› 3i49

X-ray diffraction
1.6Å resolution

Crystal Structure of AlkB in complex with Fe(II), 2-oxoglutarate and methylated trinucleotide T-meC-T

Released:
DOI: 10.2210/pdb3i49/pdb
PDB entry 3i49 coloured by chain, front view.
PDB entry 3i49 coloured by chain, side view.
PDB entry 3i49 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Enzymological and structural studies of the mechanism of promiscuous substrate recognition by the oxidative DNA repair enzyme AlkB.
Yu B, Hunt JF
Proc Natl Acad Sci U S A 106 14315-20 (2009)
PMID: 19706517

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 dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116393 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Alpha-ketoglutarate-dependent dioxygenase AlkB Chain: A
Molecule details ›
Chain: A
Length: 211 amino acids
Theoretical weight: 23.61 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P05050 (Residues: 12-216; Coverage: 95%)
Gene names: JW2200, aidD, alkB, b2212
Structure domains: Alpha-ketoglutarate-dependent dioxygenase AlkB-like
DNA (5'-D(P*TP*(ME6)P*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 3 nucleotides
Theoretical weight: 868 Da
Source organism: Escherichia coli K-12
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand AKG 1 x AKG
Ligand FE2 1 x FE2
1 modified residue:
Ligand ME6 1 x ME6

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4C
Spacegroup: P43
Unit cell:
a: 41.374Å b: 41.374Å c: 117.213Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.186 0.214
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

11 review citations

The AlkB Family of Fe(II)/α-Ketoglutarate-dependent Dioxygenases: Repairing Nucleic Acid Alkylation Damage and Beyond.
Fedeles et al. (2015)
10 more

6 mentions without citation

Enzymological and structural studies of the mechanism of promiscuous substrate recognition by the oxidative DNA repair enzyme AlkB.
Yu et al. (2009)
5 more