Y-family DNA polymerase architecture: three structural features control accurate deoxy CTP insertion opposite N2-deoxy-guanine-benzo-a-pyrene
Sholder, Gabriel D.
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Cells have lesion bypass DNA polymerases (DNAPs), often in the Y-Family, which synthesize passed DNA damage. One class of Y-Family DNAPs includes hDNAP k, EcDNAP IV and SsDbh, which insert accurately opposite N2-dG adducts, including BP-N2-dG formed from benzo[a]pyrene (BP). Another class includes hDNAP h, EcDNAP V and SsDpo4, which insert accurately opposite UV-damage. For correct Watson-Crick pairing between BP-N2-dG and dCTP, the BP moiety must be in the minor groove. On the minor groove side of the active site, k/IV/Dbh-class DNAPs have large openings that accommodate the BP moiety. Primer extension assays with purified proteins show that DNAP IV correctly inserts dCTP opposite BP more than 10-fold faster than it mis-inserts dATP, dGTP, or dTTP. In contrast, h/V/Dpo4-class DNAPs have small active site openings, which cannot accommodate BP and lead to a distorted structure and increased mutagenesis; e.g., Dpo4 has dGTP and dATP insertion rates that are 10-fold greater than those of dCTP. The opening in Dpo4 is plugged and bulky, whereas DNAP IV has a relatively spacious cavity. Consistent with this model, mutants of Dpo4 with a larger opening insert up to 10-fold more accurately opposite BP-N2-dG. Near the active site, Dpo4 has a single non-covalent bridge (NCB) between the little finger domain and the thumb-palm-fingers domain. DNAP IV and Dbh have a second, distal NCB that is 8 angstroms away from the active site towards the 3' end of the template DNA. Dpo4 becomes nearly 5-fold more accurate when mutated to carry a distal NCB, suggesting that NCB's also help control mutagenesis. Lastly, the active site of Dpo4 has a cavity in the major groove side, which may allow base flipping and dGTP insertion opposite -BP, while k/IV/Dbh-type polymerases do not. When this cavity is plugged in Dpo4 by mutagenesis or the introduction of an N-clasp motif, dGTP rates increase by nearly 20-fold. In conclusion, this data suggests that three structural regions contribute to accurate dCTP insertion opposite BP-N2-dG by k/IV/Dbh-class DNAPs: a large opening on the minor groove side near the active site, a cavity on the major groove side, and the number of non-covalent bridges between the little finger domain and the thumb-palm-fingers domain.