Binary complex crystal structure of DNA polymerase β reveals multiple conformations of the templating 8-oxoguanine lesion

Proc Natl Acad Sci U S A. 2012 Jan 3;109(1):113-8. doi: 10.1073/pnas.1112235108. Epub 2011 Dec 16.

Abstract

Oxidation of genomic DNA forms the guanine lesion 7,8-dihydro-8-oxoguanine (8-oxoG). When in the template base position during DNA synthesis the 8-oxoG lesion has dual coding potential by virtue of its anti- and syn-conformations, base pairing with cytosine and adenine, respectively. This impacts mutagenesis, because insertion of adenine opposite template 8-oxoG can result in a G to T transversion. DNA polymerases vary by orders of magnitude in their preferences for mutagenic vs. error-free 8-oxoG lesion bypass. Yet, the structural basis for lesion bypass specificity is not well understood. The DNA base excision repair enzyme DNA polymerase (pol) β is presented with gap-filling synthesis opposite 8-oxoG during repair and has similar insertion efficiencies for dCTP and dATP. We report the structure of pol β in binary complex with template 8-oxoG in a base excision repair substrate. The structure reveals both the syn- and anti-conformations of template 8-oxoG in the confines of the polymerase active site, consistent with the dual coding observed kinetically for this enzyme. A ternary complex structure of pol β with the syn-8-oxoG:anti-A Hoogsteen base pair in the closed fully assembled preinsertion active site is also reported. The syn-conformation of 8-oxoG is stabilized by minor groove hydrogen bonding between the side chain of Arg283 and O8 of 8-oxoG. An adjustment in the position of the phosphodiester backbone 5'-phosphate enables 8-oxoG to adopt the syn-conformation.

Publication types

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

MeSH terms

  • Base Pairing
  • Binding Sites
  • Crystallography, X-Ray
  • DNA Damage*
  • DNA Polymerase beta / chemistry*
  • DNA Polymerase beta / metabolism
  • Guanine / analogs & derivatives*
  • Guanine / chemistry
  • Guanine / metabolism
  • Humans
  • Models, Molecular
  • Mutagenesis / genetics
  • Protein Conformation
  • Templates, Genetic*

Substances

  • 8-hydroxyguanine
  • Guanine
  • DNA Polymerase beta

Associated data

  • PDB/3RJE
  • PDB/3RJF
  • PDB/3RJG
  • PDB/3RJH
  • PDB/3RJI
  • PDB/3RJJ
  • PDB/3RJK