Characterization of Nine Cancer-Associated Variants in Human DNA Polymerase κ

Specialized DNA damage-bypass Y-family DNA polymerases contribute to cancer prevention by providing cellular tolerance to DNA damage that can lead to mutations and contribute to cancer progression by increasing genomic instability. Y-family polymerases can also bypass DNA adducts caused by chemotherapy agents. One of the four human Y-family DNA polymerases, DNA polymerase (pol) kappa, has been shown to be specific for bypass of minor groove adducts and inhibited by major groove adducts. In addition, mutations in the gene encoding pol kappa are associated with different types of cancers as well as with chemotherapy responses. We characterized nine variants of pol kappa whose identity was inferred from cancer-associated single nucleotide polymorphisms for polymerization activity on undamaged and damaged DNA, their abilities to extend from mismatched or damaged base pairs at primer termini, and overall stability and dynamics. We find that these pol kappa variants generally fall into three categories: similar activity to wild-type (WT) pol kappa (L21F, I39T, P169T, F192C, and E292K), more active than WT pol kappa (S423R), and less active than pol kappa (R2191, R298H, and Y432S). Of these, only pol kappa variants R298H and Y432S had markedly reduced thermal stability. Molecular dynamics (MD) simulations with undamaged DNA revealed that the active variant F192C and more active variant S423R with either correct or incorrect incoming nucleotide mimic WT pol kappa with the correct incoming nucleotide, whereas the less active variants R219I, R298H, and Y432S with the correct incoming nucleotide mimic WT pol kappa with the incorrect incoming nucleotide. Thus, the observations from MD simulations suggest a possible explanation for the observed experimental results that pol kappa adopts specific active and inactive conformations that depend on both the protein variant and the identity of the DNA adduct.