1Q51
Crystal Structure of Mycobacterium tuberculosis MenB in Complex with Acetoacetyl-Coenzyme A, a Key Enzyme in Vitamin K2 Biosynthesis
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0005829 | cellular_component | cytosol |
| A | 0005886 | cellular_component | plasma membrane |
| 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 | 0034214 | biological_process | protein hexamerization |
| B | 0005829 | cellular_component | cytosol |
| B | 0005886 | cellular_component | plasma membrane |
| 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 | 0034214 | biological_process | protein hexamerization |
| C | 0005829 | cellular_component | cytosol |
| C | 0005886 | cellular_component | plasma membrane |
| 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 | 0034214 | biological_process | protein hexamerization |
| D | 0005829 | cellular_component | cytosol |
| D | 0005886 | cellular_component | plasma membrane |
| 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 | 0034214 | biological_process | protein hexamerization |
| E | 0005829 | cellular_component | cytosol |
| E | 0005886 | cellular_component | plasma membrane |
| 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 | 0034214 | biological_process | protein hexamerization |
| F | 0005829 | cellular_component | cytosol |
| F | 0005886 | cellular_component | plasma membrane |
| 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 | 0034214 | biological_process | protein hexamerization |
| G | 0005829 | cellular_component | cytosol |
| G | 0005886 | cellular_component | plasma membrane |
| G | 0008935 | molecular_function | 1,4-dihydroxy-2-naphthoyl-CoA synthase activity |
| G | 0009234 | biological_process | menaquinone biosynthetic process |
| G | 0016829 | molecular_function | lyase activity |
| G | 0034214 | biological_process | protein hexamerization |
| H | 0005829 | cellular_component | cytosol |
| H | 0005886 | cellular_component | plasma membrane |
| H | 0008935 | molecular_function | 1,4-dihydroxy-2-naphthoyl-CoA synthase activity |
| H | 0009234 | biological_process | menaquinone biosynthetic process |
| H | 0016829 | molecular_function | lyase activity |
| H | 0034214 | biological_process | protein hexamerization |
| I | 0005829 | cellular_component | cytosol |
| I | 0005886 | cellular_component | plasma membrane |
| I | 0008935 | molecular_function | 1,4-dihydroxy-2-naphthoyl-CoA synthase activity |
| I | 0009234 | biological_process | menaquinone biosynthetic process |
| I | 0016829 | molecular_function | lyase activity |
| I | 0034214 | biological_process | protein hexamerization |
| J | 0005829 | cellular_component | cytosol |
| J | 0005886 | cellular_component | plasma membrane |
| J | 0008935 | molecular_function | 1,4-dihydroxy-2-naphthoyl-CoA synthase activity |
| J | 0009234 | biological_process | menaquinone biosynthetic process |
| J | 0016829 | molecular_function | lyase activity |
| J | 0034214 | biological_process | protein hexamerization |
| K | 0005829 | cellular_component | cytosol |
| K | 0005886 | cellular_component | plasma membrane |
| K | 0008935 | molecular_function | 1,4-dihydroxy-2-naphthoyl-CoA synthase activity |
| K | 0009234 | biological_process | menaquinone biosynthetic process |
| K | 0016829 | molecular_function | lyase activity |
| K | 0034214 | biological_process | protein hexamerization |
| L | 0005829 | cellular_component | cytosol |
| L | 0005886 | cellular_component | plasma membrane |
