Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA

Escherichia coli AlkB and its human homologues ABH2 and ABH3 repair DNA/ RNA base lesions by using a direct oxidative dealkylation mechanism. ABH2 has the primary role of guarding mammalian genomes against 1- meA damage by repairing this lesion in double- stranded DNA ( dsDNA), whereas AlkB and ABH3 preferentially repair single- stranded DNA ( ssDNA) lesions and can repair damaged bases in RNA. Here we show the first crystal structures of AlkB - dsDNA and ABH2 - dsDNA complexes, stabilized by a chemical cross- linking strategy. This study reveals that AlkB uses an unprecedented base- flipping mechanism to access the damaged base: it squeezes together the two bases flanking the flipped- out one to maintain the base stack, explaining the preference of AlkB for repairing ssDNA lesions over dsDNA ones. In addition, the first crystal structure of ABH2, presented here, provides a structural basis for designing inhibitors of this human DNA repair protein.