Homology modeling of four Y-family, lesion-bypass DNA polymerases: The case that E. coli Pol IV and human Pol κ are orthologs, and E. coli Pol V and human Pol η are orthologs

Abstract

Y-family DNA polymerases (DNAPs) are a superfamily of evolutionarily related proteins that exist in cells to bypass DNA damage caused by both radiation and chemicals. Cells have multiple Y-family DNAPs, presumably to conduct translesion synthesis (TLS) on DNA lesions of varying structure and conformation. The potent, ubiquitous environmental mutagen/carcinogen benzo[ a]pyrene (B[ a]P) induces all classes of mutations with G → T base substitutions predominating. We recently showed that a G → T mutagenesis pathway for the major adduct of B[ a]P ([+ta]-B[ a]P-N 2-dG) in Escherichia coli depends on Y-family member DNAP V. Since no X-ray crystal study for DNAP V has been reported, no structure is available to help in understanding the structural basis for dATP insertion associated with G → T mutations from [+ta]-B[ a]P-N 2-dG. Herein, we do homology modeling to construct a model for UmuC, which is the polymerase subunit of DNAP V. The sequences of eight Y-family DNAPs were aligned based on the positioning of conserved amino acids and an analysis of conserved predicted secondary structure, as well as insights gained from published X-ray structures of five Y-family members. Starting coordinates for UmuC were generated from the backbone coordinates for the Y-family polymerase Dpo4 for reasons discussed, and were refined using molecular dynamics with CHARMM 27. A survey of the literature revealed that E. coli DNAP V and human DNAP η show a similar pattern of dNTP insertion opposite a variety of DNA lesions. Furthermore, E. coli DNAP IV and human DNAP κ show a similar dNTP insertional pattern with these same DNA lesions, although the insertional pattern for DNAP IV/κ differs from the pattern for DNAPs V/η. These comparisons prompted us to construct and refine models for E. coli DNAP IV and human DNAPs η and κ as well. The dNTP/template binding pocket of all four DNAPs was inspected, focusing on the array of seven amino acids that contact the base of the incoming dNTP, as well as the template base. DNAPs V and η show similarities in this array, and DNAPs IV and κ also show similarities, although the arrays are different for the two pairs of DNAPs. Thus, there is a correlation between structural similarities and insertional similarities for the pairs DNAPs V/η and DNAPs IV/κ. Although the significance of this correlation remains to be elucidated, these observations point the way for future experimental studies.