2X7J
Structure of the menaquinone biosynthesis protein MenD from Bacillus subtilis
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0009234 | biological_process | menaquinone biosynthetic process |
| A | 0016740 | molecular_function | transferase activity |
| A | 0030145 | molecular_function | manganese ion binding |
| A | 0030976 | molecular_function | thiamine pyrophosphate binding |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0070204 | molecular_function | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0009234 | biological_process | menaquinone biosynthetic process |
| B | 0016740 | molecular_function | transferase activity |
| B | 0030145 | molecular_function | manganese ion binding |
| B | 0030976 | molecular_function | thiamine pyrophosphate binding |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0070204 | molecular_function | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity |
| C | 0000287 | molecular_function | magnesium ion binding |
| C | 0003824 | molecular_function | catalytic activity |
| C | 0009234 | biological_process | menaquinone biosynthetic process |
| C | 0016740 | molecular_function | transferase activity |
| C | 0030145 | molecular_function | manganese ion binding |
| C | 0030976 | molecular_function | thiamine pyrophosphate binding |
| C | 0046872 | molecular_function | metal ion binding |
| C | 0070204 | molecular_function | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity |
| D | 0000287 | molecular_function | magnesium ion binding |
| D | 0003824 | molecular_function | catalytic activity |
| D | 0009234 | biological_process | menaquinone biosynthetic process |
| D | 0016740 | molecular_function | transferase activity |
| D | 0030145 | molecular_function | manganese ion binding |
| D | 0030976 | molecular_function | thiamine pyrophosphate binding |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0070204 | molecular_function | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 23 |
| Details | BINDING SITE FOR RESIDUE TPP A 601 |
| Chain | Residue |
| A | SER405 |
| A | ASN484 |
| A | GLY486 |
| A | GLY487 |
| A | GLY488 |
| A | ILE489 |
| A | PHE490 |
| A | MN602 |
| A | HOH2200 |
| A | HOH2213 |
| A | HOH2237 |
| A | MET406 |
| A | HOH2282 |
| B | GLU54 |
| B | GLN117 |
| B | EDO603 |
| A | ASN431 |
| A | ILE433 |
| A | ASP434 |
| A | GLY456 |
| A | ASP457 |
| A | LEU458 |
| A | SER459 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN A 602 |
| Chain | Residue |
| A | ASP457 |
| A | ASN484 |
| A | GLY486 |
| A | TPP601 |
| A | HOH2237 |
| site_id | AC3 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE EDO A 603 |
| Chain | Residue |
| A | GLY30 |
| A | SER31 |
| A | ARG32 |
| A | THR77 |
| A | ARG106 |
| A | GLN117 |
| B | PHE490 |
| B | TPP601 |
| site_id | AC4 |
| Number of Residues | 21 |
| Details | BINDING SITE FOR RESIDUE TPP B 601 |
| Chain | Residue |
| A | GLU54 |
| A | GLN117 |
| A | EDO603 |
| B | SER405 |
| B | MET406 |
| B | ASN431 |
| B | ILE433 |
| B | ASP434 |
| B | GLY456 |
| B | ASP457 |
| B | LEU458 |
| B | SER459 |
| B | ASN484 |
| B | GLY486 |
| B | GLY487 |
| B | GLY488 |
| B | ILE489 |
| B | MN602 |
| B | HOH2155 |
| B | HOH2238 |
| B | HOH2239 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN B 602 |
| Chain | Residue |
| B | ASP457 |
| B | ASN484 |
| B | GLY486 |
| B | TPP601 |
| B | HOH2239 |
| site_id | AC6 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO B 603 |
| Chain | Residue |
| A | PHE490 |
| A | TPP601 |
| B | GLY30 |
| B | SER31 |
| B | ARG32 |
| B | THR77 |
| B | GLN117 |
| site_id | AC7 |
| Number of Residues | 26 |
| Details | BINDING SITE FOR RESIDUE TPP C 601 |
| Chain | Residue |
| C | SER405 |
| C | MET406 |
| C | PRO407 |
| C | ASN431 |
| C | GLY432 |
| C | ILE433 |
| C | ASP434 |
| C | GLY456 |
| C | ASP457 |
| C | LEU458 |
