4EB4
Crystal structure of mouse thymidylate synthase in ternary complex with dUMP and Tomudex
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000900 | molecular_function | mRNA regulatory element binding translation repressor activity |
| A | 0004799 | molecular_function | thymidylate synthase activity |
| A | 0005634 | cellular_component | nucleus |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005739 | cellular_component | mitochondrion |
| A | 0005743 | cellular_component | mitochondrial inner membrane |
| A | 0005759 | cellular_component | mitochondrial matrix |
| A | 0005829 | cellular_component | cytosol |
| A | 0006231 | biological_process | dTMP biosynthetic process |
| A | 0006235 | biological_process | dTTP biosynthetic process |
| A | 0008168 | molecular_function | methyltransferase activity |
| A | 0009165 | biological_process | nucleotide biosynthetic process |
| A | 0016020 | cellular_component | membrane |
| A | 0016740 | molecular_function | transferase activity |
| A | 0016741 | molecular_function | transferase activity, transferring one-carbon groups |
| A | 0017148 | biological_process | negative regulation of translation |
| A | 0032259 | biological_process | methylation |
| A | 0035999 | biological_process | tetrahydrofolate interconversion |
| A | 0046653 | biological_process | tetrahydrofolate metabolic process |
| A | 1990825 | molecular_function | sequence-specific mRNA binding |
| B | 0000900 | molecular_function | mRNA regulatory element binding translation repressor activity |
| B | 0004799 | molecular_function | thymidylate synthase activity |
| B | 0005634 | cellular_component | nucleus |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005739 | cellular_component | mitochondrion |
| B | 0005743 | cellular_component | mitochondrial inner membrane |
| B | 0005759 | cellular_component | mitochondrial matrix |
| B | 0005829 | cellular_component | cytosol |
| B | 0006231 | biological_process | dTMP biosynthetic process |
| B | 0006235 | biological_process | dTTP biosynthetic process |
| B | 0008168 | molecular_function | methyltransferase activity |
| B | 0009165 | biological_process | nucleotide biosynthetic process |
| B | 0016020 | cellular_component | membrane |
| B | 0016740 | molecular_function | transferase activity |
| B | 0016741 | molecular_function | transferase activity, transferring one-carbon groups |
| B | 0017148 | biological_process | negative regulation of translation |
| B | 0032259 | biological_process | methylation |
| B | 0035999 | biological_process | tetrahydrofolate interconversion |
| B | 0046653 | biological_process | tetrahydrofolate metabolic process |
| B | 1990825 | molecular_function | sequence-specific mRNA binding |
| C | 0000900 | molecular_function | mRNA regulatory element binding translation repressor activity |
| C | 0004799 | molecular_function | thymidylate synthase activity |
| C | 0005634 | cellular_component | nucleus |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005739 | cellular_component | mitochondrion |
| C | 0005743 | cellular_component | mitochondrial inner membrane |
| C | 0005759 | cellular_component | mitochondrial matrix |
| C | 0005829 | cellular_component | cytosol |
| C | 0006231 | biological_process | dTMP biosynthetic process |
| C | 0006235 | biological_process | dTTP biosynthetic process |
| C | 0008168 | molecular_function | methyltransferase activity |
| C | 0009165 | biological_process | nucleotide biosynthetic process |
| C | 0016020 | cellular_component | membrane |
| C | 0016740 | molecular_function | transferase activity |
| C | 0016741 | molecular_function | transferase activity, transferring one-carbon groups |
| C | 0017148 | biological_process | negative regulation of translation |
| C | 0032259 | biological_process | methylation |
| C | 0035999 | biological_process | tetrahydrofolate interconversion |
| C | 0046653 | biological_process | tetrahydrofolate metabolic process |
| C | 1990825 | molecular_function | sequence-specific mRNA binding |
| D | 0000900 | molecular_function | mRNA regulatory element binding translation repressor activity |
