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 |