1EQB
X-RAY CRYSTAL STRUCTURE AT 2.7 ANGSTROMS RESOLUTION OF TERNARY COMPLEX BETWEEN THE Y65F MUTANT OF E-COLI SERINE HYDROXYMETHYLTRANSFERASE, GLYCINE AND 5-FORMYL TETRAHYDROFOLATE
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004372 | molecular_function | glycine hydroxymethyltransferase activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0006545 | biological_process | glycine biosynthetic process |
| A | 0006546 | biological_process | glycine catabolic process |
| A | 0006564 | biological_process | L-serine biosynthetic 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 | 0008652 | biological_process | amino acid biosynthetic process |
| A | 0008732 | molecular_function | L-allo-threonine aldolase activity |
| A | 0016020 | cellular_component | membrane |
| A | 0016740 | molecular_function | transferase activity |
| A | 0019264 | biological_process | glycine biosynthetic process from serine |
| A | 0030170 | molecular_function | pyridoxal phosphate binding |
| A | 0035999 | biological_process | tetrahydrofolate interconversion |
| A | 0042802 | molecular_function | identical protein binding |
| A | 0042803 | molecular_function | protein homodimerization activity |
| A | 0046653 | biological_process | tetrahydrofolate metabolic process |
| B | 0004372 | molecular_function | glycine hydroxymethyltransferase activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0006545 | biological_process | glycine biosynthetic process |
| B | 0006546 | biological_process | glycine catabolic process |
| B | 0006564 | biological_process | L-serine biosynthetic 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 | 0008652 | biological_process | amino acid biosynthetic process |
| B | 0008732 | molecular_function | L-allo-threonine aldolase activity |
| B | 0016020 | cellular_component | membrane |
| B | 0016740 | molecular_function | transferase activity |
| B | 0019264 | biological_process | glycine biosynthetic process from serine |
| B | 0030170 | molecular_function | pyridoxal phosphate binding |
| B | 0035999 | biological_process | tetrahydrofolate interconversion |
| B | 0042802 | molecular_function | identical protein binding |
| B | 0042803 | molecular_function | protein homodimerization activity |
| B | 0046653 | biological_process | tetrahydrofolate metabolic process |
| C | 0004372 | molecular_function | glycine hydroxymethyltransferase activity |
| C | 0005515 | molecular_function | protein binding |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005829 | cellular_component | cytosol |
| C | 0006545 | biological_process | glycine biosynthetic process |
| C | 0006546 | biological_process | glycine catabolic process |
| C | 0006564 | biological_process | L-serine biosynthetic 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 | 0008652 | biological_process | amino acid biosynthetic process |
| C | 0008732 | molecular_function | L-allo-threonine aldolase activity |
| C | 0016020 | cellular_component | membrane |
| C | 0016740 | molecular_function | transferase activity |
| C | 0019264 | biological_process | glycine biosynthetic process from serine |
| C | 0030170 | molecular_function | pyridoxal phosphate binding |
| C | 0035999 | biological_process | tetrahydrofolate interconversion |
| C | 0042802 | molecular_function | identical protein binding |
| C | 0042803 | molecular_function | protein homodimerization activity |
| C | 0046653 | biological_process | tetrahydrofolate metabolic process |
| D | 0004372 | molecular_function | glycine hydroxymethyltransferase activity |
