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 | ACT_SITE: Proton donor |
Chain | Residue | Details |
B | LYS62 | |
C | LYS62 | |
A | LYS62 |
site_id | SWS_FT_FI2 |
Number of Residues | 24 |
Details | BINDING: |
Chain | Residue | Details |
C | ASP60 | |
C | THR123 | |
C | ARG185 | |
C | GLN194 | |
C | GLY214 | |
C | ARG215 | |
A | ASP11 | |
A | LYS33 | |
A | ASP60 | |
A | THR123 | |
A | ARG185 | |
A | GLN194 | |
A | GLY214 | |
A | ARG215 | |
B | ASP11 | |
B | LYS33 | |
B | ASP60 | |
B | THR123 | |
B | ARG185 | |
B | GLN194 | |
B | GLY214 | |
B | ARG215 | |
C | ASP11 | |
C | LYS33 |
Catalytic Information from CSA
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 |