› 3buc

X-ray diffraction
2.59Å resolution

X-ray structure of human ABH2 bound to dsDNA with Mn(II) and 2KG

Released:
DOI: 10.2210/pdb3buc/pdb
PDB entry 3buc coloured by chain, front view.
PDB entry 3buc coloured by chain, side view.
PDB entry 3buc 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-116112 (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: 203 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(*DCP*DTP*DGP*DTP*DAP*DTP*(MA7)P*DAP*DCP*DTP*DGP*DCP*DG)-3') Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 3.98 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*DTP*DCP*DGP*DCP*DAP*DGP*DTP*DTP*DAP*DTP*DAP*DCP*DA)-3') Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 3.95 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand XL3 1 x XL3
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 19-BM
Spacegroup: P6522
Unit cell:
a: 77.91Å b: 77.91Å c: 226.558Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.25 0.248 0.287
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

30 review citations

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

19 mentions without citation

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