› 6fl5

X-ray diffraction
3.6Å resolution

Structure of human SHMT1-H135N-R137A-E168N mutant at 3.6 Ang. resolution

Released:
DOI: 10.2210/pdb6fl5/pdb
PDB entry 6fl5 coloured by chain, front view.
PDB entry 6fl5 coloured by chain, side view.
PDB entry 6fl5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The catalytic activity of serine hydroxymethyltransferase is essential for de novo nuclear dTMP synthesis in lung cancer cells.
Giardina G, Paone A, Tramonti A, Lucchi R, Marani M, Magnifico MC, Bouzidi A, Pontecorvi V, Guiducci G, Zamparelli C, Rinaldo S, Paiardini A, Contestabile R, Cutruzzolà F
FEBS J 285 3238-3253 (2018)
PMID: 30035852

Function and Biology Details

Reaction catalysed: 
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152736 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Serine hydroxymethyltransferase, cytosolic Chains: A, D, G, J
Molecule details ›
Chains: A, D, G, J
Length: 471 amino acids
Theoretical weight: 51.7 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P34896 (Residues: 11-481; Coverage: 98%)
Gene name: SHMT1
Sequence domains: Serine hydroxymethyltransferase

Ligands and Environments


Cofactor: Ligand PLP 4 x PLP
1 bound ligand:
Ligand CL 4 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM30A
Spacegroup: P43212
Unit cell:
a: 139.719Å b: 139.719Å c: 267.377Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.263 0.262 0.277
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

The multifaceted role of vitamin B6 in cancer: Drosophila as a model system to investigate DNA damage.
Contestabile et al. (2020)
3 more

4 mentions without citation

A Review of Small-Molecule Inhibitors of One-Carbon Enzymes: SHMT2 and MTHFD2 in the Spotlight.
Cuthbertson et al. (2021)
3 more