› 2fdh

X-ray diffraction
2.1Å resolution

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

Released:
DOI: 10.2210/pdb2fdh/pdb
PDB entry 2fdh coloured by chain, front view.
PDB entry 2fdh coloured by chain, side view.
PDB entry 2fdh coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB.
Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC, Gibney BR, Hunt JF
Nature 439 879-84 (2006)
PMID: 16482161

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 domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115250 (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 BL21(DE3)
UniProt:
  • Canonical: P05050 (Residues: 12-216; Coverage: 95%)
Gene names: JW2200, aidD, alkB, b2212
Structure domains: Alpha-ketoglutarate-dependent dioxygenase AlkB-like
5'-D(P*TP*(MA7)P*T)-3' Chain: B
Molecule details ›
Chain: B
Length: 3 nucleotides
Theoretical weight: 892 Da
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: RIGAKU RU200
Spacegroup: P43
Unit cell:
a: 40.68Å b: 40.68Å c: 118.3Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.187 0.228
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

33 review citations

TETonic shift: biological roles of TET proteins in DNA demethylation and transcription.
Pastor et al. (2013)
32 more

4 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)
3 more