› 3khc

X-ray diffraction
2.2Å resolution

Crystal Structure of Escherichia coli AlkB in complex with ssDNA containing a 1-methylguanine lesion

Released:
DOI: 10.2210/pdb3khc/pdb
PDB entry 3khc coloured by chain, front view.
PDB entry 3khc coloured by chain, side view.
PDB entry 3khc coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Structural and mutational analysis of Escherichia coli AlkB provides insight into substrate specificity and DNA damage searching.
Holland PJ, Hollis T
PLoS One 5 e8680 (2010)
PMID: 20084272

Function and Biology Details

Reaction catalysed: 
DNA-base-CH(3) + 2-oxoglutarate + O(2) = DNA-base + formaldehyde + succinate + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116477 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Alpha-ketoglutarate-dependent dioxygenase AlkB Chains: A, B
Molecule details ›
Chains: A, B
Length: 219 amino acids
Theoretical weight: 24.35 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P05050 (Residues: 1-216; Coverage: 100%)
Gene names: JW2200, aidD, alkB, b2212
Structure domains: Alpha-ketoglutarate-dependent dioxygenase AlkB-like
DNA (5'-D(P*TP*AP*(MG1)P*TP*GP*CP*CP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 8 nucleotides
Theoretical weight: 2.43 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided
DNA (5'-D(P*GP*CP*AP*T)-3') Chain: D
Molecule details ›
Chain: D
Length: 4 nucleotides
Theoretical weight: 1.19 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CO 2 x CO
Ligand AKG 2 x AKG
1 modified residue:
Ligand MG1 1 x MG1

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: C2
Unit cell:
a: 147.809Å b: 41.441Å c: 85.622Å
α: 90° β: 120.98° γ: 90°
R-values:
R R work R free
0.214 0.211 0.273
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

DNA repair by reversal of DNA damage.
Yi et al. (2013)
5 more

3 mentions without citation

Discovery of novel 2-aryl-4-benzoyl-imidazoles targeting the colchicines binding site in tubulin as potential anticancer agents.
Chen et al. (2010)
2 more