3T89
Crystal structure of Escherichia coli MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase in vitamin K2 biosynthesis
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005829 | cellular_component | cytosol |
| A | 0008935 | molecular_function | 1,4-dihydroxy-2-naphthoyl-CoA synthase activity |
| A | 0009234 | biological_process | menaquinone biosynthetic process |
| A | 0016829 | molecular_function | lyase activity |
| A | 0071890 | molecular_function | bicarbonate binding |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005829 | cellular_component | cytosol |
| B | 0008935 | molecular_function | 1,4-dihydroxy-2-naphthoyl-CoA synthase activity |
| B | 0009234 | biological_process | menaquinone biosynthetic process |
| B | 0016829 | molecular_function | lyase activity |
| B | 0071890 | molecular_function | bicarbonate binding |
| C | 0003824 | molecular_function | catalytic activity |
| C | 0005515 | molecular_function | protein binding |
| C | 0005829 | cellular_component | cytosol |
| C | 0008935 | molecular_function | 1,4-dihydroxy-2-naphthoyl-CoA synthase activity |
| C | 0009234 | biological_process | menaquinone biosynthetic process |
| C | 0016829 | molecular_function | lyase activity |
| C | 0071890 | molecular_function | bicarbonate binding |
| D | 0003824 | molecular_function | catalytic activity |
| D | 0005515 | molecular_function | protein binding |
| D | 0005829 | cellular_component | cytosol |
| D | 0008935 | molecular_function | 1,4-dihydroxy-2-naphthoyl-CoA synthase activity |
| D | 0009234 | biological_process | menaquinone biosynthetic process |
| D | 0016829 | molecular_function | lyase activity |
| D | 0071890 | molecular_function | bicarbonate binding |
| E | 0003824 | molecular_function | catalytic activity |
| E | 0005515 | molecular_function | protein binding |
| E | 0005829 | cellular_component | cytosol |
| E | 0008935 | molecular_function | 1,4-dihydroxy-2-naphthoyl-CoA synthase activity |
| E | 0009234 | biological_process | menaquinone biosynthetic process |
| E | 0016829 | molecular_function | lyase activity |
| E | 0071890 | molecular_function | bicarbonate binding |
| F | 0003824 | molecular_function | catalytic activity |
| F | 0005515 | molecular_function | protein binding |
| F | 0005829 | cellular_component | cytosol |
| F | 0008935 | molecular_function | 1,4-dihydroxy-2-naphthoyl-CoA synthase activity |
| F | 0009234 | biological_process | menaquinone biosynthetic process |
| F | 0016829 | molecular_function | lyase activity |
| F | 0071890 | molecular_function | bicarbonate binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE MLI A 301 |
| Chain | Residue |
| A | GLY132 |
| A | HOH314 |
| A | GLY133 |
| A | GLN154 |
| A | THR155 |
| A | GLY156 |
| A | SER161 |
| A | PHE162 |
| A | ASP163 |
| A | TRP184 |
| site_id | AC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL A 302 |
| Chain | Residue |
| A | THR203 |
| A | VAL205 |
| A | GLU213 |
| A | ARG216 |
| A | TRP217 |
| A | HOH462 |
| C | ARG188 |
| site_id | AC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE GOL A 303 |
| Chain | Residue |
| A | ILE174 |
| A | HOH350 |
| D | ILE174 |
| site_id | AC4 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE MLI B 301 |
| Chain | Residue |
| B | GLY132 |
| B | GLY133 |
| B | GLN154 |
| B | THR155 |
| B | GLY156 |
| B | SER161 |
| B | PHE162 |
| B | ASP163 |
| B | TRP184 |
| B | HOH525 |
| B | HOH705 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL B 302 |
| Chain | Residue |
| B | THR203 |
| B | VAL205 |
| B | GLU213 |
| B | ARG216 |
| B | TRP217 |
| E | ARG188 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE GOL B 304 |
| Chain | Residue |
| B | PHE22 |
| B | GLU23 |
| B | ILE25 |
| B | ASN40 |
| site_id | AC7 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE MLI C 301 |
| Chain | Residue |
| C | GLY132 |
| C | GLY133 |
| C | GLN154 |
| C | THR155 |
| C | GLY156 |
| C | SER161 |
| C | PHE162 |
| C | ASP163 |
| C | TRP184 |
| C | HOH437 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL C 302 |
| Chain | Residue |
| C | THR203 |
| C | VAL205 |
| C | GLU213 |
| C | ARG216 |
| C | TRP217 |
| D | ARG188 |
