› 1diz

X-ray diffraction
2.5Å resolution

CRYSTAL STRUCTURE OF E. COLI 3-METHYLADENINE DNA GLYCOSYLASE (ALKA) COMPLEXED WITH DNA

Released:
DOI: 10.2210/pdb1diz/pdb
PDB entry 1diz coloured by chain, front view.
PDB entry 1diz coloured by chain, side view.
PDB entry 1diz coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA.
Hollis T, Ichikawa Y, Ellenberger T
EMBO J 19 758-66 (2000)
PMID: 10675345

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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113681 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA-3-methyladenine glycosylase 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 282 amino acids
Theoretical weight: 31.43 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P04395 (Residues: 1-282; Coverage: 100%)
Gene names: JW2053, aidA, alkA, b2068
Sequence domains:
Structure domains:
DNA (5'-D(*GP*AP*CP*AP*TP*GP*AP*(NRI)P*TP*GP*CP*CP*T)-3') Chains: C, E
Molecule details ›
Chains: C, E
Length: 13 nucleotides
Theoretical weight: 3.84 KDa
Source organism: Escherichia coli
Expression system: Not provided
DNA (5'-D(*GP*GP*CP*AP*AP*TP*CP*AP*TP*GP*TP*CP*A)-3') Chains: D, F
Molecule details ›
Chains: D, F
Length: 13 nucleotides
Theoretical weight: 3.98 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand NA 2 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P3121
Unit cell:
a: 82.4Å b: 82.4Å c: 199.7Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.26 0.25 0.29
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

21 review citations

Base excision repair.
Krokan et al. (2013)
20 more

19 mentions without citation

AdoMet-dependent methylation, DNA methyltransferases and base flipping.
Cheng et al. (2001)
18 more