| L | 0008935 | molecular_function | 1,4-dihydroxy-2-naphthoyl-CoA synthase activity |
| L | 0009234 | biological_process | menaquinone biosynthetic process |
| L | 0016829 | molecular_function | lyase activity |
| L | 0034214 | biological_process | protein hexamerization |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE CAA K 500 |
| Chain | Residue |
| I | PHE299 |
| K | GLY105 |
| K | ASP106 |
| K | GLN107 |
| K | TRP157 |
| K | GLY160 |
| K | GLY161 |
| K | THR184 |
| K | VAL188 |
| I | LYS302 |
| K | VAL57 |
| K | ARG58 |
| K | ALA60 |
| K | PHE61 |
| K | LYS95 |
| K | SER103 |
| K | GLY104 |
| site_id | AC2 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE CAA A 501 |
| Chain | Residue |
| A | VAL57 |
| A | ARG58 |
| A | PHE61 |
| A | LYS95 |
| A | SER103 |
| A | GLY104 |
| A | GLY105 |
| A | ASP106 |
| A | GLN107 |
| A | TRP157 |
| A | GLY160 |
| A | GLY161 |
| A | THR184 |
| A | VAL188 |
| D | PHE299 |
| D | LYS302 |
| site_id | AC3 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE CAA B 502 |
| Chain | Residue |
| B | VAL57 |
| B | ARG58 |
| B | ALA60 |
| B | PHE61 |
| B | LYS95 |
| B | SER103 |
| B | GLY104 |
| B | GLY105 |
| B | ASP106 |
| B | GLN107 |
| B | TRP157 |
| B | GLY160 |
| B | GLY161 |
| B | THR184 |
| B | VAL188 |
| F | PHE299 |
| site_id | AC4 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE CAA C 503 |
| Chain | Residue |
| C | VAL57 |
| C | ARG58 |
| C | ALA60 |
| C | PHE61 |
| C | LYS95 |
| C | SER103 |
| C | GLY104 |
| C | GLY105 |
| C | ASP106 |
| C | GLN107 |
| C | TRP157 |
| C | GLY160 |
| C | GLY161 |
| C | THR184 |
| C | VAL188 |
| E | PHE299 |
| site_id | AC5 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE CAA D 504 |
| Chain | Residue |
| A | PHE299 |
| D | VAL57 |
| D | ARG58 |
| D | ALA60 |
| D | PHE61 |
| D | LYS95 |
| D | SER103 |
| D | GLY104 |
| D | GLY105 |
| D | ASP106 |
| D | GLN107 |
| D | TRP157 |
| D | GLY160 |
| D | GLY161 |
| D | THR184 |
| site_id | AC6 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE CAA E 505 |
| Chain | Residue |
| E | VAL57 |
| E | ARG58 |
| E | ALA60 |
| E | PHE61 |
| E | LYS95 |
| E | SER103 |
| E | GLY104 |
| E | GLY105 |
| E | ASP106 |
| E | GLN107 |
| E | TRP157 |
| E | GLY160 |
| E | GLY161 |
| E | THR184 |
| site_id | AC7 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE CAA F 506 |
| Chain | Residue |
| F | SER103 |
| F | GLY104 |
| F | GLY105 |
| F | ASP106 |
| F | GLN107 |
| F | TRP157 |
| F | GLY160 |
| F | GLY161 |
| F | THR184 |
| F | VAL57 |
| F | ARG58 |
| F | ALA60 |
| F | PHE61 |
| F | LYS95 |
| site_id | AC8 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE CAA G 507 |
| Chain | Residue |
| G | GLU56 |
| G | VAL57 |
| G | ARG58 |
| G | ALA60 |
| G | PHE61 |
| G | LYS95 |
| G | SER103 |
| G | GLY104 |
| G | GLY105 |
| G | ASP106 |
| G | GLN107 |
| G | TRP157 |
| G | GLY160 |
| G | GLY161 |
| G | THR184 |
| site_id | AC9 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE CAA H 508 |
| Chain | Residue |
| H | GLU56 |
| H | VAL57 |
| H | ARG58 |
| H | ALA60 |
| H | PHE61 |
| H | LYS95 |
| H | SER103 |
| H | GLY104 |
| H | GLY105 |
| H | ASP106 |
| H | GLN107 |
| H | TRP157 |
| H | GLY160 |
| H | GLY161 |
| H | THR184 |
| H | VAL188 |
| site_id | BC1 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE CAA I 509 |
| Chain | Residue |
| I | VAL57 |
| I | ARG58 |
| I | ALA60 |
| I | PHE61 |
| I | LYS95 |
| I | SER103 |
| I | GLY104 |
| I | GLY105 |
| I | ASP106 |
