DNA polymerases lose their grip.

Abstract

The African swine fever virus (ASFV) is a DNA virus that codes for two DNA polymerases: a B-family replicative DNA polymerase and a DNA polymerase (pol X) of unknown function that has sequence similarity to DNA polymerase β (pol β), a eukaryotic base excision repair enzyme in the X-family of polymerases1. Pol X is the smallest naturally occurring polymerase (174 residues, 20 kDa) and lacks accessory activities, such as the lyase activity associated with pol β. The small size of pol X makes this enzyme an ideal system for characterization by NMR. As reported on pages 936 and 942 of this issue of Nature Structural Biology, Maciejewski et al.2 and Showalter et al.3 have independently determined the solution structure of ASFV pol X. These structures represent the first solution structures of a full-length DNA polymerase. More importantly, the pol X structures provide valuable insights into how pol X can tightly bind DNA in the absence of a dedicated DNA binding subdomain and the functional significance of relative subdomain positioning upon substrate binding. These insights provide a framework in which to analyze the native function of pol X. Pol X structure The architecture of the prototypical DNA polymerase domain is likened to a right hand that can grasp DNA (for review see ref. 4), with the subdomains referred to as the fingers, palm, and thumb. The palm subdomain has three carboxylates that bind two catalytically essential metals involved in the nucleotidyl transferase reaction. Crystal structures of DNA polymerases from several polymerase families, excluding pol β, indicate that the palm subdomains are structurally homologous, but the fingers and thumb are not. The thumb and fingers subdomains have primary roles in duplex DNA binding and deoxynucleoside 5′-triphosphate (dNTP) selection, respectively. DNA polymerase β has functionally equivalent subdomains, but the topology of the palm is unique 5. The ASFV pol X shares sequence similarity with the C-terminal region of pol β