| site_id | AC9 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE MLI D 301 |
| Chain | Residue |
| D | GLY132 |
| D | GLN154 |
| D | THR155 |
| D | GLY156 |
| D | SER161 |
| D | PHE162 |
| D | ASP163 |
| D | TRP184 |
| site_id | BC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL D 302 |
| Chain | Residue |
| A | ARG188 |
| D | THR203 |
| D | VAL205 |
| D | GLU213 |
| D | ARG216 |
| D | TRP217 |
| site_id | BC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL E 303 |
| Chain | Residue |
| E | ALA172 |
| E | VAL175 |
| E | GLY176 |
| E | HOH321 |
| F | ILE174 |
| F | VAL175 |
| F | GLY176 |
| site_id | BC3 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE MLI E 301 |
| Chain | Residue |
| E | GLY132 |
| E | GLY133 |
| E | GLN154 |
| E | THR155 |
| E | GLY156 |
| E | SER161 |
| E | PHE162 |
| E | ASP163 |
| E | TRP184 |
| site_id | BC4 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL E 302 |
| Chain | Residue |
| E | THR203 |
| E | VAL205 |
| E | GLU213 |
| E | ARG216 |
| E | TRP217 |
| E | HOH343 |
| F | ARG188 |
| site_id | BC5 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE MLI F 301 |
| Chain | Residue |
| F | PHE162 |
| F | ASP163 |
| F | TRP184 |
| F | HOH495 |
| F | GLY132 |
| F | GLN154 |
| F | THR155 |
| F | GLY156 |
| F | SER161 |
| site_id | BC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL F 302 |
| Chain | Residue |
| B | ARG188 |
| F | THR203 |
| F | VAL205 |
| F | GLU213 |
| F | ARG216 |
| F | TRP217 |
Functional Information from PROSITE/UniProt
| site_id | PS00166 |
| Number of Residues | 21 |
| Details | ENOYL_COA_HYDRATASE Enoyl-CoA hydratase/isomerase signature. VAmVAGysiGGGhvlhMmCDL |
| Chain | Residue | Details |
| A | VAL123-LEU143 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 18 |
| Details | BINDING: in other chain => ECO:0000255|HAMAP-Rule:MF_01934, ECO:0000269|PubMed:21830810, ECO:0000269|PubMed:23658663 |
| Chain | Residue | Details |
| A | ARG45 | |
| D | ARG45 | |
| D | TYR129 | |
| D | THR155 | |
| E | ARG45 | |
| E | TYR129 | |
| E | THR155 | |
| F | ARG45 | |
| F | TYR129 | |
| F | THR155 | |
| A | TYR129 | |
| A | THR155 | |
| B | ARG45 | |
| B | TYR129 | |
| B | THR155 | |
| C | ARG45 | |
| C | TYR129 | |
| C | THR155 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 6 |
| Details | BINDING: in other chain => ECO:0000269|PubMed:21830810, ECO:0000269|PubMed:23658663 |
| Chain | Residue | Details |
| A | SER84 | |
| B | SER84 | |
| C | SER84 | |
| D | SER84 | |
| E | SER84 | |
| F | SER84 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 6 |
| Details | BINDING: in other chain => ECO:0000255|HAMAP-Rule:MF_01934, ECO:0000269|PubMed:21830810 |
| Chain | Residue | Details |
| A | TYR97 | |
| B | TYR97 | |
| C | TYR97 | |
| D | TYR97 | |
| E | TYR97 | |
| F | TYR97 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_01934, ECO:0000269|PubMed:22606952 |
| Chain | Residue | Details |
| A | GLN154 | |
| B | GLN154 | |
| C | GLN154 | |
| D | GLN154 | |
| E | GLN154 | |
| F | GLN154 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 6 |
| Details | BINDING: in other chain => ECO:0000255|HAMAP-Rule:MF_01934, ECO:0000269|PubMed:23658663 |
| Chain | Residue | Details |
| A | SER161 | |
| B | SER161 | |
| C | SER161 | |
| D | SER161 | |
| E | SER161 | |
| F | SER161 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_01934, ECO:0000269|PubMed:21830810 |
| Chain | Residue | Details |
| A | TYR258 | |
| B | TYR258 | |
| C | TYR258 | |
| D | TYR258 | |
| E | TYR258 | |
| F | TYR258 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_01934, ECO:0000269|PubMed:21830810, ECO:0000269|PubMed:23658663 |
| Chain | Residue | Details |
| A | LYS273 | |
| B | LYS273 | |
| C | LYS273 | |
| D | LYS273 | |
| E | LYS273 | |
| F | LYS273 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 12 |
| Details | SITE: Important for catalysis => ECO:0000255|HAMAP-Rule:MF_01934, ECO:0000305|PubMed:21830810 |
| Chain | Residue | Details |
| A | TYR97 | |
| E | TYR258 | |
| F | TYR97 | |
| F | TYR258 | |
| A | TYR258 | |
| B | TYR97 | |
| B | TYR258 | |
| C | TYR97 | |
| C | TYR258 | |
| D | TYR97 | |
| D | TYR258 | |
| E | TYR97 |
