› 9bow

X-ray diffraction
1.8Å resolution

X-ray structure of Thermus thermophilus serine hydroxymethyltransferase with PLP-L-Ser external aldimine and 5-formyltetrahydrofolate (folinic acid)

Released:
DOI: 10.2210/pdb9bow/pdb
PDB entry 9bow coloured by chain, front view.
PDB entry 9bow coloured by chain, side view.
PDB entry 9bow coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
Universality of critical active site glutamate as an acid-base catalyst in serine hydroxymethyltransferase function.
Drago VN, Phillips RS, Kovalevsky A
Chem Sci 15 12827-12844 (2024)
PMID: 39148791

Function and Biology Details

Reaction catalysed: 
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-250824 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Serine hydroxymethyltransferase Chain: A
Molecule details ›
Chain: A
Length: 402 amino acids
Theoretical weight: 44.38 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5SI56 (Residues: 6-407; Coverage: 99%)
Gene names: TTHA1524, glyA
Sequence domains: Serine hydroxymethyltransferase
Serine hydroxymethyltransferase Chain: B
Molecule details ›
Chain: B
Length: 402 amino acids
Theoretical weight: 44.15 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5SI56 (Residues: 6-407; Coverage: 99%)
Gene names: TTHA1524, glyA
Sequence domains: Serine hydroxymethyltransferase

Ligands and Environments


Cofactor: Ligand FFO 1 x FFO
3 bound ligands:
Ligand SER 1 x SER
Ligand SO4 2 x SO4
Ligand KOU 1 x KOU
1 modified residue:
Ligand LLP 1 x LLP

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P21
Unit cell:
a: 58.131Å b: 82.814Å c: 94.446Å
α: 90° β: 91.58° γ: 90°
R-values:
R R work R free
0.133 0.132 0.16
Expression system: Escherichia coli

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