Crystal structure of human ABH3 in complex with iron ion and 2- oxoglutarate
Classification:
OXIDOREDUCTASE
Technique:
X-Ray Diffraction
Resolution:
1.5
R value free:
0.191
R value observed:
0.141
R value work:
Abstract of the PDB Structure's related Publication:
Methylating agents are ubiquitous in the environment, and central in cancer therapy. The 1-methyladenine and 3-methylcytosine lesions in DNA/RNA contribute to the cytotoxicity of such agents. These lesions are directly reversed by ABH3 (hABH3) in humans and AlkB in Escherichia coli. Here, we report the structure of the hABH3 catalytic core in complex with iron and 2-oxoglutarate (2OG) at 1.5 A resolution and analyse key site-directed mutants. The hABH3 structure reveals the beta-strand jelly-roll fold that coordinates a catalytically active iron centre by a conserved His1-X-Asp/Glu-X(n)-His2 motif. This experimentally establishes hABH3 as a structural member of the Fe(II)/2OG-dependent dioxygenase superfamily, which couples substrate oxidation to conversion of 2OG into succinate and CO2. A positively charged DNA/RNA binding groove indicates a distinct nucleic acid binding conformation different from that predicted in the AlkB structure with three nucleotides. These results uncover previously unassigned key catalytic residues, identify a flexible hairpin involved in nucleotide flipping and ss/ds-DNA discrimination, and reveal self-hydroxylation of an active site leucine that may protect against uncoupled generation of dangerous oxygen radicals.
Alpha-ketoglutarate Dependent Dioxygenase Homolog 3 is an enzyme belonging to the AlkB enzyme family that utilizes non-heme iron(II), catalyzing biological oxidation (Arne Aas et al. 2003 ). ALKBH3 demethylates both ssDNA and RNA (Ougland et al. 2004 ), being involved in alkylated DNA repair that contains m1A and m3C by oxidative demethylation (Duncan et al. 2002 )
ALKBH3 demethylates m1A in 5'-untranslated regions of mRNA and in close proximity of start codons(Dominissini et al. 2016 ).ALKBH3 is mainly expressed in cytoplasm with a strong binding capability to tRNA, where tRNA demethylation is reported to be an oncogenic marker. Demethylated tRNAs are more sensitive to angiogenin cleavage (ANG) tending to generate tRNA derived smll RNAs that can ultimately strengthen the ribosome assembly and prevent apoptosis in cancer (Chen et al. 2019 ).