3G1F
Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 5,6-dihydroorotidine 5'-monophosphate
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 |
| 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 | 0016829 | molecular_function | lyase activity |
| D | 0016831 | molecular_function | carboxy-lyase activity |
| D | 0044205 | biological_process | 'de novo' UMP biosynthetic process |
| E | 0004590 | molecular_function | orotidine-5'-phosphate decarboxylase activity |
| E | 0005829 | cellular_component | cytosol |
| E | 0006207 | biological_process | 'de novo' pyrimidine nucleobase biosynthetic process |
| E | 0006221 | biological_process | pyrimidine nucleotide biosynthetic process |
| E | 0016829 | molecular_function | lyase activity |
| E | 0016831 | molecular_function | carboxy-lyase activity |
| E | 0044205 | biological_process | 'de novo' UMP biosynthetic process |
| F | 0004590 | molecular_function | orotidine-5'-phosphate decarboxylase activity |
| F | 0005829 | cellular_component | cytosol |
| F | 0006207 | biological_process | 'de novo' pyrimidine nucleobase biosynthetic process |
| F | 0006221 | biological_process | pyrimidine nucleotide biosynthetic process |
| F | 0016829 | molecular_function | lyase activity |
| F | 0016831 | molecular_function | carboxy-lyase activity |
| F | 0044205 | biological_process | 'de novo' UMP biosynthetic process |
| G | 0004590 | molecular_function | orotidine-5'-phosphate decarboxylase activity |
| G | 0005829 | cellular_component | cytosol |
| G | 0006207 | biological_process | 'de novo' pyrimidine nucleobase biosynthetic process |
| G | 0006221 | biological_process | pyrimidine nucleotide biosynthetic process |
| G | 0016829 | molecular_function | lyase activity |
| G | 0016831 | molecular_function | carboxy-lyase activity |
| G | 0044205 | biological_process | 'de novo' UMP biosynthetic process |
| H | 0004590 | molecular_function | orotidine-5'-phosphate decarboxylase activity |
| H | 0005829 | cellular_component | cytosol |
| H | 0006207 | biological_process | 'de novo' pyrimidine nucleobase biosynthetic process |
| H | 0006221 | biological_process | pyrimidine nucleotide biosynthetic process |
| H | 0016829 | molecular_function | lyase activity |
| H | 0016831 | molecular_function | carboxy-lyase activity |
| H | 0044205 | biological_process | 'de novo' UMP biosynthetic process |
| I | 0004590 | molecular_function | orotidine-5'-phosphate decarboxylase activity |
| I | 0005829 | cellular_component | cytosol |
| I | 0006207 | biological_process | 'de novo' pyrimidine nucleobase biosynthetic process |
| I | 0006221 | biological_process | pyrimidine nucleotide biosynthetic process |
| I | 0016829 | molecular_function | lyase activity |
| I | 0016831 | molecular_function | carboxy-lyase activity |
| I | 0044205 | biological_process | 'de novo' UMP biosynthetic process |
| J | 0004590 | molecular_function | orotidine-5'-phosphate decarboxylase activity |
| J | 0005829 | cellular_component | cytosol |
| J | 0006207 | biological_process | 'de novo' pyrimidine nucleobase biosynthetic process |
| J | 0006221 | biological_process | pyrimidine nucleotide biosynthetic process |
| J | 0016829 | molecular_function | lyase activity |
| J | 0016831 | molecular_function | carboxy-lyase activity |
| J | 0044205 | biological_process | 'de novo' UMP biosynthetic process |
| K | 0004590 | molecular_function | orotidine-5'-phosphate decarboxylase activity |
| K | 0005829 | cellular_component | cytosol |
| K | 0006207 | biological_process | 'de novo' pyrimidine nucleobase biosynthetic process |
| K | 0006221 | biological_process | pyrimidine nucleotide biosynthetic process |
| K | 0016829 | molecular_function | lyase activity |
| K | 0016831 | molecular_function | carboxy-lyase activity |
| K | 0044205 | biological_process | 'de novo' UMP biosynthetic process |
| L | 0004590 | molecular_function | orotidine-5'-phosphate decarboxylase activity |
| L | 0005829 | cellular_component | cytosol |
| L | 0006207 | biological_process | 'de novo' pyrimidine nucleobase biosynthetic process |
| L | 0006221 | biological_process | pyrimidine nucleotide biosynthetic process |
