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

PLoS One. 2009 Jun 2;4(6):e5766. doi: 10.1371/journal.pone.0005766.


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

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adenosine Triphosphate / chemistry*
  • Catalytic Domain
  • Crystallization
  • DNA / chemistry
  • DNA Damage
  • DNA Replication
  • DNA-Directed DNA Polymerase / chemistry*
  • DNA-Directed DNA Polymerase / metabolism*
  • Free Radicals
  • Guanine / analogs & derivatives*
  • Guanine / chemistry
  • Humans
  • Kinetics
  • Models, Genetic
  • Nucleotides / chemistry
  • Protein Conformation


  • 7,8-dihydro-8-oxoguanine
  • Free Radicals
  • Nucleotides
  • Guanine
  • Adenosine Triphosphate
  • DNA
  • DNA-Directed DNA Polymerase
  • POLK protein, human