Flipping of alkylated DNA damage bridges base and nucleotide excision repair

Abstract

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. Alkylated DNA is directly repaired by enzymes known as alkyltransferases (AGTs). A related class of enzymes, the alkyltransferase-like proteins (ATLs), can also protect against alkylation damage, but lack alkyltransferase activity. To gain insight into how this occurs, Tubbs et al. have solved the structure of a yeast ATL in the presence and absence of damaged DNA. Like AGTs, the ATL flips the alkylated base out of the DNA helix, but in this case the lesion is then acted upon by proteins of the nucleotide excision repair pathway. This 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. A class of enzymes known as alkyltransferase-like proteins (ATLs) can protect against alkylation damage to DNA. To gain insight into how this occurs, the structure of a yeast ATL has been solved in the presence and absence of damaged DNA, revealing that ATL flips the alkylated base out of the DNA helix, leaving the lesion to be acted on by proteins of the nucleotide excision repair pathway.