› 3cvs

X-ray diffraction
2.4Å resolution

Crystal Structure of an AlkA Host/Guest Complex 8oxoGuanine:Adenine Base Pair

Released:
DOI: 10.2210/pdb3cvs/pdb
PDB entry 3cvs coloured by chain, front view.
PDB entry 3cvs coloured by chain, side view.
PDB entry 3cvs coloured by chain, top view.
Source organisms:
Primary publication:
Structure of the E. coli DNA glycosylase AlkA bound to the ends of duplex DNA: a system for the structure determination of lesion-containing DNA.
Bowman BR, Lee S, Wang S, Verdine GL
Structure 16 1166-74 (2008)
PMID: 18682218

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-116153 (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:
DNA (5'-D(*DGP*DAP*DCP*DAP*DTP*DGP*DAP*(8OG)P*DTP*DGP*DCP*DC)-3') Chains: E, G
Molecule details ›
Chains: E, G
Length: 12 nucleotides
Theoretical weight: 3.7 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided
DNA (5'-D(*DGP*DGP*DCP*DAP*DAP*DTP*DCP*DAP*DTP*DGP*DTP*DC)-3') Chains: F, H
Molecule details ›
Chains: F, H
Length: 12 nucleotides
Theoretical weight: 3.66 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand 8OG 2 x 8OG

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C, null
Spacegroup: P21
Unit cell:
a: 75.174Å b: 101.247Å c: 102.917Å
α: 90° β: 94.19° γ: 90°
R-values:
R R work R free
0.219 0.219 0.27
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

DNA base repair--recognition and initiation of catalysis.
Dalhus et al. (2009)
1 more

2 mentions without citation

Golgi alpha-mannosidase II cleaves two sugars sequentially in the same catalytic site.
Shah et al. (2008)
1 more