| D | 0004799 | molecular_function | thymidylate synthase activity |
| D | 0005634 | cellular_component | nucleus |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005739 | cellular_component | mitochondrion |
| D | 0005743 | cellular_component | mitochondrial inner membrane |
| D | 0005759 | cellular_component | mitochondrial matrix |
| D | 0005829 | cellular_component | cytosol |
| D | 0006231 | biological_process | dTMP biosynthetic process |
| D | 0006235 | biological_process | dTTP biosynthetic process |
| D | 0008168 | molecular_function | methyltransferase activity |
| D | 0009165 | biological_process | nucleotide biosynthetic process |
| D | 0016020 | cellular_component | membrane |
| D | 0016740 | molecular_function | transferase activity |
| D | 0016741 | molecular_function | transferase activity, transferring one-carbon groups |
| D | 0017148 | biological_process | negative regulation of translation |
| D | 0032259 | biological_process | methylation |
| D | 0035999 | biological_process | tetrahydrofolate interconversion |
| D | 0046653 | biological_process | tetrahydrofolate metabolic process |
| D | 1990825 | molecular_function | sequence-specific mRNA binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE UMP A 401 |
| Chain | Residue |
| A | ARG44 |
| A | HIS250 |
| A | TYR252 |
| A | D16402 |
| A | HOH502 |
| A | HOH625 |
| B | ARG169 |
| B | ARG170 |
| A | CYS189 |
| A | HIS190 |
| A | GLN208 |
| A | ARG209 |
| A | SER210 |
| A | GLY211 |
| A | ASP212 |
| A | ASN220 |
| site_id | AC2 |
| Number of Residues | 21 |
| Details | BINDING SITE FOR RESIDUE D16 A 402 |
| Chain | Residue |
| A | PHE74 |
| A | ILE102 |
| A | TRP103 |
| A | ASP212 |
| A | LEU215 |
| A | GLY216 |
| A | PHE219 |
| A | ASN220 |
| A | TYR252 |
| A | LYS302 |
| A | MET303 |
| A | MET305 |
| A | ALA306 |
| A | UMP401 |
| A | HOH517 |
| A | HOH635 |
| A | HOH665 |
| A | HOH684 |
| A | HOH746 |
| A | HOH855 |
| A | HOH893 |
| site_id | AC3 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE DTT A 403 |
| Chain | Residue |
| A | GLN154 |
| A | LYS157 |
| A | VAL158 |
| A | THR161 |
| A | ASP168 |
| A | ARG170 |
| A | ILE172 |
| A | HOH550 |
| A | HOH562 |
| A | HOH631 |
| A | HOH793 |
| B | LEU181 |
| site_id | AC4 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL A 404 |
| Chain | Residue |
| A | ASP167 |
| A | VAL198 |
| A | ASN199 |
| A | HOH645 |
| A | HOH767 |
| B | LYS40 |
| B | LYS41 |
| B | GLU42 |
| site_id | AC5 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL A 405 |
| Chain | Residue |
| A | ASN177 |
| A | LYS179 |
| A | HOH702 |
| A | HOH853 |
| B | GLY137 |
| B | ASN177 |
| B | LYS179 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE GOL A 406 |
| Chain | Residue |
| A | HOH618 |
| A | HOH628 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL A 407 |
| Chain | Residue |
| A | ARG277 |
| A | LYS278 |
| A | HOH797 |
| B | LYS87 |
| B | LYS98 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 A 408 |
| Chain | Residue |
| A | ARG268 |
| A | PRO297 |
| A | HIS298 |
| A | PRO299 |
| site_id | AC9 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE UMP B 401 |
| Chain | Residue |
| A | ARG169 |
| A | ARG170 |
| B | ARG44 |
| B | CYS189 |
| B | HIS190 |
| B | GLN208 |
| B | ARG209 |
| B | SER210 |
| B | ASP212 |
| B | ASN220 |
| B | HIS250 |
| B | TYR252 |
| B | D16402 |
| B | HOH595 |
| B | HOH838 |
| site_id | BC1 |
| Number of Residues | 21 |
| Details | BINDING SITE FOR RESIDUE D16 B 402 |
| Chain | Residue |
| B | LYS302 |
| B | MET303 |
| B | MET305 |
| B | ALA306 |
| B | UMP401 |
| B | HOH570 |
| B | HOH612 |
| B | HOH679 |
| B | HOH680 |
| B | HOH715 |
| B | HOH774 |
| B | HOH832 |
| B | PHE74 |
| B | ILE102 |
| B | TRP103 |
| B | ASN106 |
| B | ASP212 |
| B | LEU215 |
| B | GLY216 |
| B | PHE219 |
| B | TYR252 |
| site_id | BC2 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE GOL B 403 |
| Chain | Residue |
| B | LEU115 |
| B | LEU181 |
| B | PRO182 |
| B | MET184 |
| B | PRO187 |
| B | HOH512 |
| B | HOH532 |
| B | HOH738 |
| B | HOH796 |
| B | HOH846 |
| site_id | BC3 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL B 404 |
| Chain | Residue |
