3GDK
Crystal structure of the orotidine 5'-monophosphate decarboxylase from Saccharomyces cerevisiae
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 | 0006222 | biological_process | UMP biosynthetic process |
| A | 0016831 | molecular_function | carboxy-lyase activity |
| A | 0044205 | biological_process | 'de novo' UMP biosynthetic process |
| A | 0055086 | biological_process | nucleobase-containing small molecule metabolic process |
| A | 0072528 | biological_process | pyrimidine-containing compound 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 | 0006222 | biological_process | UMP biosynthetic process |
| B | 0016831 | molecular_function | carboxy-lyase activity |
| B | 0044205 | biological_process | 'de novo' UMP biosynthetic process |
| B | 0055086 | biological_process | nucleobase-containing small molecule metabolic process |
| B | 0072528 | biological_process | pyrimidine-containing compound 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 | 0006222 | biological_process | UMP biosynthetic process |
| C | 0016831 | molecular_function | carboxy-lyase activity |
| C | 0044205 | biological_process | 'de novo' UMP biosynthetic process |
| C | 0055086 | biological_process | nucleobase-containing small molecule metabolic process |
| C | 0072528 | biological_process | pyrimidine-containing compound biosynthetic process |
| D | 0004590 | molecular_function | orotidine-5'-phosphate decarboxylase activity |
| D | 0005829 | cellular_component | cytosol |
| D | 0006207 | biological_process | 'de novo' pyrimidine nucleobase biosynthetic process |
| D | 0006221 | biological_process | pyrimidine nucleotide biosynthetic process |
| D | 0006222 | biological_process | UMP biosynthetic process |
| D | 0016831 | molecular_function | carboxy-lyase activity |
| D | 0044205 | biological_process | 'de novo' UMP biosynthetic process |
| D | 0055086 | biological_process | nucleobase-containing small molecule metabolic process |
| D | 0072528 | biological_process | pyrimidine-containing compound biosynthetic process |
Functional Information from PROSITE/UniProt
| site_id | PS00156 |
| Number of Residues | 14 |
| Details | OMPDECASE Orotidine 5'-phosphate decarboxylase active site. LFeDrKfaDIGnTV |
| Chain | Residue | Details |
| A | LEU88-VAL101 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | ACT_SITE: Proton donor |
| Chain | Residue | Details |
| A | LYS93 | |
| B | LYS93 | |
| C | LYS93 | |
| D | LYS93 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 20 |
| Details | BINDING: |
| Chain | Residue | Details |
| A | ASP37 | |
| B | ARG235 | |
| C | ASP37 | |
| C | LYS59 | |
| C | ASP91 | |
| C | TYR217 | |
| C | ARG235 | |
| D | ASP37 | |
| D | LYS59 | |
| D | ASP91 | |
| D | TYR217 | |
| A | LYS59 | |
| D | ARG235 | |
| A | ASP91 | |
| A | TYR217 | |
| A | ARG235 | |
| B | ASP37 | |
| B | LYS59 | |
| B | ASP91 | |
| B | TYR217 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | MOD_RES: N-acetylserine => ECO:0007744|PubMed:22814378 |
| Chain | Residue | Details |
| A | SER2 | |
| B | SER2 | |
| C | SER2 | |
| D | SER2 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 16 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:12872131 |
| Chain | Residue | Details |
| A | LYS93 | |
| C | LYS209 | |
| C | LYS253 | |
| D | LYS93 | |
| D | LYS209 | |
| D | LYS253 | |
| A | LYS209 | |
| A | LYS253 | |
| B | LYS93 | |
| B | LYS209 | |
| B | LYS253 | |
| C | LYS93 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| A | ASP91 | |
| A | LYS93 |
| site_id | CSA2 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| B | ASP91 | |
| B | LYS93 |
| site_id | CSA3 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| C | ASP91 | |
| C | LYS93 |
| site_id | CSA4 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| D | ASP91 | |
| D | LYS93 |
| site_id | CSA5 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| A | LYS59 | |
| A | ASP96 | |
| A | ASP91 | |
| A | LYS93 |
| site_id | CSA6 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| B | LYS59 | |
| B | ASP96 | |
| B | ASP91 | |
| B | LYS93 |
| site_id | CSA7 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| C | LYS59 | |
| C | ASP96 | |
| C | ASP91 | |
| C | LYS93 |
| site_id | CSA8 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| D | LYS59 | |
| D | ASP96 | |
| D | ASP91 | |
| D | LYS93 |
