ (S3 Fig). RESULTS | |
| 0 15 Activity assays experimental_method Activity assays of SePSK and AtXK-1 RESULTS | |
| 19 24 SePSK protein Activity assays of SePSK and AtXK-1 RESULTS | |
| 29 35 AtXK-1 protein Activity assays of SePSK and AtXK-1 RESULTS | |
| 71 92 structural comparison experimental_method In order to understand the function of these two kinases, we performed structural comparison using Dali server. RESULTS | |
| 99 110 Dali server experimental_method In order to understand the function of these two kinases, we performed structural comparison using Dali server. RESULTS | |
| 4 14 structures evidence The structures most closely related to SePSK are xylulose kinase, glycerol kinase and ribulose kinase, implying that SePSK and AtXK-1 might function similarly to these kinases. RESULTS | |
| 39 44 SePSK protein The structures most closely related to SePSK are xylulose kinase, glycerol kinase and ribulose kinase, implying that SePSK and AtXK-1 might function similarly to these kinases. RESULTS | |
| 49 64 xylulose kinase protein_type The structures most closely related to SePSK are xylulose kinase, glycerol kinase and ribulose kinase, implying that SePSK and AtXK-1 might function similarly to these kinases. RESULTS | |
| 66 81 glycerol kinase protein_type The structures most closely related to SePSK are xylulose kinase, glycerol kinase and ribulose kinase, implying that SePSK and AtXK-1 might function similarly to these kinases. RESULTS | |
| 86 101 ribulose kinase protein_type The structures most closely related to SePSK are xylulose kinase, glycerol kinase and ribulose kinase, implying that SePSK and AtXK-1 might function similarly to these kinases. RESULTS | |
| 117 122 SePSK protein The structures most closely related to SePSK are xylulose kinase, glycerol kinase and ribulose kinase, implying that SePSK and AtXK-1 might function similarly to these kinases. RESULTS | |
| 127 133 AtXK-1 protein The structures most closely related to SePSK are xylulose kinase, glycerol kinase and ribulose kinase, implying that SePSK and AtXK-1 might function similarly to these kinases. RESULTS | |
| 168 175 kinases protein_type The structures most closely related to SePSK are xylulose kinase, glycerol kinase and ribulose kinase, implying that SePSK and AtXK-1 might function similarly to these kinases. RESULTS | |
| 47 50 ATP chemical We first tested whether both enzymes possessed ATP hydrolysis activity in the absence of substrates. RESULTS | |
| 78 88 absence of protein_state We first tested whether both enzymes possessed ATP hydrolysis activity in the absence of substrates. RESULTS | |
| 25 30 SePSK protein As shown in Fig 2A, both SePSK and AtXK-1 exhibited ATP hydrolysis activity. RESULTS | |
| 35 41 AtXK-1 protein As shown in Fig 2A, both SePSK and AtXK-1 exhibited ATP hydrolysis activity. RESULTS | |
| 52 55 ATP chemical As shown in Fig 2A, both SePSK and AtXK-1 exhibited ATP hydrolysis activity. RESULTS | |
| 65 80 xylulose kinase protein_type This finding is in agreement with a previous result showing that xylulose kinase (PDB code: 2ITM) possessed ATP hydrolysis activity without adding substrate. RESULTS | |
| 108 111 ATP chemical This finding is in agreement with a previous result showing that xylulose kinase (PDB code: 2ITM) possessed ATP hydrolysis activity without adding substrate. RESULTS | |
| 44 49 SePSK protein To further identify the actual substrate of SePSK and AtXK-1, five different sugar molecules, including D-ribulose, L-ribulose, D-xylulose, L-xylulose and Glycerol, were used in enzymatic activity assays. RESULTS | |
| 54 60 AtXK-1 protein To further identify the actual substrate of SePSK and AtXK-1, five different sugar molecules, including D-ribulose, L-ribulose, D-xylulose, L-xylulose and Glycerol, were used in enzymatic activity assays. RESULTS | |
| 104 114 D-ribulose chemical To further identify the actual substrate of SePSK and AtXK-1, five different sugar molecules, including D-ribulose, L-ribulose, D-xylulose, L-xylulose and Glycerol, were used in enzymatic activity assays. RESULTS | |
| 116 126 L-ribulose chemical To further identify the actual substrate of SePSK and AtXK-1, five different sugar molecules, including D-ribulose, L-ribulose, D-xylulose, L-xylulose and Glycerol, were used in enzymatic activity assays. RESULTS | |
| 128 138 D-xylulose chemical To further identify the actual substrate of SePSK and AtXK-1, five different sugar molecules, including D-ribulose, L-ribulose, D-xylulose, L-xylulose and Glycerol, were used in enzymatic activity assays. RESULTS | |
| 140 150 L-xylulose chemical To further identify the actual substrate of SePSK and AtXK-1, five different sugar molecules, including D-ribulose, L-ribulose, D-xylulose, L-xylulose and Glycerol, were used in enzymatic activity assays. RESULTS | |
| 155 163 Glycerol chemical To further identify the actual substrate of SePSK and AtXK-1, five different sugar molecules, including D-ribulose, L-ribulose, D-xylulose, L-xylulose and Glycerol, were used in enzymatic activity assays. RESULTS | |
| 178 203 enzymatic activity assays experimental_method To further identify the actual substrate of SePSK and AtXK-1, five different sugar molecules, including D-ribulose, L-ribulose, D-xylulose, L-xylulose and Glycerol, were used in enzymatic activity assays. RESULTS | |
| 24 27 ATP chemical As shown in Fig 2B, the ATP hydrolysis activity of SePSK greatly increased upon adding D-ribulose than adding other potential substrates, suggesting that it has D-ribulose kinase activity. RESULTS | |
| 51 56 SePSK protein As shown in Fig 2B, the ATP hydrolysis activity of SePSK greatly increased upon adding D-ribulose than adding other potential substrates, suggesting that it has D-ribulose kinase activity. RESULTS | |
| 87 97 D-ribulose chemical As shown in Fig 2B, the ATP hydrolysis activity of SePSK greatly increased upon adding D-ribulose than adding other potential substrates, suggesting that it has D-ribulose kinase activity. RESULTS | |
| 161 178 D-ribulose kinase protein_type As shown in Fig 2B, the ATP hydrolysis activity of SePSK greatly increased upon adding D-ribulose than adding other potential substrates, suggesting that it has D-ribulose kinase activity. RESULTS | |
| 35 38 ATP chemical In contrary, limited increasing of ATP hydrolysis activity was detected for AtXK-1 upon addition of D-ribulose (Fig 2C), despite its structural similarity with SePSK. RESULTS | |
| 76 82 AtXK-1 protein In contrary, limited increasing of ATP hydrolysis activity was detected for AtXK-1 upon addition of D-ribulose (Fig 2C), despite its structural similarity with SePSK. RESULTS | |
| 100 110 D-ribulose chemical In contrary, limited increasing of ATP hydrolysis activity was detected for AtXK-1 upon addition of D-ribulose (Fig 2C), despite its structural similarity with SePSK. RESULTS | |
| 160 165 SePSK protein In contrary, limited increasing of ATP hydrolysis activity was detected for AtXK-1 upon addition of D-ribulose (Fig 2C), despite its structural similarity with SePSK. RESULTS | |
| 4 29 enzymatic activity assays experimental_method The enzymatic activity assays of SePSK and AtXK-1. FIG | |
| 33 38 SePSK protein The enzymatic activity assays of SePSK and AtXK-1. FIG | |
| 43 49 AtXK-1 protein The enzymatic activity assays of SePSK and AtXK-1. FIG | |
| 8 11 ATP chemical (A) The ATP hydrolysis activity of SePSK and AtXK-1. FIG | |
| 35 40 SePSK protein (A) The ATP hydrolysis activity of SePSK and AtXK-1. FIG | |
| 45 51 AtXK-1 protein (A) The ATP hydrolysis activity of SePSK and AtXK-1. FIG | |
| 5 10 SePSK protein Both SePSK and AtXK-1 showed ATP hydrolysis activity in the absence of substrate. FIG | |
| 15 21 AtXK-1 protein Both SePSK and AtXK-1 showed ATP hydrolysis activity in the absence of substrate. FIG | |
| 29 32 ATP chemical Both SePSK and AtXK-1 showed ATP hydrolysis activity in the absence of substrate. FIG | |
| 60 70 absence of protein_state Both SePSK and AtXK-1 showed ATP hydrolysis activity in the absence of substrate. FIG | |
| 10 13 ATP chemical While the ATP hydrolysis activity of SePSK greatly increases upon addition of D-ribulose (DR). FIG | |
| 37 42 SePSK protein While the ATP hydrolysis activity of SePSK greatly increases upon addition of D-ribulose (DR). FIG | |
| 78 88 D-ribulose chemical While the ATP hydrolysis activity of SePSK greatly increases upon addition of D-ribulose (DR). FIG | |
| 90 92 DR chemical While the ATP hydrolysis activity of SePSK greatly increases upon addition of D-ribulose (DR). FIG | |
| 8 11 ATP chemical (B) The ATP hydrolysis activity of SePSK with addition of five different substrates. FIG | |
| 35 40 SePSK protein (B) The ATP hydrolysis activity of SePSK with addition of five different substrates. FIG | |
| 19 21 DR chemical The substrates are DR (D-ribulose), LR (L-ribulose), DX (D-xylulose), LX (L-xylulose) and GLY (Glycerol). (C) The ATP hydrolysis activity of SePSK and AtXK-1 with or without D-ribulose. (D) The ATP hydrolysis activity of wild-type (WT) and single-site mutants of SePSK. FIG | |
| 23 33 D-ribulose chemical The substrates are DR (D-ribulose), LR (L-ribulose), DX (D-xylulose), LX (L-xylulose) and GLY (Glycerol). (C) The ATP hydrolysis activity of SePSK and AtXK-1 with or without D-ribulose. (D) The ATP hydrolysis activity of wild-type (WT) and single-site mutants of SePSK. FIG | |
| 36 38 LR chemical The substrates are DR (D-ribulose), LR (L-ribulose), DX (D-xylulose), LX (L-xylulose) and GLY (Glycerol). (C) The ATP hydrolysis activity of SePSK and AtXK-1 with or without D-ribulose. (D) The ATP hydrolysis activity of wild-type (WT) and single-site mutants of SePSK. FIG | |
| 40 50 L-ribulose chemical The substrates are DR (D-ribulose), LR (L-ribulose), DX (D-xylulose), LX (L-xylulose) and GLY (Glycerol). (C) The ATP hydrolysis activity of SePSK and AtXK-1 with or without D-ribulose. (D) The ATP hydrolysis activity of wild-type (WT) and single-site mutants of SePSK. FIG | |
| 53 55 DX chemical The substrates are DR (D-ribulose), LR (L-ribulose), DX (D-xylulose), LX (L-xylulose) and GLY (Glycerol). (C) The ATP hydrolysis activity of SePSK and AtXK-1 with or without D-ribulose. (D) The ATP hydrolysis activity of wild-type (WT) and single-site mutants of SePSK. FIG | |
| 57 67 D-xylulose chemical The substrates are DR (D-ribulose), LR (L-ribulose), DX (D-xylulose), LX (L-xylulose) and GLY (Glycerol). (C) The ATP hydrolysis activity of SePSK and AtXK-1 with or without D-ribulose. (D) The ATP hydrolysis activity of wild-type (WT) and single-site mutants of SePSK. FIG | |
| 70 72 LX chemical The substrates are DR (D-ribulose), LR (L-ribulose), DX (D-xylulose), LX (L-xylulose) and GLY (Glycerol). (C) The ATP hydrolysis activity of SePSK and AtXK-1 with or without D-ribulose. (D) The ATP hydrolysis activity of wild-type (WT) and single-site mutants of SePSK. FIG | |
| 74 84 L-xylulose chemical The substrates are DR (D-ribulose), LR (L-ribulose), DX (D-xylulose), LX (L-xylulose) and GLY (Glycerol). (C) The ATP hydrolysis activity of SePSK and AtXK-1 with or without D-ribulose. (D) The ATP hydrolysis activity of wild-type (WT) and single-site mutants of SePSK. FIG | |
| 90 93 GLY chemical The substrates are DR (D-ribulose), LR (L-ribulose), DX (D-xylulose), LX (L-xylulose) and GLY (Glycerol). (C) The ATP hydrolysis activity of SePSK and AtXK-1 with or without D-ribulose. (D) The ATP hydrolysis activity of wild-type (WT) and single-site mutants of SePSK. FIG | |
| 95 103 Glycerol chemical The substrates are DR (D-ribulose), LR (L-ribulose), DX (D-xylulose), LX (L-xylulose) and GLY (Glycerol). (C) The ATP hydrolysis activity of SePSK and AtXK-1 with or without D-ribulose. (D) The ATP hydrolysis activity of wild-type (WT) and single-site mutants of SePSK. FIG | |
| 114 117 ATP chemical The substrates are DR (D-ribulose), LR (L-ribulose), DX (D-xylulose), LX (L-xylulose) and GLY (Glycerol). (C) The ATP hydrolysis activity of SePSK and AtXK-1 with or without D-ribulose. (D) The ATP hydrolysis activity of wild-type (WT) and single-site mutants of SePSK. FIG | |
| 141 146 SePSK protein The substrates are DR (D-ribulose), LR (L-ribulose), DX (D-xylulose), LX (L-xylulose) and GLY (Glycerol). (C) The ATP hydrolysis activity of SePSK and AtXK-1 with or without D-ribulose. (D) The ATP hydrolysis activity of wild-type (WT) and single-site mutants of SePSK. FIG | |
| 151 157 AtXK-1 protein The substrates are DR (D-ribulose), LR (L-ribulose), DX (D-xylulose), LX (L-xylulose) and GLY (Glycerol). (C) The ATP hydrolysis activity of SePSK and AtXK-1 with or without D-ribulose. (D) The ATP hydrolysis activity of wild-type (WT) and single-site mutants of SePSK. FIG | |
| 174 184 D-ribulose chemical The substrates are DR (D-ribulose), LR (L-ribulose), DX (D-xylulose), LX (L-xylulose) and GLY (Glycerol). (C) The ATP hydrolysis activity of SePSK and AtXK-1 with or without D-ribulose. (D) The ATP hydrolysis activity of wild-type (WT) and single-site mutants of SePSK. FIG | |
| 194 197 ATP chemical The substrates are DR (D-ribulose), LR (L-ribulose), DX (D-xylulose), LX (L-xylulose) and GLY (Glycerol). (C) The ATP hydrolysis activity of SePSK and AtXK-1 with or without D-ribulose. (D) The ATP hydrolysis activity of wild-type (WT) and single-site mutants of SePSK. FIG | |
| 221 230 wild-type protein_state The substrates are DR (D-ribulose), LR (L-ribulose), DX (D-xylulose), LX (L-xylulose) and GLY (Glycerol). (C) The ATP hydrolysis activity of SePSK and AtXK-1 with or without D-ribulose. (D) The ATP hydrolysis activity of wild-type (WT) and single-site mutants of SePSK. FIG | |
| 232 234 WT protein_state The substrates are DR (D-ribulose), LR (L-ribulose), DX (D-xylulose), LX (L-xylulose) and GLY (Glycerol). (C) The ATP hydrolysis activity of SePSK and AtXK-1 with or without D-ribulose. (D) The ATP hydrolysis activity of wild-type (WT) and single-site mutants of SePSK. FIG | |