| D | 0005515 | molecular_function | protein binding |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005829 | cellular_component | cytosol |
| D | 0006545 | biological_process | glycine biosynthetic process |
| D | 0006546 | biological_process | glycine catabolic process |
| D | 0006564 | biological_process | L-serine biosynthetic 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 | 0008652 | biological_process | amino acid biosynthetic process |
| D | 0008732 | molecular_function | L-allo-threonine aldolase activity |
| D | 0016020 | cellular_component | membrane |
| D | 0016740 | molecular_function | transferase activity |
| D | 0019264 | biological_process | glycine biosynthetic process from serine |
| D | 0030170 | molecular_function | pyridoxal phosphate binding |
| D | 0035999 | biological_process | tetrahydrofolate interconversion |
| D | 0042802 | molecular_function | identical protein binding |
| D | 0042803 | molecular_function | protein homodimerization activity |
| D | 0046653 | biological_process | tetrahydrofolate metabolic process |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE GLY A 1292 |
| Chain | Residue |
| A | SER35 |
| A | SER175 |
| A | HIS203 |
| A | LYS229 |
| A | ARG363 |
| A | PLP1291 |
| A | FFO1293 |
| B | TYR55 |
| B | PHE65 |
| site_id | AC2 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GLY B 2292 |
| Chain | Residue |
| A | TYR55 |
| A | PHE65 |
| B | SER35 |
| B | HIS203 |
| B | LYS229 |
| B | ARG363 |
| B | PLP2291 |
| B | FFO2293 |
| site_id | AC3 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE GLY C 3292 |
| Chain | Residue |
| C | SER35 |
| C | HIS126 |
| C | SER175 |
| C | HIS203 |
| C | LYS229 |
| C | ARG363 |
| C | PLP3291 |
| C | FFO3293 |
| D | TYR55 |
| D | PHE65 |
| site_id | AC4 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GLY D 4292 |
| Chain | Residue |
| C | TYR55 |
| C | PHE65 |
| D | SER35 |
| D | HIS126 |
| D | HIS203 |
| D | ARG363 |
| D | PLP4291 |
| D | FFO4293 |
| site_id | AC5 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE PLP A 1291 |
| Chain | Residue |
| A | SER97 |
| A | GLY98 |
| A | SER99 |
| A | HIS126 |
| A | PHE174 |
| A | SER175 |
| A | ASP200 |
| A | HIS203 |
| A | THR226 |
| A | HIS228 |
| A | LYS229 |
| A | GLY1292 |
| B | TYR55 |
| B | GLY262 |
| B | GLY263 |
| B | HOH500 |
| B | HOH530 |
| site_id | AC6 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE FFO A 1293 |
| Chain | Residue |
| A | LEU121 |
| A | GLY125 |
| A | HIS126 |
| A | LEU127 |
| A | VAL133 |
| A | SER175 |
| A | ASN347 |
| A | SER355 |
| A | PRO356 |
| A | PHE357 |
| A | HOH693 |
| A | GLY1292 |
| B | GLU57 |
| B | TYR64 |
| B | PHE257 |
| D | SER245 |
| D | GLU246 |
| D | GLU247 |
| site_id | AC7 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE PLP B 2291 |
| Chain | Residue |
| A | TYR55 |
| A | GLY262 |
| A | GLY263 |
| A | HOH506 |
| B | SER97 |
| B | GLY98 |
| B | SER99 |
| B | HIS126 |
| B | PHE174 |
| B | SER175 |
| B | ASP200 |
| B | HIS203 |
| B | THR226 |
| B | HIS228 |
| B | LYS229 |
| B | GLY2292 |
| site_id | AC8 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE FFO B 2293 |
| Chain | Residue |
| A | GLU57 |
| A | TYR64 |
| A | PHE257 |
| B | LEU121 |
| B | GLY125 |
| B | HIS126 |
| B | LEU127 |
| B | ASN347 |
| B | SER355 |
| B | PRO356 |
| B | PHE357 |
| B | GLY2292 |
| site_id | AC9 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE PLP C 3291 |
| Chain | Residue |
| C | GLY98 |
| C | SER99 |
| C | HIS126 |
