6YRW
SHMT from Streptococcus thermophilus Tyr55Ser variant as internal aldimine and as non-covalent complex with D-Ser
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0004372 | molecular_function | glycine hydroxymethyltransferase activity |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0006545 | biological_process | glycine biosynthetic process |
| A | 0006730 | biological_process | one-carbon metabolic process |
| A | 0008652 | biological_process | amino acid biosynthetic process |
| 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 | 0046653 | biological_process | tetrahydrofolate metabolic process |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0004372 | molecular_function | glycine hydroxymethyltransferase activity |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0006545 | biological_process | glycine biosynthetic process |
| B | 0006730 | biological_process | one-carbon metabolic process |
| B | 0008652 | biological_process | amino acid biosynthetic process |
| 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 | 0046653 | biological_process | tetrahydrofolate metabolic process |
| C | 0003824 | molecular_function | catalytic activity |
| C | 0004372 | molecular_function | glycine hydroxymethyltransferase activity |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005829 | cellular_component | cytosol |
| C | 0006545 | biological_process | glycine biosynthetic process |
| C | 0006730 | biological_process | one-carbon metabolic process |
| C | 0008652 | biological_process | amino acid biosynthetic process |
| 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 | 0046653 | biological_process | tetrahydrofolate metabolic process |
| D | 0003824 | molecular_function | catalytic activity |
| D | 0004372 | molecular_function | glycine hydroxymethyltransferase activity |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005829 | cellular_component | cytosol |
| D | 0006545 | biological_process | glycine biosynthetic process |
| D | 0006730 | biological_process | one-carbon metabolic process |
| D | 0008652 | biological_process | amino acid biosynthetic process |
| 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 | 0046653 | biological_process | tetrahydrofolate metabolic process |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 14 |
| Details | binding site for residue PLP A 501 |
| Chain | Residue |
| A | SER97 |
| A | LYS230 |
| A | DSN502 |
| C | GLY261 |
| C | GLY262 |
| C | HOH657 |
| A | GLY98 |
| A | SER99 |
| A | HIS126 |
| A | ASP201 |
| A | ALA203 |
| A | HIS204 |
| A | THR227 |
| A | HIS229 |
| site_id | AC2 |
| Number of Residues | 9 |
| Details | binding site for residue DSN A 502 |
| Chain | Residue |
| A | SER35 |
| A | HIS126 |
| A | SER176 |
| A | HIS204 |
| A | LYS230 |
| A | ARG363 |
| A | PLP501 |
| A | HOH607 |
| C | TYR65 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | binding site for residue GOL A 503 |
| Chain | Residue |
| A | LEU153 |
| A | ARG180 |
| A | ASP183 |
| A | HOH644 |
| site_id | AC4 |
| Number of Residues | 9 |
| Details | binding site for residue DSN C 502 |
| Chain | Residue |
| A | GLU57 |
| A | TYR65 |
| A | HOH635 |
| C | SER35 |
| C | HIS126 |
| C | SER176 |
| C | HIS204 |
| C | ARG363 |
| C | HOH663 |
| site_id | AC5 |
| Number of Residues | 9 |
| Details | binding site for residue DSN B 502 |
| Chain | Residue |
| B | SER35 |
| B | HIS126 |
| B | SER176 |
| B | HIS204 |
| B | LYS230 |
| B | ARG363 |
| B | PLP501 |
| D | GLU57 |
| D | TYR65 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | binding site for residue GOL B 503 |
| Chain | Residue |
| B | TYR156 |
| B | ASP183 |
| B | LYS186 |
| B | HOH612 |
| B | HOH677 |
| site_id | AC7 |
| Number of Residues | 9 |
| Details | binding site for residue DSN D 502 |
| Chain | Residue |
| B | GLU57 |
| B | TYR65 |
| D | SER35 |
| D | HIS126 |
| D | SER176 |
| D | HIS204 |
| D | LYS230 |
| D | ARG363 |
| D | PLP501 |
| site_id | AC8 |
| Number of Residues | 22 |
| Details | binding site for Di-peptide PLP B 501 and LYS B 230 |
| Chain | Residue |
| B | SER35 |
| B | ASN37 |
| B | SER97 |
| B | GLY98 |
| B | SER99 |
| B | HIS126 |
| B | SER176 |
| B | ASP201 |
| B | ALA203 |
| B | HIS204 |
| B | THR227 |
| B | HIS229 |
| B | THR231 |
| B | LEU232 |
| B | ARG233 |
| B | DSN502 |
| B | HOH641 |
| B | HOH676 |
| D | GLY261 |
| D | GLY262 |
| D | HOH606 |
| D | HOH626 |
| site_id | AC9 |
| Number of Residues | 19 |
| Details | binding site for Di-peptide PLP C 501 and LYS C 230 |
| Chain | Residue |
| C | HOH650 |
| A | GLY261 |
| A | GLY262 |
| A | HOH638 |
| A | HOH661 |
| C | SER35 |
| C | ASN37 |
| C | SER97 |
| C | GLY98 |
| C | SER99 |
| C | HIS126 |
| C | ASP201 |
| C | ALA203 |
| C | HIS204 |
| C | THR227 |
| C | HIS229 |
| C | THR231 |
| C | LEU232 |
| C | ARG233 |
| site_id | AD1 |
| Number of Residues | 18 |
| Details | binding site for Di-peptide PLP D 501 and LYS D 230 |
| Chain | Residue |
| B | GLY261 |
| B | GLY262 |
| D | SER35 |
| D | ASN37 |
| D | SER97 |
| D | GLY98 |
| D | SER99 |
| D | HIS126 |
| D | ASP201 |
| D | ALA203 |
| D | HIS204 |
| D | THR227 |
| D | HIS229 |
| D | THR231 |
| D | LEU232 |
| D | ARG233 |
| D | DSN502 |
| D | HOH608 |
Functional Information from PROSITE/UniProt
| site_id | PS00096 |
| Number of Residues | 17 |
| Details | SHMT Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. HVtTTTTHKTLrGPRGG |
| Chain | Residue | Details |
| A | HIS222-GLY238 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00051 |
| Chain | Residue | Details |
| A | LEU121 | |
| D | LEU121 | |
| D | GLY125 | |
| D | SER355 | |
| A | GLY125 | |
| A | SER355 | |
| C | LEU121 | |
| C | GLY125 | |
| C | SER355 | |
| B | LEU121 | |
| B | GLY125 | |
| B | 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 |
| Chain | Residue | Details |
| A | HIS229 | |
| C | HIS229 | |
| B | HIS229 | |
| D | HIS229 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-(pyridoxal phosphate)lysine => ECO:0000255|HAMAP-Rule:MF_00051 |
| Chain | Residue | Details |
| A | LYS230 | |
| C | LYS230 | |
| B | LYS230 | |
| D | LYS230 |
