› 3d4v

X-ray diffraction
2.9Å resolution

Crystal Structure of an AlkA Host/Guest Complex N7MethylGuanine:Cytosine Base Pair

Released:
DOI: 10.2210/pdb3d4v/pdb
PDB entry 3d4v coloured by chain, front view.
PDB entry 3d4v coloured by chain, side view.
PDB entry 3d4v coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Synthesis and structure of duplex DNA containing the genotoxic nucleobase lesion N7-methylguanine.
Lee S, Bowman BR, Ueno Y, Wang S, Verdine GL
J Am Chem Soc 130 11570-1 (2008)
PMID: 18686953

Function and Biology Details

Reaction catalysed: 
Hydrolysis of alkylated DNA, releasing 3-methyladenine, 3-methylguanine, 7-methylguanine and 7-methyladenine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116170 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA-3-methyladenine glycosylase 2 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 282 amino acids
Theoretical weight: 31.43 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P04395 (Residues: 1-282; Coverage: 100%)
Gene names: JW2053, aidA, alkA, b2068
Sequence domains:
Structure domains:
5'-D(*DGP*DAP*DCP*DAP*DTP*DGP*DAP*(FMG)P*DTP*DGP*DCP*DC)-3' Chains: E, G
Molecule details ›
Chains: E, G
Length: 12 nucleotides
Theoretical weight: 3.72 KDa
Source organism: Escherichia coli
Expression system: Not provided
5'-D(*DGP*DGP*DCP*DAP*DCP*DTP*DCP*DAP*DTP*DGP*DTP*DC)-3' Chains: F, H
Molecule details ›
Chains: F, H
Length: 12 nucleotides
Theoretical weight: 3.64 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand FMG 2 x FMG

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P21
Unit cell:
a: 74.1Å b: 100.361Å c: 102.281Å
α: 90° β: 94.45° γ: 90°
R-values:
R R work R free
0.208 0.208 0.275
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

5 review citations

Bacterial sigma factors: a historical, structural, and genomic perspective.
Feklístov et al. (2014)
4 more

2 mentions without citation

Detection of damaged DNA bases by DNA glycosylase enzymes.
Friedman et al. (2010)
1 more