Alkyltransferase-like proteins (ATLs) share functional motifs with the cancer chemotherapy target O6-alkylguanine-DNA alkyltransferase (AGT) and paradoxically protect cells from the biological effects of DNA alkylation damage, despite lacking the reactive cysteine and alkyltransferase activity of AGT. Here we determine Schizosaccharomyces pombe ATL structures without and with damaged DNA containing the endogenous lesion O6-methylguanine or cigarette-smoke-derived O6-4-(3-pyridyl)-4-oxobutylguanine. These results reveal non-enzymatic DNA nucleotide flipping plus increased DNA distortion and binding pocket size compared to AGT. Our analysis of lesion-binding site conservation identifies new ATLs in sea anemone and ancestral archaea, indicating that ATL interactions are ancestral to present-day repair pathways in all domains of life. Genetic connections to mammalian XPG (also known as ERCC5) and ERCC1 in S. pombe homologues Rad13 and Swi10 and biochemical interactions with Escherichia coli UvrA and UvrC combined with structural results reveal that ATLs sculpt alkylated DNA to create a genetic and structural intersection of base damage processing with nucleotide excision repair.
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Acknowledgements We thank C. C. Vu and J. Gong for aiding in the synthesis of O6-pobG oligomers, M. N. Boddy, J. Prudden and A. Sarker for performing genetics and biochemical experiments, G. Guenther, S. Pebernard, R. S. Williams, J. J. Perry, B. R. Chapados, M. Bjorås, D. S. Shin, K. Hitomi, C. Hitomi, E. D. Getzoff, G. Williams, S. Tsutakawa and P. K. Cooper for suggestions, and the staff at the Advanced Light Source (ALS) SIBYLS beamline and the Stanford Synchrotron Radiation Laboratory (SSRL). Operations at SSRL and ALS are supported by the US Department of Energy and NIH. This work was supported by National Institutes of Health grants CA097209 (J.A.T., A.E.P.), CA018137 (A.E.P.), GM070662 (M.G.F.), and CA59887 (L.A.P.), The Skaggs Institute for Chemical Biology (J.L.T.), North West Cancer Research Fund grant CR675 (O.F.), Cancer Research-UK (G.P.M.) and CHEMORES (G.P.M.).