| C | PHE174 |
| C | SER175 |
| C | ASP200 |
| C | HIS203 |
| C | THR226 |
| C | HIS228 |
| C | LYS229 |
| C | GLY3292 |
| D | TYR55 |
| D | GLY262 |
| D | GLY263 |
| D | HOH504 |
| C | SER97 |
| site_id | BC1 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE FFO C 3293 |
| Chain | Residue |
| B | SER245 |
| B | GLU246 |
| B | GLU247 |
| C | LEU121 |
| C | GLY124 |
| C | GLY125 |
| C | HIS126 |
| C | LEU127 |
| C | VAL133 |
| C | ASN347 |
| C | SER355 |
| C | PRO356 |
| C | PHE357 |
| C | HOH692 |
| C | GLY3292 |
| D | GLU57 |
| D | TYR64 |
| D | PHE257 |
| site_id | BC2 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE PLP D 4291 |
| Chain | Residue |
| C | TYR55 |
| C | GLY262 |
| C | GLY263 |
| C | HOH505 |
| D | SER97 |
| D | GLY98 |
| D | SER99 |
| D | HIS126 |
| D | PHE174 |
| D | SER175 |
| D | ASP200 |
| D | HIS203 |
| D | THR226 |
| D | HIS228 |
| D | LYS229 |
| D | GLY4292 |
| site_id | BC3 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE FFO D 4293 |
| Chain | Residue |
| C | GLU57 |
| C | TYR64 |
| C | PHE257 |
| D | LEU121 |
| D | GLY125 |
| D | HIS126 |
| D | LEU127 |
| D | ASN347 |
| D | SER355 |
| D | PRO356 |
| D | PHE357 |
| D | GLY4292 |
Functional Information from PROSITE/UniProt
| site_id | PS00096 |
| Number of Residues | 17 |
| Details | SHMT Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. HVvTTTTHKTLaGPRGG |
| Chain | Residue | Details |
| A | HIS221-GLY237 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00051, ECO:0000305|PubMed:10656824, ECO:0000305|PubMed:10858298, ECO:0007744|PDB:1DFO, ECO:0007744|PDB:1EQB |
| Chain | Residue | Details |
| A | LEU121 | |
| D | LEU121 | |
| D | GLY125 | |
| D | SER355 | |
| A | GLY125 | |
| A | SER355 | |
| B | LEU121 | |
| B | GLY125 | |
| B | SER355 | |
| C | LEU121 | |
| C | GLY125 | |
| C | SER355 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | SITE: Plays an important role in substrate specificity => ECO:0000255|HAMAP-Rule:MF_00051, ECO:0000269|PubMed:1517215 |
| Chain | Residue | Details |
| A | HIS228 | |
| B | HIS228 | |
| C | HIS228 | |
| D | HIS228 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 12 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000269|PubMed:18723842 |
| Chain | Residue | Details |
| A | LYS54 | |
| D | LYS54 | |
| D | LYS285 | |
| D | LYS375 | |
| A | LYS285 | |
| A | LYS375 | |
| B | LYS54 | |
| B | LYS285 | |
| B | LYS375 | |
| C | LYS54 | |
| C | LYS285 | |
| C | LYS375 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-(pyridoxal phosphate)lysine => ECO:0000255|HAMAP-Rule:MF_00051, ECO:0000269|PubMed:19883126, ECO:0007744|PDB:3G8M |
| Chain | Residue | Details |
| A | LYS229 | |
| B | LYS229 | |
| C | LYS229 | |
| D | LYS229 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 8 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:21151122 |
| Chain | Residue | Details |
| A | LYS250 | |
| A | LYS354 | |
| B | LYS250 | |
| B | LYS354 | |
| C | LYS250 | |
| C | LYS354 | |
| D | LYS250 | |
| D | LYS354 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 32 |
| Details | BINDING: BINDING => ECO:0000305|PubMed:10656824, ECO:0000305|PubMed:10858298, ECO:0007744|PDB:1DFO, ECO:0007744|PDB:1EQB |
| Chain | Residue | Details |
| A | SER35 | |
| B | TYR55 | |
| B | SER99 | |
| B | SER175 | |
| B | HIS203 | |
| B | GLU246 | |
| B | GLY263 | |
| B | ARG363 | |
| C | SER35 | |
| C | TYR55 | |
| C | SER99 | |
| A | TYR55 | |
| C | SER175 | |
| C | HIS203 | |
| C | GLU246 | |
| C | GLY263 | |
| C | ARG363 | |
| D | SER35 | |