| 263 268 SePSK protein The substrates are DR (D-ribulose), LR (L-ribulose), DX (D-xylulose), LX (L-xylulose) and GLY (Glycerol). (C) The ATP hydrolysis activity of SePSK and AtXK-1 with or without D-ribulose. (D) The ATP hydrolysis activity of wild-type (WT) and single-site mutants of SePSK. FIG | |
| 29 34 SePSK protein Three single-site mutants of SePSK are D8A-SePSK, T11A-SePSK and D221A-SePSK. FIG | |
| 39 42 D8A mutant Three single-site mutants of SePSK are D8A-SePSK, T11A-SePSK and D221A-SePSK. FIG | |
| 43 48 SePSK protein Three single-site mutants of SePSK are D8A-SePSK, T11A-SePSK and D221A-SePSK. FIG | |
| 50 54 T11A mutant Three single-site mutants of SePSK are D8A-SePSK, T11A-SePSK and D221A-SePSK. FIG | |
| 55 60 SePSK protein Three single-site mutants of SePSK are D8A-SePSK, T11A-SePSK and D221A-SePSK. FIG | |
| 65 70 D221A mutant Three single-site mutants of SePSK are D8A-SePSK, T11A-SePSK and D221A-SePSK. FIG | |
| 71 76 SePSK protein Three single-site mutants of SePSK are D8A-SePSK, T11A-SePSK and D221A-SePSK. FIG | |
| 4 7 ATP chemical The ATP hydrolysis activity measured via luminescent ADP-Glo assay (Promega). FIG | |
| 41 66 luminescent ADP-Glo assay experimental_method The ATP hydrolysis activity measured via luminescent ADP-Glo assay (Promega). FIG | |
| 41 46 SePSK protein To understand the catalytic mechanism of SePSK, we performed structural comparisons among xylulose kinase, glycerol kinase, ribulose kinase and SePSK. RESULTS | |
| 61 83 structural comparisons experimental_method To understand the catalytic mechanism of SePSK, we performed structural comparisons among xylulose kinase, glycerol kinase, ribulose kinase and SePSK. RESULTS | |
| 90 105 xylulose kinase protein_type To understand the catalytic mechanism of SePSK, we performed structural comparisons among xylulose kinase, glycerol kinase, ribulose kinase and SePSK. RESULTS | |
| 107 122 glycerol kinase protein_type To understand the catalytic mechanism of SePSK, we performed structural comparisons among xylulose kinase, glycerol kinase, ribulose kinase and SePSK. RESULTS | |
| 124 139 ribulose kinase protein_type To understand the catalytic mechanism of SePSK, we performed structural comparisons among xylulose kinase, glycerol kinase, ribulose kinase and SePSK. RESULTS | |
| 144 149 SePSK protein To understand the catalytic mechanism of SePSK, we performed structural comparisons among xylulose kinase, glycerol kinase, ribulose kinase and SePSK. RESULTS | |
| 53 55 D8 residue_name_number Our results suggested that three conserved residues (D8, T11 and D221 of SePSK) play an important role in SePSK function. RESULTS | |
| 57 60 T11 residue_name_number Our results suggested that three conserved residues (D8, T11 and D221 of SePSK) play an important role in SePSK function. RESULTS | |
| 65 69 D221 residue_name_number Our results suggested that three conserved residues (D8, T11 and D221 of SePSK) play an important role in SePSK function. RESULTS | |
| 73 78 SePSK protein Our results suggested that three conserved residues (D8, T11 and D221 of SePSK) play an important role in SePSK function. RESULTS | |
| 106 111 SePSK protein Our results suggested that three conserved residues (D8, T11 and D221 of SePSK) play an important role in SePSK function. RESULTS | |
| 0 9 Mutations experimental_method Mutations of the corresponding residue in xylulose kinase and glycerol kinase from Escherichia coli greatly reduced their activity. RESULTS | |
| 42 57 xylulose kinase protein_type Mutations of the corresponding residue in xylulose kinase and glycerol kinase from Escherichia coli greatly reduced their activity. RESULTS | |
| 62 77 glycerol kinase protein_type Mutations of the corresponding residue in xylulose kinase and glycerol kinase from Escherichia coli greatly reduced their activity. RESULTS | |
| 83 99 Escherichia coli species Mutations of the corresponding residue in xylulose kinase and glycerol kinase from Escherichia coli greatly reduced their activity. RESULTS | |
| 52 57 SePSK protein To identify the function of these three residues of SePSK, we constructed D8A, T11A and D221A mutants. RESULTS | |
| 74 77 D8A mutant To identify the function of these three residues of SePSK, we constructed D8A, T11A and D221A mutants. RESULTS | |
| 79 83 T11A mutant To identify the function of these three residues of SePSK, we constructed D8A, T11A and D221A mutants. RESULTS | |
| 88 93 D221A mutant To identify the function of these three residues of SePSK, we constructed D8A, T11A and D221A mutants. RESULTS | |
| 94 101 mutants protein_state To identify the function of these three residues of SePSK, we constructed D8A, T11A and D221A mutants. RESULTS | |
| 6 31 enzymatic activity assays experimental_method Using enzymatic activity assays, we found that all of these mutants exhibit much lower activity of ATP hydrolysis after adding D-ribulose than that of wild type, indicating the possibility that these three residues are involved in the catalytic process of phosphorylation D-ribulose and are vital for the function of SePSK (Fig 2D). RESULTS | |
| 99 102 ATP chemical Using enzymatic activity assays, we found that all of these mutants exhibit much lower activity of ATP hydrolysis after adding D-ribulose than that of wild type, indicating the possibility that these three residues are involved in the catalytic process of phosphorylation D-ribulose and are vital for the function of SePSK (Fig 2D). RESULTS | |
| 127 137 D-ribulose chemical Using enzymatic activity assays, we found that all of these mutants exhibit much lower activity of ATP hydrolysis after adding D-ribulose than that of wild type, indicating the possibility that these three residues are involved in the catalytic process of phosphorylation D-ribulose and are vital for the function of SePSK (Fig 2D). RESULTS | |
| 151 160 wild type protein_state Using enzymatic activity assays, we found that all of these mutants exhibit much lower activity of ATP hydrolysis after adding D-ribulose than that of wild type, indicating the possibility that these three residues are involved in the catalytic process of phosphorylation D-ribulose and are vital for the function of SePSK (Fig 2D). RESULTS | |
| 256 271 phosphorylation ptm Using enzymatic activity assays, we found that all of these mutants exhibit much lower activity of ATP hydrolysis after adding D-ribulose than that of wild type, indicating the possibility that these three residues are involved in the catalytic process of phosphorylation D-ribulose and are vital for the function of SePSK (Fig 2D). RESULTS | |
| 272 282 D-ribulose chemical Using enzymatic activity assays, we found that all of these mutants exhibit much lower activity of ATP hydrolysis after adding D-ribulose than that of wild type, indicating the possibility that these three residues are involved in the catalytic process of phosphorylation D-ribulose and are vital for the function of SePSK (Fig 2D). RESULTS | |
| 317 322 SePSK protein Using enzymatic activity assays, we found that all of these mutants exhibit much lower activity of ATP hydrolysis after adding D-ribulose than that of wild type, indicating the possibility that these three residues are involved in the catalytic process of phosphorylation D-ribulose and are vital for the function of SePSK (Fig 2D). RESULTS | |
| 0 5 SePSK protein SePSK and AtXK-1 possess a similar ATP binding site RESULTS | |
| 10 16 AtXK-1 protein SePSK and AtXK-1 possess a similar ATP binding site RESULTS | |
| 35 51 ATP binding site site SePSK and AtXK-1 possess a similar ATP binding site RESULTS | |
| 39 44 SePSK protein To obtain more detailed information of SePSK and AtXK-1 in complex with ATP, we soaked the apo-crystals in the reservoir adding cofactor ATP, and obtained the structures of SePSK and AtXK-1 bound with ATP at the resolution of 2.3 Γ and 1.8 Γ , respectively. RESULTS | |
| 49 55 AtXK-1 protein To obtain more detailed information of SePSK and AtXK-1 in complex with ATP, we soaked the apo-crystals in the reservoir adding cofactor ATP, and obtained the structures of SePSK and AtXK-1 bound with ATP at the resolution of 2.3 Γ and 1.8 Γ , respectively. RESULTS | |
| 56 71 in complex with protein_state To obtain more detailed information of SePSK and AtXK-1 in complex with ATP, we soaked the apo-crystals in the reservoir adding cofactor ATP, and obtained the structures of SePSK and AtXK-1 bound with ATP at the resolution of 2.3 Γ and 1.8 Γ , respectively. RESULTS | |
| 72 75 ATP chemical To obtain more detailed information of SePSK and AtXK-1 in complex with ATP, we soaked the apo-crystals in the reservoir adding cofactor ATP, and obtained the structures of SePSK and AtXK-1 bound with ATP at the resolution of 2.3 Γ and 1.8 Γ , respectively. RESULTS | |
| 80 86 soaked experimental_method To obtain more detailed information of SePSK and AtXK-1 in complex with ATP, we soaked the apo-crystals in the reservoir adding cofactor ATP, and obtained the structures of SePSK and AtXK-1 bound with ATP at the resolution of 2.3 Γ and 1.8 Γ , respectively. RESULTS | |
| 91 94 apo protein_state To obtain more detailed information of SePSK and AtXK-1 in complex with ATP, we soaked the apo-crystals in the reservoir adding cofactor ATP, and obtained the structures of SePSK and AtXK-1 bound with ATP at the resolution of 2.3 Γ and 1.8 Γ , respectively. RESULTS | |
| 95 103 crystals evidence To obtain more detailed information of SePSK and AtXK-1 in complex with ATP, we soaked the apo-crystals in the reservoir adding cofactor ATP, and obtained the structures of SePSK and AtXK-1 bound with ATP at the resolution of 2.3 Γ and 1.8 Γ , respectively. RESULTS | |
| 137 140 ATP chemical To obtain more detailed information of SePSK and AtXK-1 in complex with ATP, we soaked the apo-crystals in the reservoir adding cofactor ATP, and obtained the structures of SePSK and AtXK-1 bound with ATP at the resolution of 2.3 Γ and 1.8 Γ , respectively. RESULTS | |
| 159 169 structures evidence To obtain more detailed information of SePSK and AtXK-1 in complex with ATP, we soaked the apo-crystals in the reservoir adding cofactor ATP, and obtained the structures of SePSK and AtXK-1 bound with ATP at the resolution of 2.3 Γ and 1.8 Γ , respectively. RESULTS | |
| 173 178 SePSK protein To obtain more detailed information of SePSK and AtXK-1 in complex with ATP, we soaked the apo-crystals in the reservoir adding cofactor ATP, and obtained the structures of SePSK and AtXK-1 bound with ATP at the resolution of 2.3 Γ and 1.8 Γ , respectively. RESULTS | |
| 183 189 AtXK-1 protein To obtain more detailed information of SePSK and AtXK-1 in complex with ATP, we soaked the apo-crystals in the reservoir adding cofactor ATP, and obtained the structures of SePSK and AtXK-1 bound with ATP at the resolution of 2.3 Γ and 1.8 Γ , respectively. RESULTS | |
| 190 200 bound with protein_state To obtain more detailed information of SePSK and AtXK-1 in complex with ATP, we soaked the apo-crystals in the reservoir adding cofactor ATP, and obtained the structures of SePSK and AtXK-1 bound with ATP at the resolution of 2.3 Γ and 1.8 Γ , respectively. RESULTS | |
| 201 204 ATP chemical To obtain more detailed information of SePSK and AtXK-1 in complex with ATP, we soaked the apo-crystals in the reservoir adding cofactor ATP, and obtained the structures of SePSK and AtXK-1 bound with ATP at the resolution of 2.3 Γ and 1.8 Γ , respectively. RESULTS | |
| 8 18 structures evidence In both structures, a strong electron density was found in the conserved ATP binding pocket, but can only be fitted with an ADP molecule (S4 Fig). RESULTS | |
| 29 45 electron density evidence In both structures, a strong electron density was found in the conserved ATP binding pocket, but can only be fitted with an ADP molecule (S4 Fig). RESULTS | |
| 63 72 conserved protein_state In both structures, a strong electron density was found in the conserved ATP binding pocket, but can only be fitted with an ADP molecule (S4 Fig). RESULTS | |
| 73 91 ATP binding pocket site In both structures, a strong electron density was found in the conserved ATP binding pocket, but can only be fitted with an ADP molecule (S4 Fig). RESULTS | |
| 124 127 ADP chemical In both structures, a strong electron density was found in the conserved ATP binding pocket, but can only be fitted with an ADP molecule (S4 Fig). RESULTS | |
| 13 23 structures evidence Thus the two structures were named ADP-SePSK and ADP-AtXK-1, respectively. RESULTS | |
| 35 44 ADP-SePSK complex_assembly Thus the two structures were named ADP-SePSK and ADP-AtXK-1, respectively. RESULTS | |
| 49 59 ADP-AtXK-1 complex_assembly Thus the two structures were named ADP-SePSK and ADP-AtXK-1, respectively. RESULTS | |
| 19 37 electron densities evidence The extremely weak electron densities of ATP Ξ³-phosphate in both structures suggest that the Ξ³-phosphate group of ATP is either flexible or hydrolyzed by SePSK and AtXK-1. RESULTS | |
| 47 56 phosphate chemical The extremely weak electron densities of ATP Ξ³-phosphate in both structures suggest that the Ξ³-phosphate group of ATP is either flexible or hydrolyzed by SePSK and AtXK-1. RESULTS | |
| 65 75 structures evidence The extremely weak electron densities of ATP Ξ³-phosphate in both structures suggest that the Ξ³-phosphate group of ATP is either flexible or hydrolyzed by SePSK and AtXK-1. RESULTS | |
| 95 104 phosphate chemical The extremely weak electron densities of ATP Ξ³-phosphate in both structures suggest that the Ξ³-phosphate group of ATP is either flexible or hydrolyzed by SePSK and AtXK-1. RESULTS | |
