1LS3
Crystal Structure of the Complex between Rabbit Cytosolic Serine Hydroxymethyltransferase and TriGlu-5-formyl-tetrahydrofolate
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000900 | molecular_function | mRNA regulatory element binding translation repressor activity |
| A | 0004372 | molecular_function | glycine hydroxymethyltransferase activity |
| A | 0005634 | cellular_component | nucleus |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0006544 | biological_process | glycine metabolic process |
| A | 0006563 | biological_process | L-serine metabolic process |
| A | 0006565 | biological_process | L-serine catabolic process |
| A | 0006730 | biological_process | one-carbon metabolic process |
| A | 0008270 | molecular_function | zinc ion binding |
| A | 0009113 | biological_process | purine nucleobase biosynthetic process |
| A | 0016740 | molecular_function | transferase activity |
| A | 0017148 | biological_process | negative regulation of translation |
| A | 0019264 | biological_process | glycine biosynthetic process from serine |
| A | 0030170 | molecular_function | pyridoxal phosphate binding |
| A | 0035999 | biological_process | tetrahydrofolate interconversion |
| A | 0036094 | molecular_function | small molecule binding |
| A | 0042802 | molecular_function | identical protein binding |
| A | 0042803 | molecular_function | protein homodimerization activity |
| A | 0046653 | biological_process | tetrahydrofolate metabolic process |
| A | 0046655 | biological_process | folic acid metabolic process |
| A | 0048027 | molecular_function | mRNA 5'-UTR binding |
| A | 0050897 | molecular_function | cobalt ion binding |
| A | 0051289 | biological_process | protein homotetramerization |
| A | 0070905 | molecular_function | serine binding |
| A | 1904482 | biological_process | cellular response to tetrahydrofolate |
| A | 1990830 | biological_process | cellular response to leukemia inhibitory factor |
| B | 0000900 | molecular_function | mRNA regulatory element binding translation repressor activity |
| B | 0004372 | molecular_function | glycine hydroxymethyltransferase activity |
| B | 0005634 | cellular_component | nucleus |
| B | 0005654 | cellular_component | nucleoplasm |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0006544 | biological_process | glycine metabolic process |
| B | 0006563 | biological_process | L-serine metabolic process |
| B | 0006565 | biological_process | L-serine catabolic process |
| B | 0006730 | biological_process | one-carbon metabolic process |
| B | 0008270 | molecular_function | zinc ion binding |
| B | 0009113 | biological_process | purine nucleobase biosynthetic process |
| B | 0016740 | molecular_function | transferase activity |
| B | 0017148 | biological_process | negative regulation of translation |
| B | 0019264 | biological_process | glycine biosynthetic process from serine |
| B | 0030170 | molecular_function | pyridoxal phosphate binding |
| B | 0035999 | biological_process | tetrahydrofolate interconversion |
| B | 0036094 | molecular_function | small molecule binding |
| B | 0042802 | molecular_function | identical protein binding |
| B | 0042803 | molecular_function | protein homodimerization activity |
| B | 0046653 | biological_process | tetrahydrofolate metabolic process |
| B | 0046655 | biological_process | folic acid metabolic process |
| B | 0048027 | molecular_function | mRNA 5'-UTR binding |
| B | 0050897 | molecular_function | cobalt ion binding |
| B | 0051289 | biological_process | protein homotetramerization |
| B | 0070905 | molecular_function | serine binding |
| B | 1904482 | biological_process | cellular response to tetrahydrofolate |
| B | 1990830 | biological_process | cellular response to leukemia inhibitory factor |
| C | 0000900 | molecular_function | mRNA regulatory element binding translation repressor activity |
| C | 0004372 | molecular_function | glycine hydroxymethyltransferase activity |
| C | 0005634 | cellular_component | nucleus |
| C | 0005654 | cellular_component | nucleoplasm |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005829 | cellular_component | cytosol |
| C | 0006544 | biological_process | glycine metabolic process |
| C | 0006563 | biological_process | L-serine metabolic process |
| C | 0006565 | biological_process | L-serine catabolic process |
| C | 0006730 | biological_process | one-carbon metabolic process |
| C | 0008270 | molecular_function | zinc ion binding |
| C | 0009113 | biological_process | purine nucleobase biosynthetic process |
| C | 0016740 | molecular_function | transferase activity |