| A | LYS40 |
| A | LYS41 |
| A | GLU42 |
| A | HOH741 |
| B | ASP167 |
| B | VAL198 |
| B | ASN199 |
| B | HOH740 |
| site_id | BC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL B 405 |
| Chain | Residue |
| B | HIS22 |
| B | GLU24 |
| B | LEU25 |
| B | PRO269 |
| B | HOH566 |
| site_id | BC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MES B 406 |
| Chain | Residue |
| B | ARG36 |
| B | CYS37 |
| B | GLY38 |
| B | PHE39 |
| B | LYS40 |
| B | HOH843 |
| site_id | BC6 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE UMP C 401 |
| Chain | Residue |
| C | ARG44 |
| C | CYS189 |
| C | HIS190 |
| C | ARG209 |
| C | SER210 |
| C | ASP212 |
| C | GLY216 |
| C | ASN220 |
| C | HIS250 |
| C | TYR252 |
| C | D16402 |
| C | HOH505 |
| C | HOH694 |
| D | ARG169 |
| D | ARG170 |
| site_id | BC7 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE D16 C 402 |
| Chain | Residue |
| C | PHE74 |
| C | ARG101 |
| C | ASP212 |
| C | LEU215 |
| C | GLY216 |
| C | PHE219 |
| C | TYR252 |
| C | UMP401 |
| C | HOH564 |
| C | HOH618 |
| C | HOH622 |
| C | HOH680 |
| C | HOH741 |
| site_id | BC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE GOL C 403 |
| Chain | Residue |
| C | ARG21 |
| C | ARG58 |
| C | HOH606 |
| C | HOH754 |
| site_id | BC9 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE UMP D 401 |
| Chain | Residue |
| C | ARG169 |
| C | ARG170 |
| D | ARG44 |
| D | CYS189 |
| D | HIS190 |
| D | ARG209 |
| D | SER210 |
| D | GLY211 |
| D | ASP212 |
| D | GLY216 |
| D | ASN220 |
| D | HIS250 |
| D | TYR252 |
| D | D16402 |
| D | HOH566 |
| site_id | CC1 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE D16 D 402 |
| Chain | Residue |
| D | PHE74 |
| D | ILE102 |
| D | ASP212 |
| D | LEU215 |
| D | GLY216 |
| D | PHE219 |
| D | TYR252 |
| D | LYS302 |
| D | MET303 |
| D | UMP401 |
| D | HOH603 |
| D | HOH686 |
| D | HOH699 |
| site_id | CC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL D 403 |
| Chain | Residue |
| D | ARG36 |
| D | CYS37 |
| D | GLY38 |
| D | PHE39 |
| D | GOL404 |
| site_id | CC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE GOL D 404 |
| Chain | Residue |
| C | ASN199 |
| D | PHE39 |
| D | LYS40 |
| D | GOL403 |
Functional Information from PROSITE/UniProt
| site_id | PS00091 |
| Number of Residues | 29 |
| Details | THYMIDYLATE_SYNTHASE Thymidylate synthase active site. RriImcaWNpkdlplma.....LpPCHalcQFyV |
| Chain | Residue | Details |
| A | ARG169-VAL197 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | ACT_SITE: Nucleophile => ECO:0000250|UniProtKB:P0A884 |
| Chain | Residue | Details |
| A | CYS189 | |
| B | CYS189 | |
| C | CYS189 | |
| D | CYS189 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 8 |
| Details | BINDING: in other chain => ECO:0000250|UniProtKB:P0A884 |
| Chain | Residue | Details |
| A | ARG44 | |
| A | ASN220 | |
| B | ARG44 | |
| B | ASN220 | |
| C | ARG44 | |
| C | ASN220 | |
| D | ARG44 | |
| D | ASN220 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:P45352 |
| Chain | Residue | Details |
| A | ARG169 | |
| B | ARG169 | |
| C | ARG169 | |
| D | ARG169 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 12 |
| Details | BINDING: in other chain => ECO:0000250|UniProtKB:P45352 |
| Chain | Residue | Details |
| A | CYS189 | |
| D | CYS189 | |
| D | ARG209 | |
| D | HIS250 | |
| A | ARG209 | |
| A | HIS250 | |
| B | CYS189 | |
| B | ARG209 | |
| B | HIS250 | |
| C | CYS189 | |
| C | ARG209 | |
| C | HIS250 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:P0A884 |
| Chain | Residue | Details |
| A | ASP212 | |
| A | ALA306 | |
| B | ASP212 | |
| B | ALA306 | |
| C | ASP212 | |
| C | ALA306 | |
| D | ASP212 | |
| D | ALA306 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P04818 |
| Chain | Residue | Details |
| A | SER108 | |
| B | SER108 | |
| C | SER108 | |
| D | SER108 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 12 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0000250|UniProtKB:P04818 |
| Chain | Residue | Details |
| A | LYS286 | |
| D | LYS286 | |
| D | LYS302 | |
| A | LYS302 | |
| B | LYS286 | |
| B | LYS302 | |
| C | LYS286 | |
| C | LYS302 |