| 114 117 ATP chemical The extremely weak electron densities of ATP Ξ³-phosphate in both structures suggest that the Ξ³-phosphate group of ATP is either flexible or hydrolyzed by SePSK and AtXK-1. RESULTS | |
| 154 159 SePSK protein The extremely weak electron densities of ATP Ξ³-phosphate in both structures suggest that the Ξ³-phosphate group of ATP is either flexible or hydrolyzed by SePSK and AtXK-1. RESULTS | |
| 164 170 AtXK-1 protein The extremely weak electron densities of ATP Ξ³-phosphate in both structures suggest that the Ξ³-phosphate group of ATP is either flexible or hydrolyzed by SePSK and AtXK-1. RESULTS | |
| 36 61 enzymatic activity assays experimental_method This result was consistent with our enzymatic activity assays where SePSK and AtXK-1 showed ATP hydrolysis activity without adding any substrates (Fig 2A and 2C). RESULTS | |
| 68 73 SePSK protein This result was consistent with our enzymatic activity assays where SePSK and AtXK-1 showed ATP hydrolysis activity without adding any substrates (Fig 2A and 2C). RESULTS | |
| 78 84 AtXK-1 protein This result was consistent with our enzymatic activity assays where SePSK and AtXK-1 showed ATP hydrolysis activity without adding any substrates (Fig 2A and 2C). RESULTS | |
| 92 95 ATP chemical This result was consistent with our enzymatic activity assays where SePSK and AtXK-1 showed ATP hydrolysis activity without adding any substrates (Fig 2A and 2C). RESULTS | |
| 23 26 ATP chemical To avoid hydrolysis of ATP, we soaked the crystals of apo-SePSK and apo-AtXK-1 into the reservoir adding AMP-PNP. RESULTS | |
| 31 37 soaked experimental_method To avoid hydrolysis of ATP, we soaked the crystals of apo-SePSK and apo-AtXK-1 into the reservoir adding AMP-PNP. RESULTS | |
| 42 50 crystals evidence To avoid hydrolysis of ATP, we soaked the crystals of apo-SePSK and apo-AtXK-1 into the reservoir adding AMP-PNP. RESULTS | |
| 54 57 apo protein_state To avoid hydrolysis of ATP, we soaked the crystals of apo-SePSK and apo-AtXK-1 into the reservoir adding AMP-PNP. RESULTS | |
| 58 63 SePSK protein To avoid hydrolysis of ATP, we soaked the crystals of apo-SePSK and apo-AtXK-1 into the reservoir adding AMP-PNP. RESULTS | |
| 68 71 apo protein_state To avoid hydrolysis of ATP, we soaked the crystals of apo-SePSK and apo-AtXK-1 into the reservoir adding AMP-PNP. RESULTS | |
| 72 78 AtXK-1 protein To avoid hydrolysis of ATP, we soaked the crystals of apo-SePSK and apo-AtXK-1 into the reservoir adding AMP-PNP. RESULTS | |
| 105 112 AMP-PNP chemical To avoid hydrolysis of ATP, we soaked the crystals of apo-SePSK and apo-AtXK-1 into the reservoir adding AMP-PNP. RESULTS | |
| 27 45 electron densities evidence However, we found that the electron densities of Ξ³-phosphate group of AMP-PNP (AMP-PNP Ξ³-phosphate) are still weak in the AMP-PNP-SePSK and AMP-PNP-AtXK-1 structures, suggesting high flexibility of ATP-Ξ³-phosphate. RESULTS | |
| 51 60 phosphate chemical However, we found that the electron densities of Ξ³-phosphate group of AMP-PNP (AMP-PNP Ξ³-phosphate) are still weak in the AMP-PNP-SePSK and AMP-PNP-AtXK-1 structures, suggesting high flexibility of ATP-Ξ³-phosphate. RESULTS | |
| 70 77 AMP-PNP chemical However, we found that the electron densities of Ξ³-phosphate group of AMP-PNP (AMP-PNP Ξ³-phosphate) are still weak in the AMP-PNP-SePSK and AMP-PNP-AtXK-1 structures, suggesting high flexibility of ATP-Ξ³-phosphate. RESULTS | |
| 79 86 AMP-PNP chemical However, we found that the electron densities of Ξ³-phosphate group of AMP-PNP (AMP-PNP Ξ³-phosphate) are still weak in the AMP-PNP-SePSK and AMP-PNP-AtXK-1 structures, suggesting high flexibility of ATP-Ξ³-phosphate. RESULTS | |
| 89 98 phosphate chemical However, we found that the electron densities of Ξ³-phosphate group of AMP-PNP (AMP-PNP Ξ³-phosphate) are still weak in the AMP-PNP-SePSK and AMP-PNP-AtXK-1 structures, suggesting high flexibility of ATP-Ξ³-phosphate. RESULTS | |
| 122 135 AMP-PNP-SePSK complex_assembly However, we found that the electron densities of Ξ³-phosphate group of AMP-PNP (AMP-PNP Ξ³-phosphate) are still weak in the AMP-PNP-SePSK and AMP-PNP-AtXK-1 structures, suggesting high flexibility of ATP-Ξ³-phosphate. RESULTS | |
| 140 154 AMP-PNP-AtXK-1 complex_assembly However, we found that the electron densities of Ξ³-phosphate group of AMP-PNP (AMP-PNP Ξ³-phosphate) are still weak in the AMP-PNP-SePSK and AMP-PNP-AtXK-1 structures, suggesting high flexibility of ATP-Ξ³-phosphate. RESULTS | |
| 155 165 structures evidence However, we found that the electron densities of Ξ³-phosphate group of AMP-PNP (AMP-PNP Ξ³-phosphate) are still weak in the AMP-PNP-SePSK and AMP-PNP-AtXK-1 structures, suggesting high flexibility of ATP-Ξ³-phosphate. RESULTS | |
| 198 201 ATP chemical However, we found that the electron densities of Ξ³-phosphate group of AMP-PNP (AMP-PNP Ξ³-phosphate) are still weak in the AMP-PNP-SePSK and AMP-PNP-AtXK-1 structures, suggesting high flexibility of ATP-Ξ³-phosphate. RESULTS | |
| 204 213 phosphate chemical However, we found that the electron densities of Ξ³-phosphate group of AMP-PNP (AMP-PNP Ξ³-phosphate) are still weak in the AMP-PNP-SePSK and AMP-PNP-AtXK-1 structures, suggesting high flexibility of ATP-Ξ³-phosphate. RESULTS | |
| 6 15 phosphate chemical The Ξ³-phosphate group of ATP is transferred to the sugar substrate during the reaction process, so this flexibility might be important for the ability of these kinases. RESULTS | |
| 25 28 ATP chemical The Ξ³-phosphate group of ATP is transferred to the sugar substrate during the reaction process, so this flexibility might be important for the ability of these kinases. RESULTS | |
| 51 56 sugar chemical The Ξ³-phosphate group of ATP is transferred to the sugar substrate during the reaction process, so this flexibility might be important for the ability of these kinases. RESULTS | |
| 160 167 kinases protein_type The Ξ³-phosphate group of ATP is transferred to the sugar substrate during the reaction process, so this flexibility might be important for the ability of these kinases. RESULTS | |
| 12 22 structures evidence The overall structures as well as the coordination modes of ADP and AMP-PNP in the AMP-PNP-AtXK-1, ADP-AtXK-1, ADP-SePSK and AMP-PNP-SePSK structures are nearly identical (S5 Fig), therefore the structure of AMP-PNP-SePSK is used here to describe the structural details and to compare with those of other family members. RESULTS | |
| 60 63 ADP chemical The overall structures as well as the coordination modes of ADP and AMP-PNP in the AMP-PNP-AtXK-1, ADP-AtXK-1, ADP-SePSK and AMP-PNP-SePSK structures are nearly identical (S5 Fig), therefore the structure of AMP-PNP-SePSK is used here to describe the structural details and to compare with those of other family members. RESULTS | |
| 68 75 AMP-PNP chemical The overall structures as well as the coordination modes of ADP and AMP-PNP in the AMP-PNP-AtXK-1, ADP-AtXK-1, ADP-SePSK and AMP-PNP-SePSK structures are nearly identical (S5 Fig), therefore the structure of AMP-PNP-SePSK is used here to describe the structural details and to compare with those of other family members. RESULTS | |
| 83 97 AMP-PNP-AtXK-1 complex_assembly The overall structures as well as the coordination modes of ADP and AMP-PNP in the AMP-PNP-AtXK-1, ADP-AtXK-1, ADP-SePSK and AMP-PNP-SePSK structures are nearly identical (S5 Fig), therefore the structure of AMP-PNP-SePSK is used here to describe the structural details and to compare with those of other family members. RESULTS | |
| 99 109 ADP-AtXK-1 complex_assembly The overall structures as well as the coordination modes of ADP and AMP-PNP in the AMP-PNP-AtXK-1, ADP-AtXK-1, ADP-SePSK and AMP-PNP-SePSK structures are nearly identical (S5 Fig), therefore the structure of AMP-PNP-SePSK is used here to describe the structural details and to compare with those of other family members. RESULTS | |
| 111 120 ADP-SePSK complex_assembly The overall structures as well as the coordination modes of ADP and AMP-PNP in the AMP-PNP-AtXK-1, ADP-AtXK-1, ADP-SePSK and AMP-PNP-SePSK structures are nearly identical (S5 Fig), therefore the structure of AMP-PNP-SePSK is used here to describe the structural details and to compare with those of other family members. RESULTS | |
| 125 138 AMP-PNP-SePSK complex_assembly The overall structures as well as the coordination modes of ADP and AMP-PNP in the AMP-PNP-AtXK-1, ADP-AtXK-1, ADP-SePSK and AMP-PNP-SePSK structures are nearly identical (S5 Fig), therefore the structure of AMP-PNP-SePSK is used here to describe the structural details and to compare with those of other family members. RESULTS | |
| 139 149 structures evidence The overall structures as well as the coordination modes of ADP and AMP-PNP in the AMP-PNP-AtXK-1, ADP-AtXK-1, ADP-SePSK and AMP-PNP-SePSK structures are nearly identical (S5 Fig), therefore the structure of AMP-PNP-SePSK is used here to describe the structural details and to compare with those of other family members. RESULTS | |
| 195 204 structure evidence The overall structures as well as the coordination modes of ADP and AMP-PNP in the AMP-PNP-AtXK-1, ADP-AtXK-1, ADP-SePSK and AMP-PNP-SePSK structures are nearly identical (S5 Fig), therefore the structure of AMP-PNP-SePSK is used here to describe the structural details and to compare with those of other family members. RESULTS | |
| 208 221 AMP-PNP-SePSK complex_assembly The overall structures as well as the coordination modes of ADP and AMP-PNP in the AMP-PNP-AtXK-1, ADP-AtXK-1, ADP-SePSK and AMP-PNP-SePSK structures are nearly identical (S5 Fig), therefore the structure of AMP-PNP-SePSK is used here to describe the structural details and to compare with those of other family members. RESULTS | |
| 24 29 SePSK protein As shown in Fig 3A, one SePSK protein molecule is in an asymmetric unit with one AMP-PNP molecule. RESULTS | |
| 81 88 AMP-PNP chemical As shown in Fig 3A, one SePSK protein molecule is in an asymmetric unit with one AMP-PNP molecule. RESULTS | |
| 4 11 AMP-PNP chemical The AMP-PNP is bound at the domain II, where it fits well inside a positively charged groove. RESULTS | |
| 28 37 domain II structure_element The AMP-PNP is bound at the domain II, where it fits well inside a positively charged groove. RESULTS | |
| 67 92 positively charged groove site The AMP-PNP is bound at the domain II, where it fits well inside a positively charged groove. RESULTS | |
| 4 26 AMP-PNP binding pocket site The AMP-PNP binding pocket consists of four Ξ±-helices (Ξ±26, Ξ±28, Ξ±27 and Ξ±30) and forms a shape resembling a half-fist (Fig 3A and 3B). RESULTS | |
| 39 53 four Ξ±-helices structure_element The AMP-PNP binding pocket consists of four Ξ±-helices (Ξ±26, Ξ±28, Ξ±27 and Ξ±30) and forms a shape resembling a half-fist (Fig 3A and 3B). RESULTS | |
| 55 58 Ξ±26 structure_element The AMP-PNP binding pocket consists of four Ξ±-helices (Ξ±26, Ξ±28, Ξ±27 and Ξ±30) and forms a shape resembling a half-fist (Fig 3A and 3B). RESULTS | |
| 60 63 Ξ±28 structure_element The AMP-PNP binding pocket consists of four Ξ±-helices (Ξ±26, Ξ±28, Ξ±27 and Ξ±30) and forms a shape resembling a half-fist (Fig 3A and 3B). RESULTS | |
| 65 68 Ξ±27 structure_element The AMP-PNP binding pocket consists of four Ξ±-helices (Ξ±26, Ξ±28, Ξ±27 and Ξ±30) and forms a shape resembling a half-fist (Fig 3A and 3B). RESULTS | |
| 73 76 Ξ±30 structure_element The AMP-PNP binding pocket consists of four Ξ±-helices (Ξ±26, Ξ±28, Ξ±27 and Ξ±30) and forms a shape resembling a half-fist (Fig 3A and 3B). RESULTS | |
| 90 118 shape resembling a half-fist protein_state The AMP-PNP binding pocket consists of four Ξ±-helices (Ξ±26, Ξ±28, Ξ±27 and Ξ±30) and forms a shape resembling a half-fist (Fig 3A and 3B). RESULTS | |
| 22 29 AMP-PNP chemical The head group of the AMP-PNP is embedded in a pocket surrounded by Trp383, Asn380, Gly376 and Gly377. RESULTS | |
| 47 53 pocket site The head group of the AMP-PNP is embedded in a pocket surrounded by Trp383, Asn380, Gly376 and Gly377. RESULTS | |
| 68 74 Trp383 residue_name_number The head group of the AMP-PNP is embedded in a pocket surrounded by Trp383, Asn380, Gly376 and Gly377. RESULTS | |
| 76 82 Asn380 residue_name_number The head group of the AMP-PNP is embedded in a pocket surrounded by Trp383, Asn380, Gly376 and Gly377. RESULTS | |
| 84 90 Gly376 residue_name_number The head group of the AMP-PNP is embedded in a pocket surrounded by Trp383, Asn380, Gly376 and Gly377. RESULTS | |
| 95 101 Gly377 residue_name_number The head group of the AMP-PNP is embedded in a pocket surrounded by Trp383, Asn380, Gly376 and Gly377. RESULTS | |
| 19 26 AMP-PNP chemical The purine ring of AMP-PNP is positioned in parallel to the indole ring of Trp383. RESULTS | |
| 75 81 Trp383 residue_name_number The purine ring of AMP-PNP is positioned in parallel to the indole ring of Trp383. RESULTS | |
| 19 34 hydrogen-bonded bond_interaction In addition, it is hydrogen-bonded with the side chain amide of Asn380 (Fig 3B). RESULTS | |
| 64 70 Asn380 residue_name_number In addition, it is hydrogen-bonded with the side chain amide of Asn380 (Fig 3B). RESULTS | |
| 12 19 AMP-PNP chemical The tail of AMP-PNP points to the hinge region of SePSK, and its Ξ±-phosphate and Ξ²-phosphate groups are stabilized by Gly376 and Ser243, respectively. RESULTS | |
| 34 46 hinge region structure_element The tail of AMP-PNP points to the hinge region of SePSK, and its Ξ±-phosphate and Ξ²-phosphate groups are stabilized by Gly376 and Ser243, respectively. RESULTS | |
| 50 55 SePSK protein The tail of AMP-PNP points to the hinge region of SePSK, and its Ξ±-phosphate and Ξ²-phosphate groups are stabilized by Gly376 and Ser243, respectively. RESULTS | |
