2.0Å resolution crystal structure of human polκ reveals a new catalytic function of N-clasp in DNA replication

Human polymerase kappa (pol kappa) is a distinctY-family DNA polymerase with a unique N-terminal N-clasp domain. The N-clasp renders polies high efficiency and accuracy in DNA replication and lesion bypass. How N-clasp empowers pol kappa in replication remains unclear due to the disordering of N-clasp. Here, we present a 2.0-angstrom resolution crystal structure of a pol kappa ternary complex with DNA and an incoming nucleotide. The structure-function study reveals an ordered N-clasp domain that brings conserved and functionally important residues in contact with the replicating basepair in the active site and contributes to the nucleotidyl transfer reaction. Particularly, a fully ordered Lys25 from the N-clasp domain is in H-bonding with the and gamma-phosphates of the incoming nucleotide. K25A mutation reduces the polymerase activity of pol kappa significantly. This lysine is structurally analogous to a conserved lysine in the A-family DNA polymerases in the closed form. In contrast, Lys25 in the previous structures of pol kappa does not have any contacts with the incoming nucleotide, resembling an open form of a DNA polymerase. Based on structural and functional similarity, we propose a local open/closed mechanism for pol kappa in DNA replication catalysis, which mimics the common mechanism for all DNA polymerases.