| C | 0017148 | biological_process | negative regulation of translation |
| C | 0019264 | biological_process | glycine biosynthetic process from serine |
| C | 0030170 | molecular_function | pyridoxal phosphate binding |
| C | 0035999 | biological_process | tetrahydrofolate interconversion |
| C | 0036094 | molecular_function | small molecule binding |
| C | 0042802 | molecular_function | identical protein binding |
| C | 0042803 | molecular_function | protein homodimerization activity |
| C | 0046653 | biological_process | tetrahydrofolate metabolic process |
| C | 0046655 | biological_process | folic acid metabolic process |
| C | 0048027 | molecular_function | mRNA 5'-UTR binding |
| C | 0050897 | molecular_function | cobalt ion binding |
| C | 0051289 | biological_process | protein homotetramerization |
| C | 0070905 | molecular_function | serine binding |
| C | 1904482 | biological_process | cellular response to tetrahydrofolate |
| C | 1990830 | biological_process | cellular response to leukemia inhibitory factor |
| D | 0000900 | molecular_function | mRNA regulatory element binding translation repressor activity |
| D | 0004372 | molecular_function | glycine hydroxymethyltransferase activity |
| D | 0005634 | cellular_component | nucleus |
| D | 0005654 | cellular_component | nucleoplasm |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005829 | cellular_component | cytosol |
| D | 0006544 | biological_process | glycine metabolic process |
| D | 0006563 | biological_process | L-serine metabolic process |
| D | 0006565 | biological_process | L-serine catabolic process |
| D | 0006730 | biological_process | one-carbon metabolic process |
| D | 0008270 | molecular_function | zinc ion binding |
| D | 0009113 | biological_process | purine nucleobase biosynthetic process |
| D | 0016740 | molecular_function | transferase activity |
| D | 0017148 | biological_process | negative regulation of translation |
| D | 0019264 | biological_process | glycine biosynthetic process from serine |
| D | 0030170 | molecular_function | pyridoxal phosphate binding |
| D | 0035999 | biological_process | tetrahydrofolate interconversion |
| D | 0036094 | molecular_function | small molecule binding |
| D | 0042802 | molecular_function | identical protein binding |
| D | 0042803 | molecular_function | protein homodimerization activity |
| D | 0046653 | biological_process | tetrahydrofolate metabolic process |
| D | 0046655 | biological_process | folic acid metabolic process |
| D | 0048027 | molecular_function | mRNA 5'-UTR binding |
| D | 0050897 | molecular_function | cobalt ion binding |
| D | 0051289 | biological_process | protein homotetramerization |
| D | 0070905 | molecular_function | serine binding |
| D | 1904482 | biological_process | cellular response to tetrahydrofolate |
| D | 1990830 | biological_process | cellular response to leukemia inhibitory factor |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE PLP A 419A |
| Chain | Residue |
| A | SER97 |
| A | THR226 |
| A | HIS228 |
| A | LYS229 |
| A | GLY420 |
| A | HOH506 |
| A | HOH515 |
| B | TYR55 |
| B | GLY262 |
| B | GLY263 |
| A | GLY98 |
| A | SER99 |
| A | HIS126 |
| A | THR174 |
| A | SER175 |
| A | ASP200 |
| A | ALA202 |
| A | HIS203 |
| site_id | AC2 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GLY A 420B |
| Chain | Residue |
| A | SER35 |
| A | HIS126 |
| A | SER175 |
| A | LYS229 |
| A | ARG363 |
| A | PLP419 |
| A | HOH515 |
| B | TYR65 |
| site_id | AC3 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE PLP C 419A |
| Chain | Residue |
| C | SER97 |
| C | GLY98 |
| C | SER99 |
| C | HIS126 |
| C | THR174 |
| C | SER175 |
| C | ASP200 |
| C | ALA202 |
| C | HIS203 |
| C | THR226 |
| C | HIS228 |
| C | LYS229 |
| C | GLY420 |
| D | TYR55 |
| D | GLY262 |
| D | GLY263 |
| site_id | AC4 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GLY C 420B |
| Chain | Residue |
| C | SER35 |
| C | SER175 |
| C | HIS203 |
| C | LYS229 |
| C | ARG363 |
| C | PLP419 |
| D | TYR65 |
| site_id | AC5 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE PLP B 419A |
| Chain | Residue |
| A | TYR55 |
| A | GLY262 |
| A | GLY263 |
| B | SER97 |
| B | GLY98 |
| B | SER99 |
| B | HIS126 |
| B | THR174 |
| B | SER175 |
| B | ASP200 |
| B | ALA202 |
| B | HIS203 |
| B | THR226 |
| B | HIS228 |
| B | LYS229 |
| site_id | AC6 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE TGF B 420C |
| Chain | Residue |
| A | GLU57 |
| A | TYR64 |
| A | TYR65 |
| A | PHE257 |
| B | LEU121 |
| B | GLY124 |
| B | GLY125 |
| B | HIS126 |
