› 3bty

X-ray diffraction
2.35Å resolution

Crystal structure of human ABH2 bound to dsDNA containing 1meA through cross-linking away from active site

Released:
DOI: 10.2210/pdb3bty/pdb
PDB entry 3bty coloured by chain, front view.
PDB entry 3bty coloured by chain, side view.
PDB entry 3bty 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-116109 (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

1 bound ligand:
Ligand XL3 1 x XL3
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: 77.915Å b: 77.915Å c: 226.04Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.225 0.223 0.259
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

36 review citations

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

6 mentions without citation

DNA repair by reversal of DNA damage.
Yi et al. (2013)
5 more