| I | GLN107 |
| I | TRP157 |
| I | GLY160 |
| I | GLY161 |
| I | THR184 |
| I | VAL188 |
| site_id | BC2 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE CAA J 510 |
| Chain | Residue |
| G | PHE299 |
| G | LYS302 |
| J | VAL57 |
| J | ARG58 |
| J | ALA60 |
| J | LYS95 |
| J | SER103 |
| J | GLY104 |
| J | GLY105 |
| J | ASP106 |
| J | GLN107 |
| J | TRP157 |
| J | GLY160 |
| J | GLY161 |
| J | THR184 |
| site_id | BC3 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE CAA L 511 |
| Chain | Residue |
| H | PHE299 |
| H | LYS302 |
| L | VAL57 |
| L | ARG58 |
| L | ALA60 |
| L | PHE61 |
| L | LYS95 |
| L | SER103 |
| L | GLY104 |
| L | GLY105 |
| L | ASP106 |
| L | GLN107 |
| L | TRP157 |
| L | GLY160 |
| L | GLY161 |
| L | THR184 |
| L | VAL188 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 12 |
| Details | BINDING: in other chain => ECO:0000255|HAMAP-Rule:MF_01934, ECO:0000269|PubMed:12909628, ECO:0000269|PubMed:21830810 |
| Chain | Residue | Details |
| A | ARG58 | |
| J | ARG58 | |
| K | ARG58 | |
| L | ARG58 | |
| B | ARG58 | |
| C | ARG58 | |
| D | ARG58 | |
| E | ARG58 | |
| F | ARG58 | |
| G | ARG58 | |
| H | ARG58 | |
| I | ARG58 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 12 |
| Details | BINDING: in other chain => ECO:0000269|PubMed:12909628, ECO:0000269|PubMed:21830810 |
| Chain | Residue | Details |
| A | LYS95 | |
| J | LYS95 | |
| K | LYS95 | |
| L | LYS95 | |
| B | LYS95 | |
| C | LYS95 | |
| D | LYS95 | |
| E | LYS95 | |
| F | LYS95 | |
| G | LYS95 | |
| H | LYS95 | |
| I | LYS95 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 12 |
| Details | BINDING: in other chain => ECO:0000255|HAMAP-Rule:MF_01934, ECO:0000269|PubMed:12909628, ECO:0000269|PubMed:16131752, ECO:0000269|PubMed:21830810 |
| Chain | Residue | Details |
| A | SER103 | |
| J | SER103 | |
| K | SER103 | |
| L | SER103 | |
| B | SER103 | |
| C | SER103 | |
| D | SER103 | |
| E | SER103 | |
| F | SER103 | |
| G | SER103 | |
| H | SER103 | |
| I | SER103 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 12 |
| Details | BINDING: in other chain => ECO:0000250|UniProtKB:P0ABU0, ECO:0000255|HAMAP-Rule:MF_01934 |
| Chain | Residue | Details |
| A | TYR115 | |
| J | TYR115 | |
| K | TYR115 | |
| L | TYR115 | |
| B | TYR115 | |
| C | TYR115 | |
| D | TYR115 | |
| E | TYR115 | |
| F | TYR115 | |
| G | TYR115 | |
| H | TYR115 | |
| I | TYR115 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 24 |
| Details | BINDING: in other chain => ECO:0000255|HAMAP-Rule:MF_01934, ECO:0000269|PubMed:12909628 |
| Chain | Residue | Details |
| A | TRP157 | |
| E | THR184 | |
| F | TRP157 | |
| F | THR184 | |
| G | TRP157 | |
| G | THR184 | |
| H | TRP157 | |
| H | THR184 | |
| I | TRP157 | |
| I | THR184 | |
| J | TRP157 | |
| A | THR184 | |
| J | THR184 | |
| K | TRP157 | |
| K | THR184 | |
| L | TRP157 | |
| L | THR184 | |
| B | TRP157 | |
| B | THR184 | |
| C | TRP157 | |
| C | THR184 | |
| D | TRP157 | |
| D | THR184 | |
| E | TRP157 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 12 |
| Details | BINDING: in other chain => ECO:0000255|HAMAP-Rule:MF_01934, ECO:0000305|PubMed:21830810 |
| Chain | Residue | Details |
| A | SER190 | |
| J | SER190 | |
| K | SER190 | |
| L | SER190 | |
| B | SER190 | |
| C | SER190 | |
| D | SER190 | |
| E | SER190 | |
| F | SER190 | |
| G | SER190 | |
| H | SER190 | |
| I | SER190 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 24 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:P0ABU0, ECO:0000255|HAMAP-Rule:MF_01934 |