| 67 76 phosphate chemical The tail of AMP-PNP points to the hinge region of SePSK, and its Ξ±-phosphate and Ξ²-phosphate groups are stabilized by Gly376 and Ser243, respectively. RESULTS | |
| 83 92 phosphate chemical The tail of AMP-PNP points to the hinge region of SePSK, and its Ξ±-phosphate and Ξ²-phosphate groups are stabilized by Gly376 and Ser243, respectively. RESULTS | |
| 118 124 Gly376 residue_name_number The tail of AMP-PNP points to the hinge region of SePSK, and its Ξ±-phosphate and Ξ²-phosphate groups are stabilized by Gly376 and Ser243, respectively. RESULTS | |
| 129 135 Ser243 residue_name_number The tail of AMP-PNP points to the hinge region of SePSK, and its Ξ±-phosphate and Ξ²-phosphate groups are stabilized by Gly376 and Ser243, respectively. RESULTS | |
| 15 24 structure evidence Together, this structure clearly shows that the AMP-PNP-Ξ²-phosphate is sticking out of the ATP binding pocket, thus the Ξ³-phosphate group is at the empty space between domain I and domain II and is unconstrained in its movement by the protein. RESULTS | |
| 48 55 AMP-PNP chemical Together, this structure clearly shows that the AMP-PNP-Ξ²-phosphate is sticking out of the ATP binding pocket, thus the Ξ³-phosphate group is at the empty space between domain I and domain II and is unconstrained in its movement by the protein. RESULTS | |
| 58 67 phosphate chemical Together, this structure clearly shows that the AMP-PNP-Ξ²-phosphate is sticking out of the ATP binding pocket, thus the Ξ³-phosphate group is at the empty space between domain I and domain II and is unconstrained in its movement by the protein. RESULTS | |
| 91 109 ATP binding pocket site Together, this structure clearly shows that the AMP-PNP-Ξ²-phosphate is sticking out of the ATP binding pocket, thus the Ξ³-phosphate group is at the empty space between domain I and domain II and is unconstrained in its movement by the protein. RESULTS | |
| 122 131 phosphate chemical Together, this structure clearly shows that the AMP-PNP-Ξ²-phosphate is sticking out of the ATP binding pocket, thus the Ξ³-phosphate group is at the empty space between domain I and domain II and is unconstrained in its movement by the protein. RESULTS | |
| 168 176 domain I structure_element Together, this structure clearly shows that the AMP-PNP-Ξ²-phosphate is sticking out of the ATP binding pocket, thus the Ξ³-phosphate group is at the empty space between domain I and domain II and is unconstrained in its movement by the protein. RESULTS | |
| 181 190 domain II structure_element Together, this structure clearly shows that the AMP-PNP-Ξ²-phosphate is sticking out of the ATP binding pocket, thus the Ξ³-phosphate group is at the empty space between domain I and domain II and is unconstrained in its movement by the protein. RESULTS | |
| 0 9 Structure evidence Structure of SePSK in complex with AMP-PNP. FIG | |
| 13 18 SePSK protein Structure of SePSK in complex with AMP-PNP. FIG | |
| 19 34 in complex with protein_state Structure of SePSK in complex with AMP-PNP. FIG | |
| 35 42 AMP-PNP chemical Structure of SePSK in complex with AMP-PNP. FIG | |
| 8 24 electron density evidence (A) The electron density of AMP-PNP. FIG | |
| 28 35 AMP-PNP chemical (A) The electron density of AMP-PNP. FIG | |
| 4 9 SePSK protein The SePSK structure is shown in the electrostatic potential surface mode. FIG | |
| 10 19 structure evidence The SePSK structure is shown in the electrostatic potential surface mode. FIG | |
| 4 11 AMP-PNP chemical The AMP-PNP is depicted as sticks with its ΗFoΗ-ΗFcΗ map contoured at 3 Ο shown as cyan mesh. FIG | |
| 43 56 ΗFoΗ-ΗFcΗ map evidence The AMP-PNP is depicted as sticks with its ΗFoΗ-ΗFcΗ map contoured at 3 Ο shown as cyan mesh. FIG | |
| 8 30 AMP-PNP binding pocket site (B) The AMP-PNP binding pocket. FIG | |
| 12 19 AMP-PNP chemical The head of AMP-PNP is sandwiched by four residues (Leu293, Gly376, Gly377 and Trp383). FIG | |
| 23 36 sandwiched by bond_interaction The head of AMP-PNP is sandwiched by four residues (Leu293, Gly376, Gly377 and Trp383). FIG | |
| 52 58 Leu293 residue_name_number The head of AMP-PNP is sandwiched by four residues (Leu293, Gly376, Gly377 and Trp383). FIG | |
| 60 66 Gly376 residue_name_number The head of AMP-PNP is sandwiched by four residues (Leu293, Gly376, Gly377 and Trp383). FIG | |
| 68 74 Gly377 residue_name_number The head of AMP-PNP is sandwiched by four residues (Leu293, Gly376, Gly377 and Trp383). FIG | |
| 79 85 Trp383 residue_name_number The head of AMP-PNP is sandwiched by four residues (Leu293, Gly376, Gly377 and Trp383). FIG | |
| 9 18 Ξ±-helices structure_element The four Ξ±-helices (Ξ±26, Ξ±28, Ξ±27 and Ξ±30) are labeled in red. FIG | |
| 20 23 Ξ±26 structure_element The four Ξ±-helices (Ξ±26, Ξ±28, Ξ±27 and Ξ±30) are labeled in red. FIG | |
| 25 28 Ξ±28 structure_element The four Ξ±-helices (Ξ±26, Ξ±28, Ξ±27 and Ξ±30) are labeled in red. FIG | |
| 30 33 Ξ±27 structure_element The four Ξ±-helices (Ξ±26, Ξ±28, Ξ±27 and Ξ±30) are labeled in red. FIG | |
| 38 41 Ξ±30 structure_element The four Ξ±-helices (Ξ±26, Ξ±28, Ξ±27 and Ξ±30) are labeled in red. FIG | |
| 4 11 AMP-PNP chemical The AMP-PNP and coordinated residues are shown as sticks. FIG | |
| 14 36 substrate binding site site The potential substrate binding site in SePSK RESULTS | |
| 40 45 SePSK protein The potential substrate binding site in SePSK RESULTS | |
| 21 36 activity assays experimental_method The results from our activity assays suggested that SePSK has D-ribulose kinase activity. RESULTS | |
| 52 57 SePSK protein The results from our activity assays suggested that SePSK has D-ribulose kinase activity. RESULTS | |
| 62 79 D-ribulose kinase protein_type The results from our activity assays suggested that SePSK has D-ribulose kinase activity. RESULTS | |
| 53 58 SePSK protein To better understand the interaction pattern between SePSK and D-ribulose, the apo-SePSK crystals were soaked into the reservoir with 10 mM D-ribulose (RBL) and the RBL-SePSK structure was solved. RESULTS | |
| 63 73 D-ribulose chemical To better understand the interaction pattern between SePSK and D-ribulose, the apo-SePSK crystals were soaked into the reservoir with 10 mM D-ribulose (RBL) and the RBL-SePSK structure was solved. RESULTS | |
| 79 82 apo protein_state To better understand the interaction pattern between SePSK and D-ribulose, the apo-SePSK crystals were soaked into the reservoir with 10 mM D-ribulose (RBL) and the RBL-SePSK structure was solved. RESULTS | |
| 83 88 SePSK protein To better understand the interaction pattern between SePSK and D-ribulose, the apo-SePSK crystals were soaked into the reservoir with 10 mM D-ribulose (RBL) and the RBL-SePSK structure was solved. RESULTS | |
| 89 114 crystals were soaked into experimental_method To better understand the interaction pattern between SePSK and D-ribulose, the apo-SePSK crystals were soaked into the reservoir with 10 mM D-ribulose (RBL) and the RBL-SePSK structure was solved. RESULTS | |
| 119 128 reservoir experimental_method To better understand the interaction pattern between SePSK and D-ribulose, the apo-SePSK crystals were soaked into the reservoir with 10 mM D-ribulose (RBL) and the RBL-SePSK structure was solved. RESULTS | |
| 140 150 D-ribulose chemical To better understand the interaction pattern between SePSK and D-ribulose, the apo-SePSK crystals were soaked into the reservoir with 10 mM D-ribulose (RBL) and the RBL-SePSK structure was solved. RESULTS | |
| 152 155 RBL chemical To better understand the interaction pattern between SePSK and D-ribulose, the apo-SePSK crystals were soaked into the reservoir with 10 mM D-ribulose (RBL) and the RBL-SePSK structure was solved. RESULTS | |
| 165 174 RBL-SePSK complex_assembly To better understand the interaction pattern between SePSK and D-ribulose, the apo-SePSK crystals were soaked into the reservoir with 10 mM D-ribulose (RBL) and the RBL-SePSK structure was solved. RESULTS | |
| 175 184 structure evidence To better understand the interaction pattern between SePSK and D-ribulose, the apo-SePSK crystals were soaked into the reservoir with 10 mM D-ribulose (RBL) and the RBL-SePSK structure was solved. RESULTS | |
| 189 195 solved experimental_method To better understand the interaction pattern between SePSK and D-ribulose, the apo-SePSK crystals were soaked into the reservoir with 10 mM D-ribulose (RBL) and the RBL-SePSK structure was solved. RESULTS | |
| 33 51 electron densities evidence As shown in S6 Fig, two residual electron densities are visible in domain I, which can be interpreted as two D-ribulose molecules with reasonable fit. RESULTS | |
| 67 75 domain I structure_element As shown in S6 Fig, two residual electron densities are visible in domain I, which can be interpreted as two D-ribulose molecules with reasonable fit. RESULTS | |
| 109 119 D-ribulose chemical As shown in S6 Fig, two residual electron densities are visible in domain I, which can be interpreted as two D-ribulose molecules with reasonable fit. RESULTS | |
| 76 86 D-ribulose chemical As shown in Fig 4A, the nearest distance between the carbon skeleton of two D-ribulose molecules are approx. RESULTS | |
| 7 11 RBL1 residue_name_number 7.1 Γ (RBL1-C4 and RBL2-C1). RESULTS | |
| 19 23 RBL2 residue_name_number 7.1 Γ (RBL1-C4 and RBL2-C1). RESULTS | |
| 0 4 RBL1 residue_name_number RBL1 is located in the pocket consisting of Ξ±21 and the loop between Ξ²6 and Ξ²7. RESULTS | |
| 23 29 pocket site RBL1 is located in the pocket consisting of Ξ±21 and the loop between Ξ²6 and Ξ²7. RESULTS | |
| 44 47 Ξ±21 structure_element RBL1 is located in the pocket consisting of Ξ±21 and the loop between Ξ²6 and Ξ²7. RESULTS | |
| 56 60 loop structure_element RBL1 is located in the pocket consisting of Ξ±21 and the loop between Ξ²6 and Ξ²7. RESULTS | |
| 69 78 Ξ²6 and Ξ²7 structure_element RBL1 is located in the pocket consisting of Ξ±21 and the loop between Ξ²6 and Ξ²7. RESULTS | |
| 17 21 RBL1 residue_name_number The O4 and O5 of RBL1 are coordinated with the side chain carboxyl group of Asp221. RESULTS | |
| 26 42 coordinated with bond_interaction The O4 and O5 of RBL1 are coordinated with the side chain carboxyl group of Asp221. RESULTS | |
| 76 82 Asp221 residue_name_number The O4 and O5 of RBL1 are coordinated with the side chain carboxyl group of Asp221. RESULTS | |
| 23 27 RBL1 residue_name_number Furthermore, the O2 of RBL1 interacts with the main chain amide nitrogen of Ser72 (Fig 4B). RESULTS | |
| 28 42 interacts with bond_interaction Furthermore, the O2 of RBL1 interacts with the main chain amide nitrogen of Ser72 (Fig 4B). RESULTS | |
| 76 81 Ser72 residue_name_number Furthermore, the O2 of RBL1 interacts with the main chain amide nitrogen of Ser72 (Fig 4B). RESULTS | |
| 5 11 pocket site This pocket is at a similar position of substrate binding site of other sugar kinase, such as L-ribulokinase (PDB code: 3QDK) (S7 Fig). RESULTS | |
| 40 62 substrate binding site site This pocket is at a similar position of substrate binding site of other sugar kinase, such as L-ribulokinase (PDB code: 3QDK) (S7 Fig). RESULTS | |
| 72 84 sugar kinase protein_type This pocket is at a similar position of substrate binding site of other sugar kinase, such as L-ribulokinase (PDB code: 3QDK) (S7 Fig). RESULTS | |
| 94 108 L-ribulokinase protein This pocket is at a similar position of substrate binding site of other sugar kinase, such as L-ribulokinase (PDB code: 3QDK) (S7 Fig). RESULTS | |
| 9 30 structural comparison experimental_method However, structural comparison shows that the substrate ligating residues between the two structures are not strictly conserved. RESULTS | |
| 90 100 structures evidence However, structural comparison shows that the substrate ligating residues between the two structures are not strictly conserved. RESULTS | |
| 105 127 not strictly conserved protein_state However, structural comparison shows that the substrate ligating residues between the two structures are not strictly conserved. RESULTS | |
| 13 23 structures evidence Based on the structures, the ligating residues of RBL1 in RBL-SePSK structure are Ser72, Asp221 and Ser222, and the interacting residues of L-ribulose with L-ribulokinase are Ala96, Lys208, Asp274 and Glu329 (S7 Fig). RESULTS | |
| 50 54 RBL1 residue_name_number Based on the structures, the ligating residues of RBL1 in RBL-SePSK structure are Ser72, Asp221 and Ser222, and the interacting residues of L-ribulose with L-ribulokinase are Ala96, Lys208, Asp274 and Glu329 (S7 Fig). RESULTS | |
| 58 67 RBL-SePSK complex_assembly Based on the structures, the ligating residues of RBL1 in RBL-SePSK structure are Ser72, Asp221 and Ser222, and the interacting residues of L-ribulose with L-ribulokinase are Ala96, Lys208, Asp274 and Glu329 (S7 Fig). RESULTS | |
| 68 77 structure evidence Based on the structures, the ligating residues of RBL1 in RBL-SePSK structure are Ser72, Asp221 and Ser222, and the interacting residues of L-ribulose with L-ribulokinase are Ala96, Lys208, Asp274 and Glu329 (S7 Fig). RESULTS | |
| 82 87 Ser72 residue_name_number Based on the structures, the ligating residues of RBL1 in RBL-SePSK structure are Ser72, Asp221 and Ser222, and the interacting residues of L-ribulose with L-ribulokinase are Ala96, Lys208, Asp274 and Glu329 (S7 Fig). RESULTS | |
| 89 95 Asp221 residue_name_number Based on the structures, the ligating residues of RBL1 in RBL-SePSK structure are Ser72, Asp221 and Ser222, and the interacting residues of L-ribulose with L-ribulokinase are Ala96, Lys208, Asp274 and Glu329 (S7 Fig). RESULTS | |
| 100 106 Ser222 residue_name_number Based on the structures, the ligating residues of RBL1 in RBL-SePSK structure are Ser72, Asp221 and Ser222, and the interacting residues of L-ribulose with L-ribulokinase are Ala96, Lys208, Asp274 and Glu329 (S7 Fig). RESULTS | |
