Structure of human DNA polymerase κ inserting dATP opposite an 8-OxoG DNA lesion

Rodrigo Vasquez-Del Carpio, Timothy D. Silverstein, Samer Lone, Michael K. Swan, Jayati R. Choudhury, Robert E. Johnson, Satya Prakash, Louise Prakash, Aneel K. Aggarwal

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Abstract

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 (Polk) 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 Polk's preference for insertion of an A opposite 8-oxoG lesion, we have solved the structure of Polk 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 Polk 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 Polk is more efficient at inserting an A opposite the 8-oxoG lesion than a C. The structure also provides a basis for why Polk is more efficient at inserting an A opposite the lesion than other Y-family DNA polymerases.

Original languageEnglish (US)
Article numbere5766
JournalPLoS One
Volume4
Issue number6
DOIs
StatePublished - Jun 2 2009

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ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Vasquez-Del Carpio, R., Silverstein, T. D., Lone, S., Swan, M. K., Choudhury, J. R., Johnson, R. E., Prakash, S., Prakash, L., & Aggarwal, A. K. (2009). Structure of human DNA polymerase κ inserting dATP opposite an 8-OxoG DNA lesion. PLoS One, 4(6), [e5766]. https://doi.org/10.1371/journal.pone.0005766