2.0?A resolution crystal structure of human pol? reveals a new catalytic function of N-clasp in DNA replication.

ABSTRACT: Human polymerase kappa (pol?) is a distinct Y-family DNA polymerase with a unique N-terminal N-clasp domain. The N-clasp renders pol?'s high efficiency and accuracy in DNA replication and lesion bypass. How N-clasp empowers pol? in replication remains unclear due to the disordering of N-clasp. Here, we present a 2.0-Å resolution crystal structure of a pol? 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 ?-phosphates of the incoming nucleotide. K25A mutation reduces the polymerase activity of pol? 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? 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? in DNA replication catalysis, which mimics the common mechanism for all DNA polymerases.

SUBMITTER: Jha V 

PROVIDER: S-EPMC6181923 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature