› 3o1s

X-ray diffraction
1.58Å resolution

Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase

Released:
DOI: 10.2210/pdb3o1s/pdb
PDB entry 3o1s coloured by chain, front view.
PDB entry 3o1s coloured by chain, side view.
PDB entry 3o1s coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase.
Yi C, Jia G, Hou G, Dai Q, Zhang W, Zheng G, Jian X, Yang CG, Cui Q, He C
OpenAccess logo Nature 468 330-3 (2010)
PMID: 21068844

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-507756 (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: 206 amino acids
Theoretical weight: 22.96 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(*AP*GP*GP*TP*AP*AP*(MDQ)P*AP*CP*CP*GP*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.76 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided
DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-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 FE 1 x FE
Ligand SIN 1 x SIN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P21
Unit cell:
a: 41.4Å b: 75.95Å c: 51.74Å
α: 90° β: 107.85° γ: 90°
R-values:
R R work R free
0.2 0.198 0.243
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

18 review citations

Vitamins C and E: beneficial effects from a mechanistic perspective.
Traber et al. (2011)
17 more

6 mentions without citation

Nucleic acid oxidation in DNA damage repair and epigenetics.
Zheng et al. (2014)
5 more