| Chain | Residue | Details |
| A | TYR287 | |
| E | LYS302 | |
| F | TYR287 | |
| F | LYS302 | |
| G | TYR287 | |
| G | LYS302 | |
| H | TYR287 | |
| H | LYS302 | |
| I | TYR287 | |
| I | LYS302 | |
| J | TYR287 | |
| A | LYS302 | |
| J | LYS302 | |
| K | TYR287 | |
| K | LYS302 | |
| L | TYR287 | |
| L | LYS302 | |
| B | TYR287 | |
| B | LYS302 | |
| C | TYR287 | |
| C | LYS302 | |
| D | TYR287 | |
| D | LYS302 | |
| E | TYR287 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 12 |
| Details | SITE: Important for catalysis => ECO:0000250|UniProtKB:P0ABU0, ECO:0000255|HAMAP-Rule:MF_01934 |
| Chain | Residue | Details |
| A | TYR115 | |
| J | TYR115 | |
| K | TYR115 | |
| L | TYR115 | |
| B | TYR115 | |
| C | TYR115 | |
| D | TYR115 | |
| E | TYR115 | |
| F | TYR115 | |
| G | TYR115 | |
| H | TYR115 | |
| I | TYR115 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 12 |
| Details | SITE: Important for catalysis => ECO:0000255|HAMAP-Rule:MF_01934, ECO:0000305|PubMed:20643650, ECO:0000305|PubMed:21830810 |
| Chain | Residue | Details |
| A | ASP185 | |
| J | ASP185 | |
| K | ASP185 | |
| L | ASP185 | |
| B | ASP185 | |
| C | ASP185 | |
| D | ASP185 | |
| E | ASP185 | |
| F | ASP185 | |
| G | ASP185 | |
| H | ASP185 | |
| I | ASP185 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 12 |
| Details | SITE: Important for catalysis => ECO:0000250|UniProtKB:P0ABU0, ECO:0000255|HAMAP-Rule:MF_01934, ECO:0000305|PubMed:12909628 |
| Chain | Residue | Details |
| A | TYR287 | |
| J | TYR287 | |
| K | TYR287 | |
| L | TYR287 | |
| B | TYR287 | |
| C | TYR287 | |
| D | TYR287 | |
| E | TYR287 | |
| F | TYR287 | |
| G | TYR287 | |
| H | TYR287 | |
| I | TYR287 |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 6 |
| Details | M-CSA 346 |
| Chain | Residue | Details |
| A | GLY105 | electrostatic stabiliser, hydrogen bond donor |
| A | TYR115 | electrostatic stabiliser, hydrogen bond donor, steric role |
| A | GLY161 | electrostatic stabiliser, hydrogen bond donor |
| A | ASP185 | activator |
| A | SER190 | activator |
| A | TYR287 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role |
| site_id | MCSA2 |
| Number of Residues | 6 |
| Details | M-CSA 346 |
| Chain | Residue | Details |
| B | GLY105 | electrostatic stabiliser, hydrogen bond donor |
| B | TYR115 | electrostatic stabiliser, hydrogen bond donor, steric role |
| B | GLY161 | electrostatic stabiliser, hydrogen bond donor |
| B | ASP185 | activator |
| B | SER190 | activator |
| B | TYR287 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role |
| site_id | MCSA3 |
| Number of Residues | 6 |
| Details | M-CSA 346 |
| Chain | Residue | Details |
| C | GLY105 | electrostatic stabiliser, hydrogen bond donor |
| C | TYR115 | electrostatic stabiliser, hydrogen bond donor, steric role |
| C | GLY161 | electrostatic stabiliser, hydrogen bond donor |
| C | ASP185 | activator |
| C | SER190 | activator |
| C | TYR287 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role |
| site_id | MCSA4 |
| Number of Residues | 6 |
| Details | M-CSA 346 |
| Chain | Residue | Details |
| D | GLY105 | electrostatic stabiliser, hydrogen bond donor |
| D | TYR115 | electrostatic stabiliser, hydrogen bond donor, steric role |
| D | GLY161 | electrostatic stabiliser, hydrogen bond donor |
| D | ASP185 | activator |
| D | SER190 | activator |
| D | TYR287 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role |
