1DBT
CRYSTAL STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM BACILLUS SUBTILIS COMPLEXED WITH UMP
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004590 | molecular_function | orotidine-5'-phosphate decarboxylase activity |
| A | 0005829 | cellular_component | cytosol |
| A | 0006207 | biological_process | 'de novo' pyrimidine nucleobase biosynthetic process |
| A | 0006221 | biological_process | pyrimidine nucleotide biosynthetic process |
| A | 0016829 | molecular_function | lyase activity |
| A | 0016831 | molecular_function | carboxy-lyase activity |
| A | 0044205 | biological_process | 'de novo' UMP biosynthetic process |
| B | 0004590 | molecular_function | orotidine-5'-phosphate decarboxylase activity |
| B | 0005829 | cellular_component | cytosol |
| B | 0006207 | biological_process | 'de novo' pyrimidine nucleobase biosynthetic process |
| B | 0006221 | biological_process | pyrimidine nucleotide biosynthetic process |
| B | 0016829 | molecular_function | lyase activity |
| B | 0016831 | molecular_function | carboxy-lyase activity |
| B | 0044205 | biological_process | 'de novo' UMP biosynthetic process |
| C | 0004590 | molecular_function | orotidine-5'-phosphate decarboxylase activity |
| C | 0005829 | cellular_component | cytosol |
| C | 0006207 | biological_process | 'de novo' pyrimidine nucleobase biosynthetic process |
| C | 0006221 | biological_process | pyrimidine nucleotide biosynthetic process |
| C | 0016829 | molecular_function | lyase activity |
| C | 0016831 | molecular_function | carboxy-lyase activity |
| C | 0044205 | biological_process | 'de novo' UMP biosynthetic process |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE U5P A 250 |
| Chain | Residue |
| A | ASP11 |
| A | VAL212 |
| A | GLY214 |
| A | ARG215 |
| A | HOH254 |
| A | HOH255 |
| A | HOH268 |
| A | HOH273 |
| B | ASP65 |
| B | ILE66 |
| B | THR69 |
| A | LYS33 |
| A | LYS62 |
| A | LEU122 |
| A | THR123 |
| A | VAL160 |
| A | PRO182 |
| A | ARG185 |
| A | GLN194 |
| site_id | AC2 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE U5P B 251 |
| Chain | Residue |
| A | ASP65 |
| A | ILE66 |
| A | THR69 |
| B | ASP11 |
| B | LYS33 |
| B | LYS62 |
| B | LEU122 |
| B | THR123 |
| B | VAL160 |
| B | PRO182 |
| B | ARG185 |
| B | GLN194 |
| B | VAL212 |
| B | GLY214 |
| B | ARG215 |
| B | HOH264 |
| B | HOH271 |
| B | HOH278 |
| B | HOH284 |
| site_id | AC3 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE U5P C 252 |
| Chain | Residue |
| C | ASP11 |
| C | LYS33 |
| C | LYS62 |
| C | ASP65 |
| C | ILE66 |
| C | THR69 |
| C | LEU122 |
| C | THR123 |
| C | VAL160 |
| C | PRO182 |
| C | ARG185 |
| C | GLN194 |
| C | VAL212 |
| C | GLY214 |
| C | ARG215 |
| C | HOH256 |
| C | HOH261 |
| C | HOH264 |
| C | HOH275 |
Functional Information from PROSITE/UniProt
| site_id | PS00156 |
| Number of Residues | 14 |
| Details | OMPDECASE Orotidine 5'-phosphate decarboxylase active site. LFlDlKlhDIPtTV |
| Chain | Residue | Details |
| A | LEU57-VAL70 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 3 |
| Details | Active site: {"description":"Proton donor"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 48 |
| Details | Binding site: {} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 3 |
| Details | a catalytic site defined by CSA, PubMed 10681442, 11114509, 19472232 |
| Chain | Residue | Details |
| A | LYS62 | |
| A | ASP60 | |
| B | ASP65 |
| site_id | MCSA1 |
| Number of Residues | 6 |
| Details | M-CSA 50 |
| Chain | Residue | Details |
| A | LYS33 | electrostatic destabiliser, electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor |
| A | ASP60 | activator, electrostatic destabiliser, hydrogen bond acceptor, repulsive charge-charge interaction |
| A | LYS62 | activator, electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| A | ASP65 | activator, electrostatic stabiliser, hydrogen bond acceptor |
| A | THR123 | electrostatic stabiliser, hydrogen bond donor |
| A | ARG215 | electrostatic destabiliser, hydrogen bond donor |
| site_id | MCSA2 |
| Number of Residues | 6 |
| Details | M-CSA 50 |
| Chain | Residue | Details |
| B | LYS33 | electrostatic destabiliser, electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor |
| B | ASP60 | activator, electrostatic destabiliser, hydrogen bond acceptor, repulsive charge-charge interaction |
| B | LYS62 | activator, electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| B | ASP65 | activator, electrostatic stabiliser, hydrogen bond acceptor |
| B | THR123 | electrostatic stabiliser, hydrogen bond donor |
| B | ARG215 | electrostatic destabiliser, hydrogen bond donor |
| site_id | MCSA3 |
| Number of Residues | 6 |
| Details | M-CSA 50 |
| Chain | Residue | Details |
| C | LYS33 | electrostatic destabiliser, electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor |
| C | ASP60 | activator, electrostatic destabiliser, hydrogen bond acceptor, repulsive charge-charge interaction |
| C | LYS62 | activator, electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| C | ASP65 | activator, electrostatic stabiliser, hydrogen bond acceptor |
| C | THR123 | electrostatic stabiliser, hydrogen bond donor |
| C | ARG215 | electrostatic destabiliser, hydrogen bond donor |