| L | 0016829 | molecular_function | lyase activity |
| L | 0016831 | molecular_function | carboxy-lyase activity |
| L | 0044205 | biological_process | 'de novo' UMP biosynthetic process |
| M | 0004590 | molecular_function | orotidine-5'-phosphate decarboxylase activity |
| M | 0005829 | cellular_component | cytosol |
| M | 0006207 | biological_process | 'de novo' pyrimidine nucleobase biosynthetic process |
| M | 0006221 | biological_process | pyrimidine nucleotide biosynthetic process |
| M | 0016829 | molecular_function | lyase activity |
| M | 0016831 | molecular_function | carboxy-lyase activity |
| M | 0044205 | biological_process | 'de novo' UMP biosynthetic process |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE 2OM A 229 |
| Chain | Residue |
| A | ASP20 |
| A | GLY202 |
| A | ARG203 |
| A | HOH234 |
| A | HOH240 |
| A | HOH246 |
| B | ASP75 |
| B | ILE76 |
| B | THR79 |
| A | LYS42 |
| A | ASP70 |
| A | LYS72 |
| A | MET126 |
| A | SER127 |
| A | PRO180 |
| A | GLN185 |
| A | VAL201 |
| site_id | AC2 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE 2OM B 229 |
| Chain | Residue |
| A | ASP75 |
| A | ILE76 |
| A | THR79 |
| B | ASP20 |
| B | LYS42 |
| B | ASP70 |
| B | LYS72 |
| B | MET126 |
| B | SER127 |
| B | PRO180 |
| B | VAL182 |
| B | GLN185 |
| B | GLY202 |
| B | ARG203 |
| site_id | AC3 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE 2OM C 229 |
| Chain | Residue |
| C | ASP20 |
| C | LYS42 |
| C | ASP70 |
| C | LYS72 |
| C | ILE96 |
| C | MET126 |
| C | SER127 |
| C | PRO180 |
| C | GLN185 |
| C | GLY202 |
| C | ARG203 |
| C | HOH236 |
| C | HOH238 |
| D | ASP75 |
| D | ILE76 |
| D | THR79 |
| site_id | AC4 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE 2OM D 229 |
| Chain | Residue |
| C | ASP75 |
| C | THR79 |
| D | ASP20 |
| D | LYS42 |
| D | ASP70 |
| D | LYS72 |
| D | MET126 |
| D | SER127 |
| D | PRO180 |
| D | ALA184 |
| D | GLN185 |
| D | GLY202 |
| D | ARG203 |
| D | TYR206 |
| site_id | AC5 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE 2OM E 229 |
| Chain | Residue |
| E | ASP20 |
| E | LYS42 |
| E | ASP70 |
| E | LYS72 |
| E | ILE96 |
| E | MET126 |
| E | SER127 |
| E | PRO180 |
| E | VAL182 |
| E | GLN185 |
| E | GLY202 |
| E | ARG203 |
| F | ASP75 |
| F | ILE76 |
| F | THR79 |
| site_id | AC6 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE 2OM F 229 |
| Chain | Residue |
| E | ASP75 |
| E | THR79 |
| F | ASP20 |
| F | LYS42 |
| F | ASP70 |
| F | LYS72 |
| F | LEU123 |
| F | MET126 |
| F | SER127 |
| F | PRO180 |
| F | VAL182 |
| F | ALA184 |
| F | GLN185 |
| F | GLY202 |
| F | ARG203 |
| site_id | AC7 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE 2OM G 229 |
| Chain | Residue |
| G | VAL182 |
| G | GLN185 |
| G | GLY202 |
| G | ARG203 |
| H | ASP75 |
| H | ILE76 |
| H | THR79 |
| G | ASP20 |
| G | LYS42 |
| G | ASP70 |
| G | LYS72 |
| G | ILE96 |
| G | MET126 |
| G | SER127 |
| G | PRO180 |
| site_id | AC8 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE 2OM H 229 |
| Chain | Residue |
| G | ASP75 |
| G | ILE76 |
| G | THR79 |
| H | ASP20 |
| H | LYS42 |
| H | ASP70 |
| H | LYS72 |
| H | MET126 |
| H | SER127 |
| H | PRO180 |
| H | VAL182 |
| H | GLN185 |
| H | GLY202 |
| H | ARG203 |
| site_id | AC9 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE 2OM I 229 |
| Chain | Residue |
| I | ASP20 |
| I | LYS42 |
| I | ASP70 |
| I | LYS72 |
| I | LEU123 |
| I | MET126 |
| I | SER127 |
| I | GLY183 |
| I | ALA184 |
| I | GLN185 |
| I | GLY202 |
| I | ARG203 |
| I | TYR206 |
| I | HOH235 |
| J | ASP75 |
| J | ILE76 |
| J | THR79 |
| site_id | BC1 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE 2OM J 229 |
| Chain | Residue |
| I | ASP75 |
| I | ILE76 |
| I | THR79 |
| J | ASP20 |
| J | LYS42 |
| J | ASP70 |
| J | LYS72 |
| J | MET126 |
| J | SER127 |
| J | PRO180 |
| J | GLN185 |
| J | GLY202 |
| J | ARG203 |
| site_id | BC2 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE 2OM K 229 |
| Chain | Residue |
| K | ASP20 |
| K | LYS42 |
| K | ASP70 |
| K | LYS72 |
| K | MET126 |
| K | SER127 |
| K | PRO180 |
| K | GLN185 |
| K | GLY202 |
| K | ARG203 |
| L | ASP75 |
