› 3bkz

X-ray diffraction
1.65Å resolution

X-ray structure of E coli AlkB crosslinked to dsDNA in the active site

Released:
DOI: 10.2210/pdb3bkz/pdb
PDB entry 3bkz coloured by chain, front view.
PDB entry 3bkz coloured by chain, side view.
PDB entry 3bkz coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA.
Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C
Nature 452 961-5 (2008)
PMID: 18432238

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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116095 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Alpha-ketoglutarate-dependent dioxygenase AlkB Chain: A
Molecule details ›
Chain: A
Length: 201 amino acids
Theoretical weight: 22.29 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P05050 (Residues: 14-214; Coverage: 93%)
Gene names: JW2200, aidD, alkB, b2212
Structure domains: Alpha-ketoglutarate-dependent dioxygenase AlkB-like
DNA (5'-D(*DTP*DAP*DGP*DGP*DTP*DAP*DAP*DCP*DAP*DTP*DCP*DGP*DT)-3') Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 4.05 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided
DNA (5'-D(*DAP*DAP*DCP*DGP*DAP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DT)-3') Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 3.93 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MN 1 x MN
Ligand AKG 1 x AKG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-BM-D
Spacegroup: P21
Unit cell:
a: 41.397Å b: 75.507Å c: 46.788Å
α: 90° β: 105.45° γ: 90°
R-values:
R R work R free
0.189 0.188 0.212
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

37 review citations

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

5 mentions without citation

Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA.
Yang et al. (2008)
4 more