Background: Oxygen-free radicals formed during normal aerobic cellular metabolism attack bases in DNA and 7,8-dihydro-8-oxoguanine (8-oxoG) is one of the major lesions formed. It is amongst the most mutagenic lesions in cells because of its dual coding potential, wherein 8-oxoG(syn) can pair with an A in addition to normal base pairing of 8-oxoG(anti) with a C. Human DNA polymerase κ (Polκ) is a member of the newly discovered Y-family of DNA polymerases that possess the ability to replicate through DNA lesions. To understand the basis of Polκ's preference for insertion of an A opposite 8-oxoG lesion, we have solved the structure of Polκ in ternary complex with a template-primer presenting 8-oxoG in the active site and with dATP as the incoming nucleotide.
Methodology and Principal Findings: We show that the Polκ active site is well-adapted to accommodate 8-oxoG in the syn conformation. That is, the polymerase and the bound template-primer are almost identical in their conformations to that in the ternary complex with undamaged DNA. There is no steric hindrance to accommodating 8-oxoG in the syn conformation for Hoogsteen base-paring with incoming dATP.
Conclusions and Significance: The structure we present here is the first for a eukaryotic translesion synthesis (TLS) DNA polymerase with an 8-oxoG:A base pair in the active site. The structure shows why Polκ is more efficient at inserting an A opposite the 8-oxoG lesion than a C. The structure also provides a basis for why Polκ is more efficient at inserting an A opposite the lesion than other Y-family DNA polymerases.
Carpio RV-D, Silverstein TD, Lone S, Swan MK, Choudhury JR, et al. (2009) Structure of Human DNA Polymerase k Inserting dATP Opposite an 8-OxoG DNA Lesion. PLoS ONE 4(6): e5766. https://doi.org/10.1371/journal.pone.0005766
Virtual Commons Citation
Carpio, Rodrigo Vasquez-Del; Silverstein, Timothy D.; Lone, Samer; Swan, Michael K.; Choudhury, Jayati R.; Johnson, Robert E.; Prakash, Satya; Prakash, Louise; and Aggarwal, Aneel K. (2009). Structure of Human DNA Polymerase κ Inserting dATP Opposite an 8-OxoG DNA Lesion. In Chemical Sciences Faculty Publications. Paper 5.
Available at: https://vc.bridgew.edu/chem_fac/5