| L | ILE76 |
| L | THR79 |
| site_id | BC3 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE 2OM L 229 |
| Chain | Residue |
| K | ASP75 |
| K | ILE76 |
| K | THR79 |
| L | ASP20 |
| L | LYS42 |
| L | ASP70 |
| L | LYS72 |
| L | MET126 |
| L | SER127 |
| L | PRO180 |
| L | GLY183 |
| L | GLN185 |
| L | VAL201 |
| L | GLY202 |
| L | ARG203 |
| L | TYR206 |
| site_id | BC4 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE 2OM M 229 |
| Chain | Residue |
| M | ASP20 |
| M | LYS42 |
| M | ASP70 |
| M | LYS72 |
| M | ASP75 |
| M | ILE76 |
| M | THR79 |
| M | MET126 |
| M | SER127 |
| M | PRO180 |
| M | GLN185 |
| M | GLY202 |
| M | ARG203 |
| M | HOH237 |
Functional Information from PROSITE/UniProt
| site_id | PS00156 |
| Number of Residues | 14 |
| Details | OMPDECASE Orotidine 5'-phosphate decarboxylase active site. IIaDfKvaDIPeTN |
| Chain | Residue | Details |
| A | ILE67-ASN80 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 13 |
| Details | Active site: {"description":"Proton donor"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 312 |
| Details | Binding site: {} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| A | LYS72 | |
| A | ASP70 |
| site_id | CSA10 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| J | LYS72 | |
| J | ASP70 |
| site_id | CSA11 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| K | LYS72 | |
| K | ASP70 |
| site_id | CSA12 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| L | LYS72 | |
| L | ASP70 |
| site_id | CSA13 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| M | LYS72 | |
| M | ASP70 |
| site_id | CSA14 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| A | LYS42 | |
| A | ASP75 | |
| A | LYS72 | |
| A | ASP70 |
| site_id | CSA15 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| B | LYS42 | |
| B | ASP75 | |
| B | LYS72 | |
| B | ASP70 |
| site_id | CSA16 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| C | LYS42 | |
| C | ASP75 | |
| C | LYS72 | |
| C | ASP70 |
| site_id | CSA17 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| D | LYS42 | |
| D | ASP75 | |
| D | LYS72 | |
| D | ASP70 |
| site_id | CSA18 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| E | LYS42 | |
| E | ASP75 | |
| E | LYS72 | |
| E | ASP70 |
| site_id | CSA19 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| F | LYS42 | |
| F | ASP75 | |
| F | LYS72 | |
| F | ASP70 |
| site_id | CSA2 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| B | LYS72 | |
| B | ASP70 |
| site_id | CSA20 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| G | LYS42 | |
| G | ASP75 | |
| G | LYS72 | |
| G | ASP70 |
| site_id | CSA21 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| H | LYS42 | |
| H | ASP75 | |
| H | LYS72 | |
| H | ASP70 |
| site_id | CSA22 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| I | LYS42 | |
| I | ASP75 | |
| I | LYS72 | |
| I | ASP70 |
| site_id | CSA23 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| J | LYS42 | |
| J | ASP75 | |
| J | LYS72 | |
| J | ASP70 |
| site_id | CSA24 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| K | LYS42 | |
| K | ASP75 | |
| K | LYS72 | |
| K | ASP70 |
| site_id | CSA25 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| L | LYS42 | |
| L | ASP75 | |
| L | LYS72 | |
| L | ASP70 |
| site_id | CSA26 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| M | LYS42 | |
| M | ASP75 | |
| M | LYS72 | |
| M | ASP70 |
| site_id | CSA3 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| C | LYS72 | |
| C | ASP70 |
| site_id | CSA4 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| D | LYS72 | |
| D | ASP70 |
| site_id | CSA5 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| E | LYS72 | |
| E | ASP70 |
| site_id | CSA6 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| F | LYS72 | |
| F | ASP70 |
| site_id | CSA7 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| G | LYS72 | |
| G | ASP70 |
| site_id | CSA8 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| H | LYS72 | |
| H | ASP70 |
| site_id | CSA9 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dbt |
| Chain | Residue | Details |
| I | LYS72 | |
| I | ASP70 |
