Architecture of Y-family DNA polymerases relevant to translesion DNA synthesis as revealed in structural and molecular modeling studies

Abstract

DNA adducts, which block replicative DNA polymerases (DNAPs), are often bypassed by lesion-bypass DNAPs, which are mostly in the Y-Family. Y-Family DNAPs can do non-mutagenic or mutagenic dNTP insertion, and understanding this difference is important, because mutations transform normal into tumorigenic cells. Y-Family DNAP architecture that dictates mechanism, as revealed in structural and modeling studies, is considered. Steps from adduct blockage of replicative DNAPs, to bypass by a lesion-bypass DNAP, to resumption of synthesis by a replicative DNAP are described. Catalytic steps and protein conformational changes are considered. One adduct is analyzed in greater detail: the major benzo[a]pyrene adduct (B [a] P-N2 -dG), which is bypassed non-mutagenically (dCTP insertion) by Y-family DNAPs in the IV/κ -class and mutagenically (dATP insertion) by V/η -class Y-Family DNAPs. Important architectural differences between IV/κ -class versus V/η -class DNAPs are discussed, including insights gained by analyzing ∼400 sequences each for bacterial DNAPs IV and V, along with sequences from eukaryotic DNAPs kappa, eta and iota. The little finger domains of Y-Family DNAPs do not show sequence conservation; however, their structures are remarkably similar due to the presence of a core of hydrophobic amino acids, whose exact identity is less important than the hydrophobic amino acid spacing. © 2010 Sushil Chandani et al.