› 1g55

X-ray diffraction
1.8Å resolution

Structure of human DNMT2, an enigmatic DNA methyltransferase homologue

Released:
DOI: 10.2210/pdb1g55/pdb
PDB entry 1g55 coloured by chain, front view.
PDB entry 1g55 coloured by chain, side view.
PDB entry 1g55 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of human DNMT2, an enigmatic DNA methyltransferase homolog that displays denaturant-resistant binding to DNA.
Dong A, Yoder JA, Zhang X, Zhou L, Bestor TH, Cheng X
Nucleic Acids Res 29 439-48 (2001)
PMID: 11139614

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + cytosine(38) in tRNA = S-adenosyl-L-homocysteine + 5-methylcytosine(38) in tRNA
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127060 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA (cytosine(38)-C(5))-methyltransferase Chain: A
Molecule details ›
Chain: A
Length: 343 amino acids
Theoretical weight: 39.28 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O14717 (Residues: 2-391; Coverage: 88%)
Gene names: DNMT2, TRDMT1
Sequence domains: C-5 cytosine-specific DNA methylase
Structure domains:

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
3 bound ligands:
Ligand SO4 1 x SO4
Ligand BME 1 x BME
Ligand GOL 1 x GOL
1 modified residue:
Ligand CSO 2 x CSO

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12C
Spacegroup: I41
Unit cell:
a: 116.5Å b: 116.5Å c: 69.8Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.21 0.25
Expression system: Escherichia coli

Quick links

Citations

44 review citations

Eukaryotic cytosine methyltransferases.
Goll et al. (2005)
43 more

18 mentions without citation

Many paths to methyltransfer: a chronicle of convergence.
Schubert et al. (2003)
17 more