Published on April 28, 2014 in J Biol Chem volume None.
PubMed ID: 24778178
N6-Methyladenosine (m6A) is the most prevalent internal RNA modification in eukaryotes. ALKBH5 belongs to the AlkB family of dioxygenases and has been shown to specifically demethylate m6A in single stranded RNA. Here we report crystal structures of ALKBH5 in the presence of either its cofactors or the ALKBH5 inhibitor citrate. Catalytic assays demonstrate that the ALKBH5 catalytic domain can demethylate both ssRNA and ssDNA. We identify the tricarboxylic acid (TCA) cycle intermediate citrate as a modest inhibitor of ALKHB5 (IC50: ~488 muM). The structural analysis reveals that a loop region of ALKBH5 is immobilized by a disulfide bond which apparently excludes the binding of dsDNA to ALKBH5. We identify the m6A binding pocket of ALKBH5 and the key residues involved in m6A recognition using mutagenesis and ITC binding experiments.