| D | TYR55 | |
| D | SER99 | |
| D | SER175 | |
| D | HIS203 | |
| A | SER99 | |
| D | GLU246 | |
| D | GLY263 | |
| D | ARG363 | |
| A | SER175 | |
| A | HIS203 | |
| A | GLU246 | |
| A | GLY263 | |
| A | ARG363 | |
| B | SER35 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000305|PubMed:10656824, ECO:0007744|PDB:1DFO |
| Chain | Residue | Details |
| A | PHE65 | |
| B | PHE65 | |
| C | PHE65 | |
| D | PHE65 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:19883126, ECO:0007744|PDB:3G8M |
| Chain | Residue | Details |
| A | HIS228 | |
| A | ARG235 | |
| B | HIS228 | |
| B | ARG235 | |
| C | HIS228 | |
| C | ARG235 | |
| D | HIS228 | |
| D | ARG235 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 8 |
| Details | SITE: Transaldimination and stability |
| Chain | Residue | Details |
| A | TYR55 | |
| A | ARG235 | |
| B | TYR55 | |
| B | ARG235 | |
| C | TYR55 | |
| C | ARG235 | |
| D | TYR55 | |
| D | ARG235 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 24 |
| Details | MOD_RES: N6-succinyllysine => ECO:0000269|PubMed:21151122 |
| Chain | Residue | Details |
| A | LYS62 | |
| B | LYS293 | |
| B | LYS331 | |
| B | LYS346 | |
| C | LYS62 | |
| C | LYS242 | |
| C | LYS277 | |
| C | LYS293 | |
| C | LYS331 | |
| C | LYS346 | |
| D | LYS62 | |
| A | LYS242 | |
| D | LYS242 | |
| D | LYS277 | |
| D | LYS293 | |
| D | LYS331 | |
| D | LYS346 | |
| A | LYS277 | |
| A | LYS293 | |
| A | LYS331 | |
| A | LYS346 | |
| B | LYS62 | |
| B | LYS242 | |
| B | LYS277 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| A | CYS68 |
| site_id | CSA10 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| B | LYS229 | |
| B | ASP200 | |
| B | HIS123 |
| site_id | CSA11 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| C | LYS229 | |
| C | ASP200 | |
| C | HIS123 |
| site_id | CSA12 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| D | LYS229 | |
| D | ASP200 | |
| D | HIS123 |
| site_id | CSA13 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| A | LYS229 | |
| A | HIS203 |
| site_id | CSA14 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| B | LYS229 | |
| B | HIS203 |
| site_id | CSA15 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| C | LYS229 | |
| C | HIS203 |
| site_id | CSA16 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| D | LYS229 | |
| D | HIS203 |
| site_id | CSA17 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| A | GLU69 |
| site_id | CSA18 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| B | GLU69 |
| site_id | CSA19 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| C | GLU69 |
| site_id | CSA2 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| B | CYS68 |
| site_id | CSA20 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| D | GLU69 |
| site_id | CSA3 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| C | CYS68 |
| site_id | CSA4 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| D | CYS68 |
| site_id | CSA5 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| A | THR226 | |
| A | LYS229 | |
| A | GLU57 |
| site_id | CSA6 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| B | THR226 | |
| B | LYS229 | |
| B | GLU57 |
| site_id | CSA7 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| C | THR226 | |
| C | LYS229 | |
| C | GLU57 |
| site_id | CSA8 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| D | THR226 | |
| D | LYS229 | |
| D | GLU57 |
| site_id | CSA9 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| A | LYS229 | |
| A | ASP200 | |
| A | HIS123 |
