› 3ths

X-ray diffraction
2.5Å resolution

Crystal structure of rat native liver Glycine N-methyltransferase complexed with 5-methyltetrahydrofolate pentaglutamate

Released:
DOI: 10.2210/pdb3ths/pdb
PDB entry 3ths coloured by chain, front view.
PDB entry 3ths coloured by chain, side view.
PDB entry 3ths coloured by chain, top view.
Source organism: Rattus norvegicus
Primary publication:
Differences in folate-protein interactions result in differing inhibition of native rat liver and recombinant glycine N-methyltransferase by 5-methyltetrahydrofolate.
Luka Z, Pakhomova S, Loukachevitch LV, Newcomer ME, Wagner C
Biochim Biophys Acta 1824 286-91 (2012)
PMID: 22037183

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + glycine = S-adenosyl-L-homocysteine + sarcosine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
homo tetramer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-146529 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Glycine N-methyltransferase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 293 amino acids
Theoretical weight: 32.49 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: P13255 (Residues: 2-293; Coverage: 100%)
Gene names: Fbp-cII, Gnmt
Sequence domains: Methyltransferase domain
Structure domains:
5-methyltetrahydrofolate pentaglutamate Chains: E, F
Molecule details ›
Chains: E, F
Length: 6 amino acids
Theoretical weight: 976 Da
Source organism: Rattus norvegicus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand BME 1 x BME
Ligand TAM 1 x TAM
1 modified residue:
Ligand GGL 10 x GGL

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: C2
Unit cell:
a: 193.036Å b: 61.047Å c: 146.352Å
α: 90° β: 128.92° γ: 90°
R-values:
R R work R free
0.23 0.228 0.28
Expression system: Not provided

Quick links

Citations

2 review citations

Sarcosine as a potential prostate cancer biomarker--a review.
Cernei et al. (2013)
1 more

2 mentions without citation

A novel tumor suppressor function of glycine N-methyltransferase is independent of its catalytic activity but requires nuclear localization.
DebRoy et al. (2013)
1 more