| C | SER459 |
| C | ASN484 |
| C | GLY486 |
| C | GLY487 |
| C | GLY488 |
| C | ILE489 |
| C | PHE490 |
| C | MN602 |
| C | HOH2251 |
| C | HOH2252 |
| C | HOH2253 |
| D | PRO29 |
| D | GLU54 |
| D | THR80 |
| D | GLN117 |
| D | EDO603 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN C 602 |
| Chain | Residue |
| C | HOH2253 |
| C | ASP457 |
| C | ASN484 |
| C | GLY486 |
| C | TPP601 |
| site_id | AC9 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO C 603 |
| Chain | Residue |
| C | GLY30 |
| C | SER31 |
| C | ARG32 |
| C | THR77 |
| C | GLN117 |
| D | PHE490 |
| D | TPP601 |
| site_id | BC1 |
| Number of Residues | 25 |
| Details | BINDING SITE FOR RESIDUE TPP D 601 |
| Chain | Residue |
| C | PRO29 |
| C | GLU54 |
| C | THR80 |
| C | GLN117 |
| C | EDO603 |
| D | SER405 |
| D | MET406 |
| D | ASN431 |
| D | ILE433 |
| D | ASP434 |
| D | GLY456 |
| D | ASP457 |
| D | LEU458 |
| D | SER459 |
| D | ASN484 |
| D | GLY486 |
| D | GLY487 |
| D | GLY488 |
| D | ILE489 |
| D | PHE490 |
| D | MN602 |
| D | HOH2206 |
| D | HOH2290 |
| D | HOH2291 |
| D | HOH2292 |
| site_id | BC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN D 602 |
| Chain | Residue |
| D | ASP457 |
| D | ASN484 |
| D | GLY486 |
| D | TPP601 |
| D | HOH2292 |
| site_id | BC3 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO D 603 |
| Chain | Residue |
| C | PHE490 |
| C | TPP601 |
| D | GLY30 |
| D | SER31 |
| D | ARG32 |
| D | THR77 |
| D | GLN117 |
| site_id | BC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE NA D 1581 |
| Chain | Residue |
| D | CYS40 |
| D | ALA41 |
| D | HIS43 |
| D | ILE46 |
| site_id | BC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE NA A 1581 |
| Chain | Residue |
| A | CYS40 |
| A | ALA41 |
| A | HIS43 |
| A | ILE46 |
| site_id | BC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NA B 1581 |
| Chain | Residue |
| B | CYS40 |
| B | ALA41 |
| B | HIS43 |
| B | ILE46 |
| B | HOH2022 |
| B | HOH2024 |
| site_id | BC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA C 1579 |
| Chain | Residue |
| C | CYS40 |
| C | ALA41 |
| C | HIS43 |
| C | ILE46 |
| C | HOH2015 |
| site_id | BC8 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1582 |
| Chain | Residue |
| A | ARG32 |
| A | PRO107 |
| A | LEU110 |
| A | LEU173 |
| A | ARG174 |
| A | GLU175 |
| A | HOH2283 |
| site_id | BC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1582 |
| Chain | Residue |
| B | ARG32 |
| B | PRO107 |
| B | LEU110 |
| B | LEU173 |
| B | ARG174 |
| B | GLU175 |
| site_id | CC1 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 D 1582 |
| Chain | Residue |
| D | ARG32 |
| D | PRO107 |
| D | LEU110 |
| D | ARG174 |
| D | GLU175 |
| D | HOH2041 |
| D | HOH2293 |
| site_id | CC2 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE SO4 C 1580 |
| Chain | Residue |
| C | ARG32 |
| C | PRO107 |
| C | GLU109 |
| C | LEU110 |
| C | LEU173 |
| C | ARG174 |
| C | GLU175 |
| C | HOH2254 |
| C | HOH2255 |
| site_id | CC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1583 |
| Chain | Residue |
| A | LYS276 |
| A | ARG564 |
| A | HOH2284 |
| A | HOH2285 |
| site_id | CC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1583 |
| Chain | Residue |
| B | LYS276 |
| B | ARG564 |
| B | HOH2121 |
| site_id | CC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 C 1581 |
| Chain | Residue |
| C | LYS276 |
| C | PHE492 |
| C | ARG564 |
| C | HOH2256 |
| site_id | CC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 D 1583 |
| Chain | Residue |
| D | LYS276 |
| D | PHE492 |
| D | ARG564 |
Functional Information from PROSITE/UniProt
| site_id | PS00041 |
| Number of Residues | 42 |
| Details | HTH_ARAC_FAMILY_1 Bacterial regulatory proteins, araC family signature. RVpiIVltAdrphe....LrEVGAPqAInqhflFgnfVKFftDsAL |
| Chain | Residue | Details |
| A | ARG96-LEU137 |
