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

• Published in: Nature 2008-04, Vol.452 (7190), p.961-965
• Main Authors: He, Chuan, Yang, Cai-Guang, Yi, Chengqi, Duguid, Erica M, Sullivan, Christopher T, Jian, Xing, Rice, Phoebe A
• Format: Article
• Language: English
• Subjects: Adenine - analogs & derivatives; Adenine - metabolism; AlkB Homolog 2, Alpha-Ketoglutarate-Dependent Dioxygenase; Anion exchange; Binding Sites; Biological and medical sciences; Cancer; Cross-Linking Reagents - chemistry; Crystal structure; Crystalline structure; Crystallography, X-Ray; Crystals; Data collection; Deoxyribonucleic acid; Dioxygenases - chemistry; Dioxygenases - metabolism; DNA; DNA - chemistry; DNA - metabolism; DNA Damage; DNA polymerases; DNA Repair; DNA Repair Enzymes - chemistry; DNA Repair Enzymes - metabolism; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - metabolism; E coli; Enzymes; Escherichia coli; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - metabolism; Fundamental and applied biological sciences. Psychology; Humanities and Social Sciences; Humans; Mixed Function Oxygenases - chemistry; Mixed Function Oxygenases - metabolism; Models, Molecular; Molecular biophysics; multidisciplinary; Physiological aspects; Protein Binding; Proteins; Ribonucleic acid; RNA; RNA - metabolism; RNA polymerases; Science; Science (multidisciplinary); Structure; Structure in molecular biology
• ISSN: 0028-0836; 1476-4687; 1476-4679
• DOI: 10.1038/nature06889

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. Base lesions can be directly repaired by oxidative dealkylation catalysed by AlkB in bacteria and by ABH2/ABH3 in man. Several structures of AlkB and ABH2 bound to dsDNA are solved. These structures reveal why AlkB prefers ssDNA to dsDNA substrates, and how ABH2 differs structurally, to allow it to repair dsDNA.