| 140 150 L-ribulose chemical Based on the structures, the ligating residues of RBL1 in RBL-SePSK structure are Ser72, Asp221 and Ser222, and the interacting residues of L-ribulose with L-ribulokinase are Ala96, Lys208, Asp274 and Glu329 (S7 Fig). RESULTS | |
| 156 170 L-ribulokinase protein Based on the structures, the ligating residues of RBL1 in RBL-SePSK structure are Ser72, Asp221 and Ser222, and the interacting residues of L-ribulose with L-ribulokinase are Ala96, Lys208, Asp274 and Glu329 (S7 Fig). RESULTS | |
| 175 180 Ala96 residue_name_number Based on the structures, the ligating residues of RBL1 in RBL-SePSK structure are Ser72, Asp221 and Ser222, and the interacting residues of L-ribulose with L-ribulokinase are Ala96, Lys208, Asp274 and Glu329 (S7 Fig). RESULTS | |
| 182 188 Lys208 residue_name_number Based on the structures, the ligating residues of RBL1 in RBL-SePSK structure are Ser72, Asp221 and Ser222, and the interacting residues of L-ribulose with L-ribulokinase are Ala96, Lys208, Asp274 and Glu329 (S7 Fig). RESULTS | |
| 190 196 Asp274 residue_name_number Based on the structures, the ligating residues of RBL1 in RBL-SePSK structure are Ser72, Asp221 and Ser222, and the interacting residues of L-ribulose with L-ribulokinase are Ala96, Lys208, Asp274 and Glu329 (S7 Fig). RESULTS | |
| 201 207 Glu329 residue_name_number Based on the structures, the ligating residues of RBL1 in RBL-SePSK structure are Ser72, Asp221 and Ser222, and the interacting residues of L-ribulose with L-ribulokinase are Ala96, Lys208, Asp274 and Glu329 (S7 Fig). RESULTS | |
| 0 6 Glu329 residue_name_number Glu329 in 3QDK has no counterpart in RBL-SePSK structure. RESULTS | |
| 37 46 RBL-SePSK complex_assembly Glu329 in 3QDK has no counterpart in RBL-SePSK structure. RESULTS | |
| 47 56 structure evidence Glu329 in 3QDK has no counterpart in RBL-SePSK structure. RESULTS | |
| 22 28 Lys208 residue_name_number In addition, although Lys208 of L-ribulokinase has the corresponding residue (Lys163) in RBL-SePSK structure, the hydrogen bond of Lys163 is broken because of the conformational change of two Ξ±-helices (Ξ±9 and Ξ±13) of SePSK. RESULTS | |
| 32 46 L-ribulokinase protein In addition, although Lys208 of L-ribulokinase has the corresponding residue (Lys163) in RBL-SePSK structure, the hydrogen bond of Lys163 is broken because of the conformational change of two Ξ±-helices (Ξ±9 and Ξ±13) of SePSK. RESULTS | |
| 78 84 Lys163 residue_name_number In addition, although Lys208 of L-ribulokinase has the corresponding residue (Lys163) in RBL-SePSK structure, the hydrogen bond of Lys163 is broken because of the conformational change of two Ξ±-helices (Ξ±9 and Ξ±13) of SePSK. RESULTS | |
| 89 98 RBL-SePSK complex_assembly In addition, although Lys208 of L-ribulokinase has the corresponding residue (Lys163) in RBL-SePSK structure, the hydrogen bond of Lys163 is broken because of the conformational change of two Ξ±-helices (Ξ±9 and Ξ±13) of SePSK. RESULTS | |
| 99 108 structure evidence In addition, although Lys208 of L-ribulokinase has the corresponding residue (Lys163) in RBL-SePSK structure, the hydrogen bond of Lys163 is broken because of the conformational change of two Ξ±-helices (Ξ±9 and Ξ±13) of SePSK. RESULTS | |
| 114 127 hydrogen bond bond_interaction In addition, although Lys208 of L-ribulokinase has the corresponding residue (Lys163) in RBL-SePSK structure, the hydrogen bond of Lys163 is broken because of the conformational change of two Ξ±-helices (Ξ±9 and Ξ±13) of SePSK. RESULTS | |
| 131 137 Lys163 residue_name_number In addition, although Lys208 of L-ribulokinase has the corresponding residue (Lys163) in RBL-SePSK structure, the hydrogen bond of Lys163 is broken because of the conformational change of two Ξ±-helices (Ξ±9 and Ξ±13) of SePSK. RESULTS | |
| 192 201 Ξ±-helices structure_element In addition, although Lys208 of L-ribulokinase has the corresponding residue (Lys163) in RBL-SePSK structure, the hydrogen bond of Lys163 is broken because of the conformational change of two Ξ±-helices (Ξ±9 and Ξ±13) of SePSK. RESULTS | |
| 203 205 Ξ±9 structure_element In addition, although Lys208 of L-ribulokinase has the corresponding residue (Lys163) in RBL-SePSK structure, the hydrogen bond of Lys163 is broken because of the conformational change of two Ξ±-helices (Ξ±9 and Ξ±13) of SePSK. RESULTS | |
| 210 213 Ξ±13 structure_element In addition, although Lys208 of L-ribulokinase has the corresponding residue (Lys163) in RBL-SePSK structure, the hydrogen bond of Lys163 is broken because of the conformational change of two Ξ±-helices (Ξ±9 and Ξ±13) of SePSK. RESULTS | |
| 218 223 SePSK protein In addition, although Lys208 of L-ribulokinase has the corresponding residue (Lys163) in RBL-SePSK structure, the hydrogen bond of Lys163 is broken because of the conformational change of two Ξ±-helices (Ξ±9 and Ξ±13) of SePSK. RESULTS | |
| 15 25 D-ribulose chemical The binding of D-ribulose (RBL) with SePSK. FIG | |
| 27 30 RBL chemical The binding of D-ribulose (RBL) with SePSK. FIG | |
| 37 42 SePSK protein The binding of D-ribulose (RBL) with SePSK. FIG | |
| 8 43 electrostatic potential surface map evidence (A) The electrostatic potential surface map of RBL-SePSK and a zoom-in view of RBL binding site. FIG | |
| 47 56 RBL-SePSK complex_assembly (A) The electrostatic potential surface map of RBL-SePSK and a zoom-in view of RBL binding site. FIG | |
| 79 95 RBL binding site site (A) The electrostatic potential surface map of RBL-SePSK and a zoom-in view of RBL binding site. FIG | |
| 4 8 RBL1 residue_name_number The RBL1 and RBL2 are depicted as sticks. (B) Interaction of two D-ribulose molecules (RBL1 and RBL2) with SePSK. FIG | |
| 13 17 RBL2 residue_name_number The RBL1 and RBL2 are depicted as sticks. (B) Interaction of two D-ribulose molecules (RBL1 and RBL2) with SePSK. FIG | |
| 65 75 D-ribulose chemical The RBL1 and RBL2 are depicted as sticks. (B) Interaction of two D-ribulose molecules (RBL1 and RBL2) with SePSK. FIG | |
| 87 91 RBL1 residue_name_number The RBL1 and RBL2 are depicted as sticks. (B) Interaction of two D-ribulose molecules (RBL1 and RBL2) with SePSK. FIG | |
| 96 100 RBL2 residue_name_number The RBL1 and RBL2 are depicted as sticks. (B) Interaction of two D-ribulose molecules (RBL1 and RBL2) with SePSK. FIG | |
| 107 112 SePSK protein The RBL1 and RBL2 are depicted as sticks. (B) Interaction of two D-ribulose molecules (RBL1 and RBL2) with SePSK. FIG | |
| 4 7 RBL chemical The RBL molecules (carbon atoms colored yellow) and amino acid residues of SePSK (carbon atoms colored green) involved in RBL interaction are shown as sticks. FIG | |
| 75 80 SePSK protein The RBL molecules (carbon atoms colored yellow) and amino acid residues of SePSK (carbon atoms colored green) involved in RBL interaction are shown as sticks. FIG | |
| 122 125 RBL chemical The RBL molecules (carbon atoms colored yellow) and amino acid residues of SePSK (carbon atoms colored green) involved in RBL interaction are shown as sticks. FIG | |
| 4 18 hydrogen bonds bond_interaction The hydrogen bonds are indicated by the black dashed lines and the numbers near the dashed lines are the distances (Γ ). (C) The binding affinity assays of SePSK with D-ribulose. FIG | |
| 128 151 binding affinity assays experimental_method The hydrogen bonds are indicated by the black dashed lines and the numbers near the dashed lines are the distances (Γ ). (C) The binding affinity assays of SePSK with D-ribulose. FIG | |
| 155 160 SePSK protein The hydrogen bonds are indicated by the black dashed lines and the numbers near the dashed lines are the distances (Γ ). (C) The binding affinity assays of SePSK with D-ribulose. FIG | |
| 166 176 D-ribulose chemical The hydrogen bonds are indicated by the black dashed lines and the numbers near the dashed lines are the distances (Γ ). (C) The binding affinity assays of SePSK with D-ribulose. FIG | |
| 0 25 Single-cycle kinetic data experimental_method Single-cycle kinetic data are reflecting the interaction of SePSK and D8A-SePSK with D-ribulose. FIG | |
| 60 65 SePSK protein Single-cycle kinetic data are reflecting the interaction of SePSK and D8A-SePSK with D-ribulose. FIG | |
| 70 73 D8A mutant Single-cycle kinetic data are reflecting the interaction of SePSK and D8A-SePSK with D-ribulose. FIG | |
| 74 79 SePSK protein Single-cycle kinetic data are reflecting the interaction of SePSK and D8A-SePSK with D-ribulose. FIG | |
| 85 95 D-ribulose chemical Single-cycle kinetic data are reflecting the interaction of SePSK and D8A-SePSK with D-ribulose. FIG | |
| 26 37 sensorgrams evidence It shows two experimental sensorgrams after minus the empty sensorgrams. FIG | |
| 60 71 sensorgrams evidence It shows two experimental sensorgrams after minus the empty sensorgrams. FIG | |
| 92 101 wild type protein_state The original data is shown as black curve, and the fitted data is shown as different color (wild type SePSK: red curve, D8A-SePSK: green curve). FIG | |
| 102 107 SePSK protein The original data is shown as black curve, and the fitted data is shown as different color (wild type SePSK: red curve, D8A-SePSK: green curve). FIG | |
| 120 123 D8A mutant The original data is shown as black curve, and the fitted data is shown as different color (wild type SePSK: red curve, D8A-SePSK: green curve). FIG | |
| 124 129 SePSK protein The original data is shown as black curve, and the fitted data is shown as different color (wild type SePSK: red curve, D8A-SePSK: green curve). FIG | |
| 0 26 Dissociation rate constant evidence Dissociation rate constant of wild type and D8A-SePSK are 3 ms-1 and 9 ms-1, respectively. FIG | |
| 30 39 wild type protein_state Dissociation rate constant of wild type and D8A-SePSK are 3 ms-1 and 9 ms-1, respectively. FIG | |
| 44 47 D8A mutant Dissociation rate constant of wild type and D8A-SePSK are 3 ms-1 and 9 ms-1, respectively. FIG | |
| 48 53 SePSK protein Dissociation rate constant of wild type and D8A-SePSK are 3 ms-1 and 9 ms-1, respectively. FIG | |
| 4 18 binding pocket site The binding pocket of RBL2 with relatively weak electron density is near the N-terminal region of SePSK and is negatively charged. RESULTS | |
| 22 26 RBL2 residue_name_number The binding pocket of RBL2 with relatively weak electron density is near the N-terminal region of SePSK and is negatively charged. RESULTS | |
| 48 64 electron density evidence The binding pocket of RBL2 with relatively weak electron density is near the N-terminal region of SePSK and is negatively charged. RESULTS | |
| 98 103 SePSK protein The binding pocket of RBL2 with relatively weak electron density is near the N-terminal region of SePSK and is negatively charged. RESULTS | |
| 18 22 Asp8 residue_name_number The side chain of Asp8 interacts strongly with O3 and O4 of RBL2. RESULTS | |
| 23 46 interacts strongly with bond_interaction The side chain of Asp8 interacts strongly with O3 and O4 of RBL2. RESULTS | |
| 60 64 RBL2 residue_name_number The side chain of Asp8 interacts strongly with O3 and O4 of RBL2. RESULTS | |
| 22 27 Ser12 residue_name_number The hydroxyl group of Ser12 coordinates with O2 of RBL2. RESULTS | |
| 28 44 coordinates with bond_interaction The hydroxyl group of Ser12 coordinates with O2 of RBL2. RESULTS | |
| 51 55 RBL2 residue_name_number The hydroxyl group of Ser12 coordinates with O2 of RBL2. RESULTS | |
| 32 37 Gly13 residue_name_number The backbone amide nitrogens of Gly13 and Arg15 also keep hydrogen bonds with RBL2 (Fig 4B). RESULTS | |
| 42 47 Arg15 residue_name_number The backbone amide nitrogens of Gly13 and Arg15 also keep hydrogen bonds with RBL2 (Fig 4B). RESULTS | |
| 58 72 hydrogen bonds bond_interaction The backbone amide nitrogens of Gly13 and Arg15 also keep hydrogen bonds with RBL2 (Fig 4B). RESULTS | |
| 78 82 RBL2 residue_name_number The backbone amide nitrogens of Gly13 and Arg15 also keep hydrogen bonds with RBL2 (Fig 4B). RESULTS | |
| 0 21 Structural comparison experimental_method Structural comparison of SePSK and AtXK-1 showed that while the RBL1 binding pocket is conserved, the RBL2 pocket is disrupted in AtXK-1 structure, despite the fact that the residues interacting with RBL2 are highly conserved between the two proteins. RESULTS | |
| 25 30 SePSK protein Structural comparison of SePSK and AtXK-1 showed that while the RBL1 binding pocket is conserved, the RBL2 pocket is disrupted in AtXK-1 structure, despite the fact that the residues interacting with RBL2 are highly conserved between the two proteins. RESULTS | |
| 35 41 AtXK-1 protein Structural comparison of SePSK and AtXK-1 showed that while the RBL1 binding pocket is conserved, the RBL2 pocket is disrupted in AtXK-1 structure, despite the fact that the residues interacting with RBL2 are highly conserved between the two proteins. RESULTS | |
| 64 83 RBL1 binding pocket site Structural comparison of SePSK and AtXK-1 showed that while the RBL1 binding pocket is conserved, the RBL2 pocket is disrupted in AtXK-1 structure, despite the fact that the residues interacting with RBL2 are highly conserved between the two proteins. RESULTS | |
| 87 96 conserved protein_state Structural comparison of SePSK and AtXK-1 showed that while the RBL1 binding pocket is conserved, the RBL2 pocket is disrupted in AtXK-1 structure, despite the fact that the residues interacting with RBL2 are highly conserved between the two proteins. RESULTS | |
| 102 113 RBL2 pocket site Structural comparison of SePSK and AtXK-1 showed that while the RBL1 binding pocket is conserved, the RBL2 pocket is disrupted in AtXK-1 structure, despite the fact that the residues interacting with RBL2 are highly conserved between the two proteins. RESULTS | |
| 130 136 AtXK-1 protein Structural comparison of SePSK and AtXK-1 showed that while the RBL1 binding pocket is conserved, the RBL2 pocket is disrupted in AtXK-1 structure, despite the fact that the residues interacting with RBL2 are highly conserved between the two proteins. RESULTS | |
| 137 146 structure evidence Structural comparison of SePSK and AtXK-1 showed that while the RBL1 binding pocket is conserved, the RBL2 pocket is disrupted in AtXK-1 structure, despite the fact that the residues interacting with RBL2 are highly conserved between the two proteins. RESULTS | |
| 200 204 RBL2 residue_name_number Structural comparison of SePSK and AtXK-1 showed that while the RBL1 binding pocket is conserved, the RBL2 pocket is disrupted in AtXK-1 structure, despite the fact that the residues interacting with RBL2 are highly conserved between the two proteins. RESULTS | |
| 209 225 highly conserved protein_state Structural comparison of SePSK and AtXK-1 showed that while the RBL1 binding pocket is conserved, the RBL2 pocket is disrupted in AtXK-1 structure, despite the fact that the residues interacting with RBL2 are highly conserved between the two proteins. RESULTS | |
| 7 16 RBL-SePSK complex_assembly In the RBL-SePSK structure, a 2.6 Γ hydrogen bond is present between RBL2 and Ser12 (Fig 4B), while in the AtXK-1 structure this hydrogen bond with the corresponding residue (Ser22) is broken. RESULTS | |
| 17 26 structure evidence In the RBL-SePSK structure, a 2.6 Γ hydrogen bond is present between RBL2 and Ser12 (Fig 4B), while in the AtXK-1 structure this hydrogen bond with the corresponding residue (Ser22) is broken. RESULTS | |
| 36 49 hydrogen bond bond_interaction In the RBL-SePSK structure, a 2.6 Γ hydrogen bond is present between RBL2 and Ser12 (Fig 4B), while in the AtXK-1 structure this hydrogen bond with the corresponding residue (Ser22) is broken. RESULTS | |
| 69 73 RBL2 residue_name_number In the RBL-SePSK structure, a 2.6 Γ hydrogen bond is present between RBL2 and Ser12 (Fig 4B), while in the AtXK-1 structure this hydrogen bond with the corresponding residue (Ser22) is broken. RESULTS | |
| 78 83 Ser12 residue_name_number In the RBL-SePSK structure, a 2.6 Γ hydrogen bond is present between RBL2 and Ser12 (Fig 4B), while in the AtXK-1 structure this hydrogen bond with the corresponding residue (Ser22) is broken. RESULTS | |
| 107 113 AtXK-1 protein In the RBL-SePSK structure, a 2.6 Γ hydrogen bond is present between RBL2 and Ser12 (Fig 4B), while in the AtXK-1 structure this hydrogen bond with the corresponding residue (Ser22) is broken. RESULTS | |
| 114 123 structure evidence In the RBL-SePSK structure, a 2.6 Γ hydrogen bond is present between RBL2 and Ser12 (Fig 4B), while in the AtXK-1 structure this hydrogen bond with the corresponding residue (Ser22) is broken. RESULTS | |
| 129 142 hydrogen bond bond_interaction In the RBL-SePSK structure, a 2.6 Γ hydrogen bond is present between RBL2 and Ser12 (Fig 4B), while in the AtXK-1 structure this hydrogen bond with the corresponding residue (Ser22) is broken. RESULTS | |
| 175 180 Ser22 residue_name_number In the RBL-SePSK structure, a 2.6 Γ hydrogen bond is present between RBL2 and Ser12 (Fig 4B), while in the AtXK-1 structure this hydrogen bond with the corresponding residue (Ser22) is broken. RESULTS | |
| 71 79 Ξ²-sheets structure_element This break is probably induced by the conformational change of the two Ξ²-sheets (Ξ²1 and Ξ²2), with the result that the linking loop (loop 1) is located further away from the RBL2 binding site. RESULTS | |
| 81 83 Ξ²1 structure_element This break is probably induced by the conformational change of the two Ξ²-sheets (Ξ²1 and Ξ²2), with the result that the linking loop (loop 1) is located further away from the RBL2 binding site. RESULTS | |
| 88 90 Ξ²2 structure_element This break is probably induced by the conformational change of the two Ξ²-sheets (Ξ²1 and Ξ²2), with the result that the linking loop (loop 1) is located further away from the RBL2 binding site. RESULTS | |
| 118 130 linking loop structure_element This break is probably induced by the conformational change of the two Ξ²-sheets (Ξ²1 and Ξ²2), with the result that the linking loop (loop 1) is located further away from the RBL2 binding site. RESULTS | |
| 132 138 loop 1 structure_element This break is probably induced by the conformational change of the two Ξ²-sheets (Ξ²1 and Ξ²2), with the result that the linking loop (loop 1) is located further away from the RBL2 binding site. RESULTS | |
| 173 190 RBL2 binding site site This break is probably induced by the conformational change of the two Ξ²-sheets (Ξ²1 and Ξ²2), with the result that the linking loop (loop 1) is located further away from the RBL2 binding site. RESULTS | |
| 37 43 AtXK-1 protein This change might be the reason that AtXK-1 only shows limited increasing in its ATP hydrolysis ability upon adding D-ribulose as a substrate after comparing with SePSK (Fig 2C). RESULTS | |
| 81 84 ATP chemical This change might be the reason that AtXK-1 only shows limited increasing in its ATP hydrolysis ability upon adding D-ribulose as a substrate after comparing with SePSK (Fig 2C). RESULTS | |
| 116 126 D-ribulose chemical This change might be the reason that AtXK-1 only shows limited increasing in its ATP hydrolysis ability upon adding D-ribulose as a substrate after comparing with SePSK (Fig 2C). RESULTS | |
| 163 168 SePSK protein This change might be the reason that AtXK-1 only shows limited increasing in its ATP hydrolysis ability upon adding D-ribulose as a substrate after comparing with SePSK (Fig 2C). RESULTS | |
| 4 9 SePSK protein Our SePSK structure shows that the Asp8 residue forms strong hydrogen bond with RBL2 (Fig 4B). RESULTS | |
| 10 19 structure evidence Our SePSK structure shows that the Asp8 residue forms strong hydrogen bond with RBL2 (Fig 4B). RESULTS | |
| 35 39 Asp8 residue_name_number Our SePSK structure shows that the Asp8 residue forms strong hydrogen bond with RBL2 (Fig 4B). RESULTS | |
| 61 74 hydrogen bond bond_interaction Our SePSK structure shows that the Asp8 residue forms strong hydrogen bond with RBL2 (Fig 4B). RESULTS | |
| 80 84 RBL2 residue_name_number Our SePSK structure shows that the Asp8 residue forms strong hydrogen bond with RBL2 (Fig 4B). RESULTS | |
| 17 33 enzymatic assays experimental_method In addition, our enzymatic assays indicated that Asp8 is important for the activity of SePSK (Fig 2D). RESULTS | |
| 49 53 Asp8 residue_name_number In addition, our enzymatic assays indicated that Asp8 is important for the activity of SePSK (Fig 2D). RESULTS | |
| 87 92 SePSK protein In addition, our enzymatic assays indicated that Asp8 is important for the activity of SePSK (Fig 2D). RESULTS | |
| 49 65 binding affinity evidence To further verified this result, we measured the binding affinity for D-ribulose of both wild type (WT) and D8A mutant of SePSK using a surface plasmon resonance method. RESULTS | |
| 70 80 D-ribulose chemical To further verified this result, we measured the binding affinity for D-ribulose of both wild type (WT) and D8A mutant of SePSK using a surface plasmon resonance method. RESULTS | |
| 89 98 wild type protein_state To further verified this result, we measured the binding affinity for D-ribulose of both wild type (WT) and D8A mutant of SePSK using a surface plasmon resonance method. RESULTS | |
| 100 102 WT protein_state To further verified this result, we measured the binding affinity for D-ribulose of both wild type (WT) and D8A mutant of SePSK using a surface plasmon resonance method. RESULTS | |
| 108 111 D8A mutant To further verified this result, we measured the binding affinity for D-ribulose of both wild type (WT) and D8A mutant of SePSK using a surface plasmon resonance method. RESULTS | |
| 112 118 mutant protein_state To further verified this result, we measured the binding affinity for D-ribulose of both wild type (WT) and D8A mutant of SePSK using a surface plasmon resonance method. RESULTS | |
| 122 127 SePSK protein To further verified this result, we measured the binding affinity for D-ribulose of both wild type (WT) and D8A mutant of SePSK using a surface plasmon resonance method. RESULTS | |
| 136 168 surface plasmon resonance method experimental_method To further verified this result, we measured the binding affinity for D-ribulose of both wild type (WT) and D8A mutant of SePSK using a surface plasmon resonance method. RESULTS | |
| 28 36 affinity evidence The results showed that the affinity of D8A-SePSK with D-ribulose is weaker than that of WT with a reduction of approx. RESULTS | |
| 40 43 D8A mutant The results showed that the affinity of D8A-SePSK with D-ribulose is weaker than that of WT with a reduction of approx. RESULTS | |
| 44 49 SePSK protein The results showed that the affinity of D8A-SePSK with D-ribulose is weaker than that of WT with a reduction of approx. RESULTS | |
| 55 65 D-ribulose chemical The results showed that the affinity of D8A-SePSK with D-ribulose is weaker than that of WT with a reduction of approx. RESULTS | |
| 89 91 WT protein_state The results showed that the affinity of D8A-SePSK with D-ribulose is weaker than that of WT with a reduction of approx. RESULTS | |
| 0 26 Dissociation rate constant evidence Dissociation rate constant (Kd) of wild type and D8A-SePSK are 3 ms-1 and 9 ms-1, respectively. RESULTS | |
| 28 30 Kd evidence Dissociation rate constant (Kd) of wild type and D8A-SePSK are 3 ms-1 and 9 ms-1, respectively. RESULTS | |
| 35 44 wild type protein_state Dissociation rate constant (Kd) of wild type and D8A-SePSK are 3 ms-1 and 9 ms-1, respectively. RESULTS | |
| 49 52 D8A mutant Dissociation rate constant (Kd) of wild type and D8A-SePSK are 3 ms-1 and 9 ms-1, respectively. RESULTS | |
| 53 58 SePSK protein Dissociation rate constant (Kd) of wild type and D8A-SePSK are 3 ms-1 and 9 ms-1, respectively. RESULTS | |
| 29 52 second RBL binding site site The results implied that the second RBL binding site plays a role in the D-ribulose kinase function of SePSK. RESULTS | |
| 73 90 D-ribulose kinase protein_type The results implied that the second RBL binding site plays a role in the D-ribulose kinase function of SePSK. RESULTS | |
| 103 108 SePSK protein The results implied that the second RBL binding site plays a role in the D-ribulose kinase function of SePSK. RESULTS | |
| 47 57 D-ribulose chemical However, considering the high concentration of D-ribulose used for crystal soaking, as well as the relatively weak electron density of RBL2, it is also possible that the second binding site of D-ribulose in SePSK is an artifact. RESULTS | |
| 67 82 crystal soaking experimental_method However, considering the high concentration of D-ribulose used for crystal soaking, as well as the relatively weak electron density of RBL2, it is also possible that the second binding site of D-ribulose in SePSK is an artifact. RESULTS | |
| 115 131 electron density evidence However, considering the high concentration of D-ribulose used for crystal soaking, as well as the relatively weak electron density of RBL2, it is also possible that the second binding site of D-ribulose in SePSK is an artifact. RESULTS | |
| 135 139 RBL2 residue_name_number However, considering the high concentration of D-ribulose used for crystal soaking, as well as the relatively weak electron density of RBL2, it is also possible that the second binding site of D-ribulose in SePSK is an artifact. RESULTS | |
| 170 189 second binding site site However, considering the high concentration of D-ribulose used for crystal soaking, as well as the relatively weak electron density of RBL2, it is also possible that the second binding site of D-ribulose in SePSK is an artifact. RESULTS | |
| 193 203 D-ribulose chemical However, considering the high concentration of D-ribulose used for crystal soaking, as well as the relatively weak electron density of RBL2, it is also possible that the second binding site of D-ribulose in SePSK is an artifact. RESULTS | |
| 207 212 SePSK protein However, considering the high concentration of D-ribulose used for crystal soaking, as well as the relatively weak electron density of RBL2, it is also possible that the second binding site of D-ribulose in SePSK is an artifact. RESULTS | |
| 35 40 SePSK protein Simulated conformational change of SePSK during the catalytic process RESULTS | |
| 60 68 domain I structure_element It was reported earlier that the crossing angle between the domain I and domain II in FGGY family carbohydrate kinases is different. RESULTS | |
| 73 82 domain II structure_element It was reported earlier that the crossing angle between the domain I and domain II in FGGY family carbohydrate kinases is different. RESULTS | |
| 86 118 FGGY family carbohydrate kinases protein_type It was reported earlier that the crossing angle between the domain I and domain II in FGGY family carbohydrate kinases is different. RESULTS | |
| 79 82 ATP chemical In addition, this difference may be caused by the binding of substrates and/or ATP. RESULTS | |
| 39 51 sugar kinase protein_type As reported previously, members of the sugar kinase family undergo a conformational change to narrow the crossing angle between two domains and reduce the distance between substrate and ATP in order to facilitate the catalytic reaction of phosphorylation of sugar substrates. RESULTS | |
| 186 189 ATP chemical As reported previously, members of the sugar kinase family undergo a conformational change to narrow the crossing angle between two domains and reduce the distance between substrate and ATP in order to facilitate the catalytic reaction of phosphorylation of sugar substrates. RESULTS | |
