Cryo-EM structure of Pol κ-DNA-PCNA holoenzyme and implications for polymerase switching in DNA lesion bypass

Abstract

Replacement of the stalled replicative polymerase (Pol {delta}) at a DNA lesion by the error-prone DNA polymerase {kappa} (Pol {kappa}) restarts synthesis past the lesion to prevent genome instability. The switching from Pol {delta} to Pol {kappa} is mediated by the processivity clamp PCNA but the structural basis of this mechanism is unknown. We determined the Cryo-EM structures of human Pol {kappa}-DNA-PCNA complex and of a stalled Pol {delta}-DNA-PCNA complex at 3.9 and 4.7 [A] resolution, respectively. In Pol {kappa} complex, the C-terminus of the PAD domain docks the catalytic core to one PCNA protomer in an angled orientation, bending the DNA exiting Pol {kappa} active site through PCNA. In Pol {delta} complex, the DNA is disengaged from the active site but is retained by the thumb domain. We present a model for polymerase switching facilitated by Pol {kappa} recruitment to PCNA and Pol {kappa} conformational sampling to seize the DNA from stalled Pol {delta} assisted by PCNA tilting.