Reversal of a mutator activity by a nearby fidelity-neutral substitution in the RB69 DNA polymerase binding pocket

Abstract

Phage RB69 family-B DNA polymerase is responsible for the overall high fidelity of RB69 DNA synthesis. Fidelity is compromised when conserved Tyr567, one of the residues that form the nascent polymerase base-pair binding pocket, is replaced by alanine. The Y567A mutator mutant has an enlarged binding pocket and can incorporate and extend mispairs efficiently. Ser565 is a nearby conserved residue that also contributes to the binding pocket, but a S565G replacement has only small impacts on DNA replication fidelity. When the Y567A and S565G replacements were combined, mutator activity was strongly decreased compared to that of Y567A alone. Analyses conducted both in vivo and in vitro revealed that, compared to Y567A alone, the double mutant mainly reduced base substitution mutations and to a lesser extent frameshift mutations. The decrease in mutation rates was not due to increased exonuclease activity. Based on measurements of DNA binding affinity and of mismatch insertion and extension, we propose that the recovered fidelity of the double mutant may result in part from increased dissociation of the enzyme from DNA followed by the binding of the same or another polymerase molecule in either the exonuclease or polymerase mode. An additional antimutagenic factor may be a structural alteration in the polymerase binding pocket described in the following report.