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 | 0003824 | molecular_function | catalytic activity |
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 | 0003824 | molecular_function | catalytic activity |
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 | 0003824 | molecular_function | catalytic activity |
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 | 0003824 | molecular_function | catalytic activity |
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 |