› 3bi3

X-ray diffraction
1.9Å resolution

X-ray structure of AlkB protein bound to dsDNA containing 1meA/A with cofactors

Released:
DOI: 10.2210/pdb3bi3/pdb
PDB entry 3bi3 coloured by chain, front view.
PDB entry 3bi3 coloured by chain, side view.
PDB entry 3bi3 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-116092 (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: 22.31 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P05050 (Residues: 13-213; Coverage: 93%)
Gene names: JW2200, aidD, alkB, b2212
Structure domains: Alpha-ketoglutarate-dependent dioxygenase AlkB-like
DNA (5'-D(*TP*AP*GP*GP*TP*AP*AP*(MA7)P*AP*(2YR)P*CP*GP*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 4.07 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided
DNA (5'-D(*DAP*DAP*DCP*DGP*DGP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DT)-3') Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 3.95 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
1 modified residue:
Ligand MA7 1 x MA7

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-BM-C
Spacegroup: P21
Unit cell:
a: 41.407Å b: 75.629Å c: 50.972Å
α: 90° β: 107.73° γ: 90°
R-values:
R R work R free
0.216 0.215 0.247
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

37 review citations

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

8 mentions without citation

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