| 239 254 phosphorylation ptm As reported previously, members of the sugar kinase family undergo a conformational change to narrow the crossing angle between two domains and reduce the distance between substrate and ATP in order to facilitate the catalytic reaction of phosphorylation of sugar substrates. RESULTS | |
| 16 26 structures evidence After comparing structures of apo-SePSK, RBL-SePSK and AMP-PNP-SePSK, we noticed that these structures presented here are similar. RESULTS | |
| 30 33 apo protein_state After comparing structures of apo-SePSK, RBL-SePSK and AMP-PNP-SePSK, we noticed that these structures presented here are similar. RESULTS | |
| 34 39 SePSK protein After comparing structures of apo-SePSK, RBL-SePSK and AMP-PNP-SePSK, we noticed that these structures presented here are similar. RESULTS | |
| 41 50 RBL-SePSK complex_assembly After comparing structures of apo-SePSK, RBL-SePSK and AMP-PNP-SePSK, we noticed that these structures presented here are similar. RESULTS | |
| 55 68 AMP-PNP-SePSK complex_assembly After comparing structures of apo-SePSK, RBL-SePSK and AMP-PNP-SePSK, we noticed that these structures presented here are similar. RESULTS | |
| 92 102 structures evidence After comparing structures of apo-SePSK, RBL-SePSK and AMP-PNP-SePSK, we noticed that these structures presented here are similar. RESULTS | |
| 0 11 Superposing experimental_method Superposing the structures of RBL-SePSK and AMP-PNP-SePSK, the results show that the nearest distance between AMP-PNP Ξ³-phosphate and RBL1/RBL2 is 7.5 Γ (RBL1-O5)/6.7 Γ (RBL2-O1) (S8 Fig). RESULTS | |
| 16 26 structures evidence Superposing the structures of RBL-SePSK and AMP-PNP-SePSK, the results show that the nearest distance between AMP-PNP Ξ³-phosphate and RBL1/RBL2 is 7.5 Γ (RBL1-O5)/6.7 Γ (RBL2-O1) (S8 Fig). RESULTS | |
| 30 39 RBL-SePSK complex_assembly Superposing the structures of RBL-SePSK and AMP-PNP-SePSK, the results show that the nearest distance between AMP-PNP Ξ³-phosphate and RBL1/RBL2 is 7.5 Γ (RBL1-O5)/6.7 Γ (RBL2-O1) (S8 Fig). RESULTS | |
| 44 57 AMP-PNP-SePSK complex_assembly Superposing the structures of RBL-SePSK and AMP-PNP-SePSK, the results show that the nearest distance between AMP-PNP Ξ³-phosphate and RBL1/RBL2 is 7.5 Γ (RBL1-O5)/6.7 Γ (RBL2-O1) (S8 Fig). RESULTS | |
| 110 117 AMP-PNP chemical Superposing the structures of RBL-SePSK and AMP-PNP-SePSK, the results show that the nearest distance between AMP-PNP Ξ³-phosphate and RBL1/RBL2 is 7.5 Γ (RBL1-O5)/6.7 Γ (RBL2-O1) (S8 Fig). RESULTS | |
| 120 129 phosphate chemical Superposing the structures of RBL-SePSK and AMP-PNP-SePSK, the results show that the nearest distance between AMP-PNP Ξ³-phosphate and RBL1/RBL2 is 7.5 Γ (RBL1-O5)/6.7 Γ (RBL2-O1) (S8 Fig). RESULTS | |
| 134 138 RBL1 residue_name_number Superposing the structures of RBL-SePSK and AMP-PNP-SePSK, the results show that the nearest distance between AMP-PNP Ξ³-phosphate and RBL1/RBL2 is 7.5 Γ (RBL1-O5)/6.7 Γ (RBL2-O1) (S8 Fig). RESULTS | |
| 139 143 RBL2 residue_name_number Superposing the structures of RBL-SePSK and AMP-PNP-SePSK, the results show that the nearest distance between AMP-PNP Ξ³-phosphate and RBL1/RBL2 is 7.5 Γ (RBL1-O5)/6.7 Γ (RBL2-O1) (S8 Fig). RESULTS | |
| 154 158 RBL1 residue_name_number Superposing the structures of RBL-SePSK and AMP-PNP-SePSK, the results show that the nearest distance between AMP-PNP Ξ³-phosphate and RBL1/RBL2 is 7.5 Γ (RBL1-O5)/6.7 Γ (RBL2-O1) (S8 Fig). RESULTS | |
| 170 174 RBL2 residue_name_number Superposing the structures of RBL-SePSK and AMP-PNP-SePSK, the results show that the nearest distance between AMP-PNP Ξ³-phosphate and RBL1/RBL2 is 7.5 Γ (RBL1-O5)/6.7 Γ (RBL2-O1) (S8 Fig). RESULTS | |
| 44 53 phosphate chemical This distance is too long to transfer the Ξ³-phosphate group from ATP to the substrate. RESULTS | |
| 65 68 ATP chemical This distance is too long to transfer the Ξ³-phosphate group from ATP to the substrate. RESULTS | |
| 25 30 SePSK protein Since the two domains of SePSK are widely separated in this structure, we hypothesize that our structures of SePSK represent its open form, and that a conformational rearrangement must occur to switch to the closed state in order to facilitate the catalytic process of phosphorylation of sugar substrates. RESULTS | |
| 60 69 structure evidence Since the two domains of SePSK are widely separated in this structure, we hypothesize that our structures of SePSK represent its open form, and that a conformational rearrangement must occur to switch to the closed state in order to facilitate the catalytic process of phosphorylation of sugar substrates. RESULTS | |
| 95 105 structures evidence Since the two domains of SePSK are widely separated in this structure, we hypothesize that our structures of SePSK represent its open form, and that a conformational rearrangement must occur to switch to the closed state in order to facilitate the catalytic process of phosphorylation of sugar substrates. RESULTS | |
| 109 114 SePSK protein Since the two domains of SePSK are widely separated in this structure, we hypothesize that our structures of SePSK represent its open form, and that a conformational rearrangement must occur to switch to the closed state in order to facilitate the catalytic process of phosphorylation of sugar substrates. RESULTS | |
| 129 133 open protein_state Since the two domains of SePSK are widely separated in this structure, we hypothesize that our structures of SePSK represent its open form, and that a conformational rearrangement must occur to switch to the closed state in order to facilitate the catalytic process of phosphorylation of sugar substrates. RESULTS | |
| 208 214 closed protein_state Since the two domains of SePSK are widely separated in this structure, we hypothesize that our structures of SePSK represent its open form, and that a conformational rearrangement must occur to switch to the closed state in order to facilitate the catalytic process of phosphorylation of sugar substrates. RESULTS | |
| 269 284 phosphorylation ptm Since the two domains of SePSK are widely separated in this structure, we hypothesize that our structures of SePSK represent its open form, and that a conformational rearrangement must occur to switch to the closed state in order to facilitate the catalytic process of phosphorylation of sugar substrates. RESULTS | |
| 53 63 simulation experimental_method For studying such potential conformational change, a simulation on the Hingeprot Server was performed to predict the movement of different SePSK domains. RESULTS | |
| 71 87 Hingeprot Server experimental_method For studying such potential conformational change, a simulation on the Hingeprot Server was performed to predict the movement of different SePSK domains. RESULTS | |
| 139 144 SePSK protein For studying such potential conformational change, a simulation on the Hingeprot Server was performed to predict the movement of different SePSK domains. RESULTS | |
| 24 32 domain I structure_element The results showed that domain I and domain II are closer to each other with Ala228 and Thr401 in A2 as Hinge-residues. RESULTS | |
| 37 46 domain II structure_element The results showed that domain I and domain II are closer to each other with Ala228 and Thr401 in A2 as Hinge-residues. RESULTS | |
| 77 83 Ala228 residue_name_number The results showed that domain I and domain II are closer to each other with Ala228 and Thr401 in A2 as Hinge-residues. RESULTS | |
| 88 94 Thr401 residue_name_number The results showed that domain I and domain II are closer to each other with Ala228 and Thr401 in A2 as Hinge-residues. RESULTS | |
| 98 100 A2 structure_element The results showed that domain I and domain II are closer to each other with Ala228 and Thr401 in A2 as Hinge-residues. RESULTS | |
| 104 118 Hinge-residues structure_element The results showed that domain I and domain II are closer to each other with Ala228 and Thr401 in A2 as Hinge-residues. RESULTS | |
| 28 33 SePSK protein Based on the above results, SePSK is divided into two rigid parts. RESULTS | |
| 4 12 domain I structure_element The domain I of RBL-SePSK (aa. 1β228, aa. 402β421) and the domain II of AMP-PNP-SePSK (aa. 229β401) were superposed with structures, including apo-AtXK-1, apo-SePSK, xylulose kinase from Lactobacillus acidophilus (PDB code: 3LL3) and the S58W mutant form of glycerol kinase from Escherichia coli (PDB code: 1GLJ). RESULTS | |
| 16 25 RBL-SePSK complex_assembly The domain I of RBL-SePSK (aa. 1β228, aa. 402β421) and the domain II of AMP-PNP-SePSK (aa. 229β401) were superposed with structures, including apo-AtXK-1, apo-SePSK, xylulose kinase from Lactobacillus acidophilus (PDB code: 3LL3) and the S58W mutant form of glycerol kinase from Escherichia coli (PDB code: 1GLJ). RESULTS | |
| 31 36 1β228 residue_range The domain I of RBL-SePSK (aa. 1β228, aa. 402β421) and the domain II of AMP-PNP-SePSK (aa. 229β401) were superposed with structures, including apo-AtXK-1, apo-SePSK, xylulose kinase from Lactobacillus acidophilus (PDB code: 3LL3) and the S58W mutant form of glycerol kinase from Escherichia coli (PDB code: 1GLJ). RESULTS | |
| 42 49 402β421 residue_range The domain I of RBL-SePSK (aa. 1β228, aa. 402β421) and the domain II of AMP-PNP-SePSK (aa. 229β401) were superposed with structures, including apo-AtXK-1, apo-SePSK, xylulose kinase from Lactobacillus acidophilus (PDB code: 3LL3) and the S58W mutant form of glycerol kinase from Escherichia coli (PDB code: 1GLJ). RESULTS | |
| 59 68 domain II structure_element The domain I of RBL-SePSK (aa. 1β228, aa. 402β421) and the domain II of AMP-PNP-SePSK (aa. 229β401) were superposed with structures, including apo-AtXK-1, apo-SePSK, xylulose kinase from Lactobacillus acidophilus (PDB code: 3LL3) and the S58W mutant form of glycerol kinase from Escherichia coli (PDB code: 1GLJ). RESULTS | |
| 72 85 AMP-PNP-SePSK complex_assembly The domain I of RBL-SePSK (aa. 1β228, aa. 402β421) and the domain II of AMP-PNP-SePSK (aa. 229β401) were superposed with structures, including apo-AtXK-1, apo-SePSK, xylulose kinase from Lactobacillus acidophilus (PDB code: 3LL3) and the S58W mutant form of glycerol kinase from Escherichia coli (PDB code: 1GLJ). RESULTS | |
| 91 98 229β401 residue_range The domain I of RBL-SePSK (aa. 1β228, aa. 402β421) and the domain II of AMP-PNP-SePSK (aa. 229β401) were superposed with structures, including apo-AtXK-1, apo-SePSK, xylulose kinase from Lactobacillus acidophilus (PDB code: 3LL3) and the S58W mutant form of glycerol kinase from Escherichia coli (PDB code: 1GLJ). RESULTS | |
| 105 115 superposed experimental_method The domain I of RBL-SePSK (aa. 1β228, aa. 402β421) and the domain II of AMP-PNP-SePSK (aa. 229β401) were superposed with structures, including apo-AtXK-1, apo-SePSK, xylulose kinase from Lactobacillus acidophilus (PDB code: 3LL3) and the S58W mutant form of glycerol kinase from Escherichia coli (PDB code: 1GLJ). RESULTS | |
| 121 131 structures evidence The domain I of RBL-SePSK (aa. 1β228, aa. 402β421) and the domain II of AMP-PNP-SePSK (aa. 229β401) were superposed with structures, including apo-AtXK-1, apo-SePSK, xylulose kinase from Lactobacillus acidophilus (PDB code: 3LL3) and the S58W mutant form of glycerol kinase from Escherichia coli (PDB code: 1GLJ). RESULTS | |
| 143 146 apo protein_state The domain I of RBL-SePSK (aa. 1β228, aa. 402β421) and the domain II of AMP-PNP-SePSK (aa. 229β401) were superposed with structures, including apo-AtXK-1, apo-SePSK, xylulose kinase from Lactobacillus acidophilus (PDB code: 3LL3) and the S58W mutant form of glycerol kinase from Escherichia coli (PDB code: 1GLJ). RESULTS | |
| 147 153 AtXK-1 protein The domain I of RBL-SePSK (aa. 1β228, aa. 402β421) and the domain II of AMP-PNP-SePSK (aa. 229β401) were superposed with structures, including apo-AtXK-1, apo-SePSK, xylulose kinase from Lactobacillus acidophilus (PDB code: 3LL3) and the S58W mutant form of glycerol kinase from Escherichia coli (PDB code: 1GLJ). RESULTS | |
| 155 158 apo protein_state The domain I of RBL-SePSK (aa. 1β228, aa. 402β421) and the domain II of AMP-PNP-SePSK (aa. 229β401) were superposed with structures, including apo-AtXK-1, apo-SePSK, xylulose kinase from Lactobacillus acidophilus (PDB code: 3LL3) and the S58W mutant form of glycerol kinase from Escherichia coli (PDB code: 1GLJ). RESULTS | |
| 159 164 SePSK protein The domain I of RBL-SePSK (aa. 1β228, aa. 402β421) and the domain II of AMP-PNP-SePSK (aa. 229β401) were superposed with structures, including apo-AtXK-1, apo-SePSK, xylulose kinase from Lactobacillus acidophilus (PDB code: 3LL3) and the S58W mutant form of glycerol kinase from Escherichia coli (PDB code: 1GLJ). RESULTS | |
| 166 181 xylulose kinase protein_type The domain I of RBL-SePSK (aa. 1β228, aa. 402β421) and the domain II of AMP-PNP-SePSK (aa. 229β401) were superposed with structures, including apo-AtXK-1, apo-SePSK, xylulose kinase from Lactobacillus acidophilus (PDB code: 3LL3) and the S58W mutant form of glycerol kinase from Escherichia coli (PDB code: 1GLJ). RESULTS | |
| 187 212 Lactobacillus acidophilus species The domain I of RBL-SePSK (aa. 1β228, aa. 402β421) and the domain II of AMP-PNP-SePSK (aa. 229β401) were superposed with structures, including apo-AtXK-1, apo-SePSK, xylulose kinase from Lactobacillus acidophilus (PDB code: 3LL3) and the S58W mutant form of glycerol kinase from Escherichia coli (PDB code: 1GLJ). RESULTS | |
| 238 242 S58W mutant The domain I of RBL-SePSK (aa. 1β228, aa. 402β421) and the domain II of AMP-PNP-SePSK (aa. 229β401) were superposed with structures, including apo-AtXK-1, apo-SePSK, xylulose kinase from Lactobacillus acidophilus (PDB code: 3LL3) and the S58W mutant form of glycerol kinase from Escherichia coli (PDB code: 1GLJ). RESULTS | |
