Y-Family Polymerase Conformation Is a Major Determinant of Fidelity and Translesion Specificity

Y-family polymerases help cells tolerate DNA damage by performing translesion synthesis opposite damaged DNA bases, yet they also have a high intrinsic error rate. We constructed chimeras of two closely related Y-family polymerases that display distinctly different activity profiles and found that the polypeptide linker that tethers the catalytic polymerase domain to the C-terminal DNA-binding domain is a major determinant of overall polymerase activity, nucleotide incorporation fidelity, and abasic site-bypass ability. Exchanging just 3 out of the 15 linker residues is sufficient to interconvert the polymerase activities tested. Crystal structures of four chimeras show that the conformation of the protein correlates with the identity of the interdomain linker sequence. Thus, residues that are more than 15 Å away from the active site are able to influence many aspects of polymerase activity by altering the relative orientations of the catalytic and DNA-binding domains. [Display omitted] ▸ Y-family polymerases differ in fidelity and translesion synthesis specificity ▸ Polymerase fidelity and specificity are controlled by the interdomain linker ▸ Three amino acids in the interdomain linker are sufficient to determine conformation ▸ Differences in polymerase conformation determine differences in polymerase activity By using chimeric constructs of Dbh and Dpo4, Wilson et al. show that the interdomain linker determines the fidelity and abasic-site bypass ability of the polymerases. Critical residues are distant from the active site and influence activity by altering relative orientations of the catalytic and DNA-binding domains.