› 2dpm

X-ray diffraction
1.8Å resolution

DPNM DNA ADENINE METHYLTRANSFERASE FROM STREPTOCCOCUS PNEUMONIAE COMPLEXED WITH S-ADENOSYLMETHIONINE

Released:
DOI: 10.2210/pdb2dpm/pdb
PDB entry 2dpm coloured by chain, front view.
PDB entry 2dpm coloured by chain, side view.
PDB entry 2dpm coloured by chain, top view.
Source organism: Streptococcus pneumoniae
Primary publication:
Crystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of streptococcus pneumoniae bound to S-adenosylmethionine.
Tran PH, Korszun ZR, Cerritelli S, Springhorn SS, Lacks SA
Structure 6 1563-75 (1998)
PMID: 9862809

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + adenine in DNA = S-adenosyl-L-homocysteine + N-6-methyladenine in DNA
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-137334 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Type II methyltransferase M1.DpnII Chain: A
Molecule details ›
Chain: A
Length: 284 amino acids
Theoretical weight: 32.95 KDa
Source organism: Streptococcus pneumoniae
Expression system: Escherichia coli
UniProt:
  • Canonical: P04043 (Residues: 1-284; Coverage: 100%)
Gene name: dpnM
Sequence domains: D12 class N6 adenine-specific DNA methyltransferase
Structure domains:

Ligands and Environments


Cofactor: Ligand SAM 1 x SAM
1 bound ligand:
Ligand HG 1 x HG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12C
Spacegroup: P212121
Unit cell:
a: 56.6Å b: 68.1Å c: 85.2Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.238 0.238 0.284
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases.
Jeltsch A. (2002)
4 more

15 mentions without citation

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