| 243 249 mutant protein_state The domain I of RBL-SePSK (aa. 1β228, aa. 402β421) and the domain II of AMP-PNP-SePSK (aa. 229β401) were superposed with structures, including apo-AtXK-1, apo-SePSK, xylulose kinase from Lactobacillus acidophilus (PDB code: 3LL3) and the S58W mutant form of glycerol kinase from Escherichia coli (PDB code: 1GLJ). RESULTS | |
| 258 273 glycerol kinase protein_type The domain I of RBL-SePSK (aa. 1β228, aa. 402β421) and the domain II of AMP-PNP-SePSK (aa. 229β401) were superposed with structures, including apo-AtXK-1, apo-SePSK, xylulose kinase from Lactobacillus acidophilus (PDB code: 3LL3) and the S58W mutant form of glycerol kinase from Escherichia coli (PDB code: 1GLJ). RESULTS | |
| 279 295 Escherichia coli species The domain I of RBL-SePSK (aa. 1β228, aa. 402β421) and the domain II of AMP-PNP-SePSK (aa. 229β401) were superposed with structures, including apo-AtXK-1, apo-SePSK, xylulose kinase from Lactobacillus acidophilus (PDB code: 3LL3) and the S58W mutant form of glycerol kinase from Escherichia coli (PDB code: 1GLJ). RESULTS | |
| 15 28 superposition experimental_method The results of superposition displayed different crossing angle between these two domains. RESULTS | |
| 6 19 superposition experimental_method After superposition, the distances of AMP-PNP Ξ³-phosphate and the fifth hydroxyl group of RBL1 are 7.9 Γ (superposed with AtXK-1), 7.4 Γ (superposed with SePSK), 6.6 Γ (superposed with 3LL3) and 6.1 Γ (superposed with 1GLJ). RESULTS | |
| 38 45 AMP-PNP chemical After superposition, the distances of AMP-PNP Ξ³-phosphate and the fifth hydroxyl group of RBL1 are 7.9 Γ (superposed with AtXK-1), 7.4 Γ (superposed with SePSK), 6.6 Γ (superposed with 3LL3) and 6.1 Γ (superposed with 1GLJ). RESULTS | |
| 48 57 phosphate chemical After superposition, the distances of AMP-PNP Ξ³-phosphate and the fifth hydroxyl group of RBL1 are 7.9 Γ (superposed with AtXK-1), 7.4 Γ (superposed with SePSK), 6.6 Γ (superposed with 3LL3) and 6.1 Γ (superposed with 1GLJ). RESULTS | |
| 90 94 RBL1 residue_name_number After superposition, the distances of AMP-PNP Ξ³-phosphate and the fifth hydroxyl group of RBL1 are 7.9 Γ (superposed with AtXK-1), 7.4 Γ (superposed with SePSK), 6.6 Γ (superposed with 3LL3) and 6.1 Γ (superposed with 1GLJ). RESULTS | |
| 106 116 superposed experimental_method After superposition, the distances of AMP-PNP Ξ³-phosphate and the fifth hydroxyl group of RBL1 are 7.9 Γ (superposed with AtXK-1), 7.4 Γ (superposed with SePSK), 6.6 Γ (superposed with 3LL3) and 6.1 Γ (superposed with 1GLJ). RESULTS | |
| 122 128 AtXK-1 protein After superposition, the distances of AMP-PNP Ξ³-phosphate and the fifth hydroxyl group of RBL1 are 7.9 Γ (superposed with AtXK-1), 7.4 Γ (superposed with SePSK), 6.6 Γ (superposed with 3LL3) and 6.1 Γ (superposed with 1GLJ). RESULTS | |
| 138 148 superposed experimental_method After superposition, the distances of AMP-PNP Ξ³-phosphate and the fifth hydroxyl group of RBL1 are 7.9 Γ (superposed with AtXK-1), 7.4 Γ (superposed with SePSK), 6.6 Γ (superposed with 3LL3) and 6.1 Γ (superposed with 1GLJ). RESULTS | |
| 154 159 SePSK protein After superposition, the distances of AMP-PNP Ξ³-phosphate and the fifth hydroxyl group of RBL1 are 7.9 Γ (superposed with AtXK-1), 7.4 Γ (superposed with SePSK), 6.6 Γ (superposed with 3LL3) and 6.1 Γ (superposed with 1GLJ). RESULTS | |
| 169 179 superposed experimental_method After superposition, the distances of AMP-PNP Ξ³-phosphate and the fifth hydroxyl group of RBL1 are 7.9 Γ (superposed with AtXK-1), 7.4 Γ (superposed with SePSK), 6.6 Γ (superposed with 3LL3) and 6.1 Γ (superposed with 1GLJ). RESULTS | |
| 202 212 superposed experimental_method After superposition, the distances of AMP-PNP Ξ³-phosphate and the fifth hydroxyl group of RBL1 are 7.9 Γ (superposed with AtXK-1), 7.4 Γ (superposed with SePSK), 6.6 Γ (superposed with 3LL3) and 6.1 Γ (superposed with 1GLJ). RESULTS | |
| 28 35 AMP-PNP chemical Meanwhile, the distances of AMP-PNP Ξ³-phosphate and the first hydroxyl group of RBL2 are 7.2 Γ (superposed with AtXK-1), 6.7 Γ (superposed with SePSK), 3.7 Γ (superposed with 3LL3), until AMP-PNP Ξ³-phosphate fully contacts RBL2 after superposition with 1GLJ (Fig 5). RESULTS | |
| 38 47 phosphate chemical Meanwhile, the distances of AMP-PNP Ξ³-phosphate and the first hydroxyl group of RBL2 are 7.2 Γ (superposed with AtXK-1), 6.7 Γ (superposed with SePSK), 3.7 Γ (superposed with 3LL3), until AMP-PNP Ξ³-phosphate fully contacts RBL2 after superposition with 1GLJ (Fig 5). RESULTS | |
| 80 84 RBL2 residue_name_number Meanwhile, the distances of AMP-PNP Ξ³-phosphate and the first hydroxyl group of RBL2 are 7.2 Γ (superposed with AtXK-1), 6.7 Γ (superposed with SePSK), 3.7 Γ (superposed with 3LL3), until AMP-PNP Ξ³-phosphate fully contacts RBL2 after superposition with 1GLJ (Fig 5). RESULTS | |
| 96 106 superposed experimental_method Meanwhile, the distances of AMP-PNP Ξ³-phosphate and the first hydroxyl group of RBL2 are 7.2 Γ (superposed with AtXK-1), 6.7 Γ (superposed with SePSK), 3.7 Γ (superposed with 3LL3), until AMP-PNP Ξ³-phosphate fully contacts RBL2 after superposition with 1GLJ (Fig 5). RESULTS | |
| 112 118 AtXK-1 protein Meanwhile, the distances of AMP-PNP Ξ³-phosphate and the first hydroxyl group of RBL2 are 7.2 Γ (superposed with AtXK-1), 6.7 Γ (superposed with SePSK), 3.7 Γ (superposed with 3LL3), until AMP-PNP Ξ³-phosphate fully contacts RBL2 after superposition with 1GLJ (Fig 5). RESULTS | |
| 128 138 superposed experimental_method Meanwhile, the distances of AMP-PNP Ξ³-phosphate and the first hydroxyl group of RBL2 are 7.2 Γ (superposed with AtXK-1), 6.7 Γ (superposed with SePSK), 3.7 Γ (superposed with 3LL3), until AMP-PNP Ξ³-phosphate fully contacts RBL2 after superposition with 1GLJ (Fig 5). RESULTS | |
| 144 149 SePSK protein Meanwhile, the distances of AMP-PNP Ξ³-phosphate and the first hydroxyl group of RBL2 are 7.2 Γ (superposed with AtXK-1), 6.7 Γ (superposed with SePSK), 3.7 Γ (superposed with 3LL3), until AMP-PNP Ξ³-phosphate fully contacts RBL2 after superposition with 1GLJ (Fig 5). RESULTS | |
| 159 169 superposed experimental_method Meanwhile, the distances of AMP-PNP Ξ³-phosphate and the first hydroxyl group of RBL2 are 7.2 Γ (superposed with AtXK-1), 6.7 Γ (superposed with SePSK), 3.7 Γ (superposed with 3LL3), until AMP-PNP Ξ³-phosphate fully contacts RBL2 after superposition with 1GLJ (Fig 5). RESULTS | |
| 188 195 AMP-PNP chemical Meanwhile, the distances of AMP-PNP Ξ³-phosphate and the first hydroxyl group of RBL2 are 7.2 Γ (superposed with AtXK-1), 6.7 Γ (superposed with SePSK), 3.7 Γ (superposed with 3LL3), until AMP-PNP Ξ³-phosphate fully contacts RBL2 after superposition with 1GLJ (Fig 5). RESULTS | |
| 198 207 phosphate chemical Meanwhile, the distances of AMP-PNP Ξ³-phosphate and the first hydroxyl group of RBL2 are 7.2 Γ (superposed with AtXK-1), 6.7 Γ (superposed with SePSK), 3.7 Γ (superposed with 3LL3), until AMP-PNP Ξ³-phosphate fully contacts RBL2 after superposition with 1GLJ (Fig 5). RESULTS | |
| 223 227 RBL2 residue_name_number Meanwhile, the distances of AMP-PNP Ξ³-phosphate and the first hydroxyl group of RBL2 are 7.2 Γ (superposed with AtXK-1), 6.7 Γ (superposed with SePSK), 3.7 Γ (superposed with 3LL3), until AMP-PNP Ξ³-phosphate fully contacts RBL2 after superposition with 1GLJ (Fig 5). RESULTS | |
| 234 247 superposition experimental_method Meanwhile, the distances of AMP-PNP Ξ³-phosphate and the first hydroxyl group of RBL2 are 7.2 Γ (superposed with AtXK-1), 6.7 Γ (superposed with SePSK), 3.7 Γ (superposed with 3LL3), until AMP-PNP Ξ³-phosphate fully contacts RBL2 after superposition with 1GLJ (Fig 5). RESULTS | |
| 22 26 RBL2 residue_name_number This distance between RBL2 and AMP-PNP-Ξ³-phosphate is close enough to facilitate phosphate transferring. RESULTS | |
| 31 38 AMP-PNP chemical This distance between RBL2 and AMP-PNP-Ξ³-phosphate is close enough to facilitate phosphate transferring. RESULTS | |
| 41 50 phosphate chemical This distance between RBL2 and AMP-PNP-Ξ³-phosphate is close enough to facilitate phosphate transferring. RESULTS | |
| 81 90 phosphate chemical This distance between RBL2 and AMP-PNP-Ξ³-phosphate is close enough to facilitate phosphate transferring. RESULTS | |
| 14 27 superposition experimental_method Together, our superposition results provided snapshots of the conformational changes at different catalytic stages of SePSK and potentially revealed the closed form of SePSK. RESULTS | |
| 118 123 SePSK protein Together, our superposition results provided snapshots of the conformational changes at different catalytic stages of SePSK and potentially revealed the closed form of SePSK. RESULTS | |
| 153 159 closed protein_state Together, our superposition results provided snapshots of the conformational changes at different catalytic stages of SePSK and potentially revealed the closed form of SePSK. RESULTS | |
| 168 173 SePSK protein Together, our superposition results provided snapshots of the conformational changes at different catalytic stages of SePSK and potentially revealed the closed form of SePSK. RESULTS | |
| 35 40 SePSK protein Simulated conformational change of SePSK during the catalytic process. FIG | |
| 4 14 structures evidence The structures are shown as cartoon and the ligands are shown as sticks. FIG | |
| 0 8 Domain I structure_element Domain I from D-ribulose-SePSK (green) and Domain II from AMP-PNP-SePSK (cyan) are superposed with apo-AtXK-1 (1st), apo-SePSK (2nd), 3LL3 (3rd) and 1GLJ (4th), respectively. FIG | |
| 14 30 D-ribulose-SePSK complex_assembly Domain I from D-ribulose-SePSK (green) and Domain II from AMP-PNP-SePSK (cyan) are superposed with apo-AtXK-1 (1st), apo-SePSK (2nd), 3LL3 (3rd) and 1GLJ (4th), respectively. FIG | |
| 43 52 Domain II structure_element Domain I from D-ribulose-SePSK (green) and Domain II from AMP-PNP-SePSK (cyan) are superposed with apo-AtXK-1 (1st), apo-SePSK (2nd), 3LL3 (3rd) and 1GLJ (4th), respectively. FIG | |
| 58 71 AMP-PNP-SePSK complex_assembly Domain I from D-ribulose-SePSK (green) and Domain II from AMP-PNP-SePSK (cyan) are superposed with apo-AtXK-1 (1st), apo-SePSK (2nd), 3LL3 (3rd) and 1GLJ (4th), respectively. FIG | |
| 83 93 superposed experimental_method Domain I from D-ribulose-SePSK (green) and Domain II from AMP-PNP-SePSK (cyan) are superposed with apo-AtXK-1 (1st), apo-SePSK (2nd), 3LL3 (3rd) and 1GLJ (4th), respectively. FIG | |
| 99 102 apo protein_state Domain I from D-ribulose-SePSK (green) and Domain II from AMP-PNP-SePSK (cyan) are superposed with apo-AtXK-1 (1st), apo-SePSK (2nd), 3LL3 (3rd) and 1GLJ (4th), respectively. FIG | |
| 103 109 AtXK-1 protein Domain I from D-ribulose-SePSK (green) and Domain II from AMP-PNP-SePSK (cyan) are superposed with apo-AtXK-1 (1st), apo-SePSK (2nd), 3LL3 (3rd) and 1GLJ (4th), respectively. FIG | |
| 117 120 apo protein_state Domain I from D-ribulose-SePSK (green) and Domain II from AMP-PNP-SePSK (cyan) are superposed with apo-AtXK-1 (1st), apo-SePSK (2nd), 3LL3 (3rd) and 1GLJ (4th), respectively. FIG | |
| 121 126 SePSK protein Domain I from D-ribulose-SePSK (green) and Domain II from AMP-PNP-SePSK (cyan) are superposed with apo-AtXK-1 (1st), apo-SePSK (2nd), 3LL3 (3rd) and 1GLJ (4th), respectively. FIG | |
| 92 95 RBL chemical The numbers near the black dashed lines show the distances (Γ ) between two nearest atoms of RBL and AMP-PNP. FIG | |
| 100 107 AMP-PNP chemical The numbers near the black dashed lines show the distances (Γ ) between two nearest atoms of RBL and AMP-PNP. FIG | |
| 16 49 structural and enzymatic analyses experimental_method In summary, our structural and enzymatic analyses provide evidence that SePSK shows D-ribulose kinase activity, and exhibits the conserved features of FGGY family carbohydrate kinases. RESULTS | |
| 72 77 SePSK protein In summary, our structural and enzymatic analyses provide evidence that SePSK shows D-ribulose kinase activity, and exhibits the conserved features of FGGY family carbohydrate kinases. RESULTS | |
| 84 101 D-ribulose kinase protein_type In summary, our structural and enzymatic analyses provide evidence that SePSK shows D-ribulose kinase activity, and exhibits the conserved features of FGGY family carbohydrate kinases. RESULTS | |
| 151 183 FGGY family carbohydrate kinases protein_type In summary, our structural and enzymatic analyses provide evidence that SePSK shows D-ribulose kinase activity, and exhibits the conserved features of FGGY family carbohydrate kinases. RESULTS | |
| 6 15 conserved site Three conserved residues in SePSK were identified to be essential for this function. RESULTS | |
| 28 33 SePSK protein Three conserved residues in SePSK were identified to be essential for this function. RESULTS | |
| 70 75 SePSK protein Our results provide the detailed information about the interaction of SePSK with ATP and substrates. RESULTS | |
| 81 84 ATP chemical Our results provide the detailed information about the interaction of SePSK with ATP and substrates. RESULTS | |
| 10 34 structural superposition experimental_method Moreover, structural superposition results enable us to visualize the conformational change of SePSK during the catalytic process. RESULTS | |
| 95 100 SePSK protein Moreover, structural superposition results enable us to visualize the conformational change of SePSK during the catalytic process. RESULTS | |
| 112 117 SePSK protein In conclusion, our results provide important information for a more detailed understanding of the mechanisms of SePSK and other members of FGGY family carbohydrate kinases. RESULTS | |
| 139 171 FGGY family carbohydrate kinases protein_type In conclusion, our results provide important information for a more detailed understanding of the mechanisms of SePSK and other members of FGGY family carbohydrate kinases. RESULTS | |