| B | LEU127 |
| B | LYS134 |
| B | SER175 |
| B | ASN345 |
| B | LEU357 |
| B | HOH739 |
| site_id | AC7 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE PLP D 419A |
| Chain | Residue |
| C | TYR55 |
| C | GLY262 |
| C | GLY263 |
| D | SER97 |
| D | GLY98 |
| D | SER99 |
| D | HIS126 |
| D | THR174 |
| D | SER175 |
| D | ASP200 |
| D | ALA202 |
| D | HIS203 |
| D | THR226 |
| D | HIS228 |
| D | LYS229 |
| site_id | AC8 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE TGF D 420F |
| Chain | Residue |
| D | LEU127 |
| D | LYS134 |
| D | SER175 |
| D | CYS176 |
| D | GLY331 |
| D | ASN345 |
| D | LYS346 |
| D | ASN347 |
| D | ALA356 |
| D | LEU357 |
| D | PRO359 |
| D | HOH740 |
| C | GLU57 |
| C | TYR64 |
| C | TYR65 |
| D | GLY124 |
| D | GLY125 |
| D | HIS126 |
| site_id | AC9 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE GOL D 421 |
| Chain | Residue |
| D | ASP182 |
| site_id | BC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE GOL C 421 |
| Chain | Residue |
| B | PHE418 |
| C | ASP156 |
| C | HOH679 |
| site_id | BC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE GOL B 421 |
| Chain | Residue |
| B | LEU181 |
| B | ASP182 |
| site_id | BC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE GOL B 422 |
| Chain | Residue |
| A | SER49 |
| B | ILE19 |
| B | PRO418 |
| B | PHE418 |
Functional Information from PROSITE/UniProt
| site_id | PS00096 |
| Number of Residues | 17 |
| Details | SHMT Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. HVvTTTTHKTLrGCRAG |
| Chain | Residue | Details |
| A | HIS221-GLY237 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | ACT_SITE: Nucleophile => ECO:0000305|PubMed:7358720 |
| Chain | Residue | Details |
| A | CYS176 | |
| B | CYS176 | |
| C | CYS176 | |
| D | CYS176 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | ACT_SITE: Proton donor => ECO:0000250 |
| Chain | Residue | Details |
| A | HIS228 | |
| B | HIS228 | |
| C | HIS228 | |
| D | HIS228 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | MOD_RES: N-acetylalanine => ECO:0000269|PubMed:3553178 |
| Chain | Residue | Details |
| A | ALA-21 | |
| B | ALA-21 | |
| C | ALA-21 | |
| D | ALA-21 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | MOD_RES: Deamidated asparagine; alternate => ECO:0000269|PubMed:2318867 |
| Chain | Residue | Details |
| A | ASN-17 | |
| B | ASN-17 | |
| C | ASN-17 | |
| D | ASN-17 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-(pyridoxal phosphate)lysine => ECO:0000269|PubMed:10387080 |
| Chain | Residue | Details |
| A | LYS229 | |
| B | LYS229 | |
| C | LYS229 | |
| D | LYS229 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 8 |
| Details | CROSSLNK: Isoaspartyl glycine isopeptide (Asn-Gly); alternate => ECO:0000269|PubMed:2318867 |
| Chain | Residue | Details |
| A | ASN-17 | |
| A | GLY-16 | |
| B | ASN-17 | |
| B | GLY-16 | |
| C | ASN-17 | |
| C | GLY-16 | |
| D | ASN-17 | |
| D | GLY-16 |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 6 |
| Details | M-CSA 147 |
| Chain | Residue | Details |
| A | TYR55 | steric locator |
| A | GLU57 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| A | ASP200 | electrostatic stabiliser |
| A | THR226 | electrostatic stabiliser, hydrogen bond acceptor |
| A | LYS229 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| A | ARG235 | electrostatic stabiliser |
| site_id | MCSA2 |
| Number of Residues | 6 |
| Details | M-CSA 147 |
| Chain | Residue | Details |
| B | TYR55 | steric locator |
| B | GLU57 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| B | ASP200 | electrostatic stabiliser |
| B | THR226 | electrostatic stabiliser, hydrogen bond acceptor |
| B | LYS229 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| B | ARG235 | electrostatic stabiliser |
| site_id | MCSA3 |
| Number of Residues | 6 |
| Details | M-CSA 147 |
| Chain | Residue | Details |
| C | TYR55 | steric locator |
| C | GLU57 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| C | ASP200 | electrostatic stabiliser |
| C | THR226 | electrostatic stabiliser, hydrogen bond acceptor |
| C | LYS229 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| C | ARG235 | electrostatic stabiliser |
| site_id | MCSA4 |
| Number of Residues | 6 |
| Details | M-CSA 147 |
| Chain | Residue | Details |
| D | TYR55 | steric locator |
| D | GLU57 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| D | ASP200 | electrostatic stabiliser |
| D | THR226 | electrostatic stabiliser, hydrogen bond acceptor |
| D | LYS229 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| D | ARG235 | electrostatic stabiliser |
