PMID: 30310122
Jha V, Ling H
2.0 A resolution crystal structure of human polkappa reveals a new catalytic function of N-clasp in DNA replication.
Sci Rep. 2018 Oct 11;8(1):15125. doi: 10.1038/s41598-018-33371-5.
Human polymerase kappa (polkappa) is a distinct Y-family DNA polymerase with a unique N-terminal N-clasp domain. The N-clasp renders polkappa's high efficiency and accuracy in DNA replication and lesion bypass. How N-clasp empowers polkappa in replication remains unclear due to the disordering of N-clasp. Here, we present a 2.0-A resolution crystal structure of a polkappa 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 alpha- and gamma-phosphates of the incoming nucleotide. K25A mutation reduces the polymerase activity of polkappa 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 polkappa 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 polkappa in DNA replication catalysis, which mimics the common mechanism for all DNA polymerases.