| site_id | MCSA5 |
| Number of Residues | 6 |
| Details | M-CSA 346 |
| Chain | Residue | Details |
| E | GLY105 | electrostatic stabiliser, hydrogen bond donor |
| E | TYR115 | electrostatic stabiliser, hydrogen bond donor, steric role |
| E | GLY161 | electrostatic stabiliser, hydrogen bond donor |
| E | ASP185 | activator |
| E | SER190 | activator |
| E | TYR287 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role |
| site_id | MCSA6 |
| Number of Residues | 6 |
| Details | M-CSA 346 |
| Chain | Residue | Details |
| F | GLY105 | electrostatic stabiliser, hydrogen bond donor |
| F | TYR115 | electrostatic stabiliser, hydrogen bond donor, steric role |
| F | GLY161 | electrostatic stabiliser, hydrogen bond donor |
| F | ASP185 | activator |
| F | SER190 | activator |
| F | TYR287 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role |
| site_id | MCSA7 |
| Number of Residues | 6 |
| Details | M-CSA 346 |
| Chain | Residue | Details |
| G | GLY105 | electrostatic stabiliser, hydrogen bond donor |
| G | TYR115 | electrostatic stabiliser, hydrogen bond donor, steric role |
| G | GLY161 | electrostatic stabiliser, hydrogen bond donor |
| G | ASP185 | activator |
| G | SER190 | activator |
| G | TYR287 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role |
| site_id | MCSA8 |
| Number of Residues | 6 |
| Details | M-CSA 346 |
| Chain | Residue | Details |
| H | GLY105 | electrostatic stabiliser, hydrogen bond donor |
| H | TYR115 | electrostatic stabiliser, hydrogen bond donor, steric role |
| H | GLY161 | electrostatic stabiliser, hydrogen bond donor |
| H | ASP185 | activator |
| H | SER190 | activator |
| H | TYR287 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role |
| site_id | MCSA9 |
| Number of Residues | 6 |
| Details | M-CSA 346 |
| Chain | Residue | Details |
| I | GLY105 | electrostatic stabiliser, hydrogen bond donor |
| I | TYR115 | electrostatic stabiliser, hydrogen bond donor, steric role |
| I | GLY161 | electrostatic stabiliser, hydrogen bond donor |
| I | ASP185 | activator |
| I | SER190 | activator |
| I | TYR287 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role |
| site_id | MCSA10 |
| Number of Residues | 6 |
| Details | M-CSA 346 |
| Chain | Residue | Details |
| J | GLY105 | electrostatic stabiliser, hydrogen bond donor |
| J | TYR115 | electrostatic stabiliser, hydrogen bond donor, steric role |
| J | GLY161 | electrostatic stabiliser, hydrogen bond donor |
| J | ASP185 | activator |
| J | SER190 | activator |
| J | TYR287 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role |
| site_id | MCSA11 |
| Number of Residues | 6 |
| Details | M-CSA 346 |
| Chain | Residue | Details |
| K | GLY105 | electrostatic stabiliser, hydrogen bond donor |
| K | TYR115 | electrostatic stabiliser, hydrogen bond donor, steric role |
| K | GLY161 | electrostatic stabiliser, hydrogen bond donor |
| K | ASP185 | activator |
| K | SER190 | activator |
| K | TYR287 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role |
| site_id | MCSA12 |
| Number of Residues | 6 |
| Details | M-CSA 346 |
| Chain | Residue | Details |
| L | GLY105 | electrostatic stabiliser, hydrogen bond donor |
| L | TYR115 | electrostatic stabiliser, hydrogen bond donor, steric role |
| L | GLY161 | electrostatic stabiliser, hydrogen bond donor |
| L | ASP185 | activator |
| L | SER190 | activator |
| L | TYR287 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role |
