› 2iuw

X-ray diffraction
1.5Å resolution

Crystal structure of human ABH3 in complex with iron ion and 2- oxoglutarate

Released:
DOI: 10.2210/pdb2iuw/pdb
PDB entry 2iuw coloured by chain, front view.
PDB entry 2iuw coloured by chain, side view.
PDB entry 2iuw coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Human ABH3 structure and key residues for oxidative demethylation to reverse DNA/RNA damage.
Sundheim O, Vågbø CB, Bjørås M, Sousa MM, Talstad V, Aas PA, Drabløs F, Krokan HE, Tainer JA, Slupphaug G
EMBO J 25 3389-97 (2006)
PMID: 16858410

Function and Biology Details

Reactions catalysed: 
DNA-base-CH(3) + 2-oxoglutarate + O(2) = DNA-base + formaldehyde + succinate + CO(2)
N(1)-methyladenine in mRNA + 2-oxoglutarate + O(2) = adenine in mRNA + formaldehyde + succinate + CO(2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188692 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3 Chain: A
Molecule details ›
Chain: A
Length: 238 amino acids
Theoretical weight: 27.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96Q83 (Residues: 62-286; Coverage: 79%)
Gene names: ABH3, ALKBH3, DEPC1
Sequence domains: 2OG-Fe(II) oxygenase superfamily
Structure domains: Alpha-ketoglutarate-dependent dioxygenase AlkB-like

Ligands and Environments

3 bound ligands:
Ligand FE 3 x FE
Ligand AKG 1 x AKG
Ligand BME 4 x BME
1 modified residue:
Ligand LED 1 x LED

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: I41
Unit cell:
a: 119.955Å b: 119.955Å c: 40.554Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.14 not available 0.191
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

25 review citations

Mononuclear non-heme iron enzymes with the 2-His-1-carboxylate facial triad: recent developments in enzymology and modeling studies.
Bruijnincx et al. (2008)
24 more

31 mentions without citation

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