› 3btx

X-ray diffraction
2Å resolution

X-ray structure of human ABH2 bound to dsDNA through active site cross-linking

Released:
DOI: 10.2210/pdb3btx/pdb
PDB entry 3btx coloured by chain, front view.
PDB entry 3btx coloured by chain, side view.
PDB entry 3btx coloured by chain, top view.
Source organism: Homo sapiens
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:
  • not assigned
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116108 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA oxidative demethylase ALKBH2 Chain: A
Molecule details ›
Chain: A
Length: 204 amino acids
Theoretical weight: 23.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q6NS38 (Residues: 56-258; Coverage: 78%)
Gene names: ABH2, ALKBH2
Sequence domains: 2OG-Fe(II) oxygenase superfamily
Structure domains: Alpha-ketoglutarate-dependent dioxygenase AlkB-like
DNA (5'-D(*CP*TP*GP*TP*AP*TP*(2YR)P*AP*TP*TP*GP*CP*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 4.02 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*DTP*DCP*DGP*DCP*DAP*DAP*DTP*DAP*DAP*DTP*DAP*DCP*DA)-3') Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 3.94 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-BM
Spacegroup: P6522
Unit cell:
a: 78.14Å b: 78.14Å c: 229.59Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.22 0.219 0.228
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

37 review citations

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

6 mentions without citation

The roles of Jumonji-type oxygenases in human disease.
Johansson et al. (2014)
5 more