Structural insights into DNA polymerase X from African swine fever virus in the presence of oxoG lesions

Abstract

DNA polymerase X (pol X) from the African swine fever virus is a 174‐amino‐acid repair polymerase that participates in a viral Base Excision Repair pathway and is characterized by low fidelity. Pol X is homologous to human DNA polymerase β, but lacks the fingers subdomain. An essential feature of pol X is that insertion rate is of the G:G mispair is comparable to that of the four Watson Crick base pairs. Molecular dynamic studies of polX/DNA complexes suggest an induced fit mechanism for this enzyme. Interestingly, an active closed conformation is achieved also in simulations that contain the G:G mispair, in agreement with the kinetic data. Here we present molecular dynamic simulations of pol X/DNA complexes in which the templating base pair opposite to the incoming nucleotide contains the damaged base 7,8‐Dihydro‐8‐oxoguanine (oxoG). OxoG is known to be one of the major known products of oxidation of DNA by reactive oxygen species (ROS). Since the African swine fever virus's components are in an active state of respiration, it is not unreasonable to think that the virus may encounter this common ROS‐induced DNA lesion. According to kinetics data, pol X readily accommodates A opposite to oxoG, with efficiency even higher than the non‐damaged G:C base pair. The goal of this molecular dynamic study is to help interpret, at an atomistic level, the kinetics data. Support provided by NSF grant MCB‐0316771 and NIH grant R01 ES01269.