Structural basis for the inefficient nucleotide incorporation opposite cisplatin-DNA lesion by human DNA polymerase β

J Biol Chem. 2014 Nov 7;289(45):31341-8. doi: 10.1074/jbc.M114.605451. Epub 2014 Sep 18.


Human DNA polymerase β (polβ) has been suggested to play a role in cisplatin resistance, especially in polβ-overexpressing cancer cells. Polβ has been shown to accurately albeit slowly bypass the cisplatin-1,2-d(GpG) (Pt-GG) intramolecular cross-link in vitro. Currently, the structural basis for the inefficient Pt-GG bypass mechanism of polβ is unknown. To gain structural insights into the mechanism, we determined two ternary structures of polβ incorporating dCTP opposite the templating Pt-GG lesion in the presence of the active site Mg(2+) or Mn(2+). The Mg(2+)-bound structure shows that the bulky Pt-GG adduct is accommodated in the polβ active site without any steric hindrance. In addition, both guanines of the Pt-GG lesion form Watson-Crick base pairing with the primer terminus dC and the incoming dCTP, providing the structural basis for the accurate bypass of the Pt-GG adduct by polβ. The Mn(2+)-bound structure shows that polβ adopts a catalytically suboptimal semiclosed conformation during the insertion of dCTP opposite the templating Pt-GG, explaining the inefficient replication across the Pt-GG lesion by polβ. Overall, our studies provide the first structural insights into the mechanism of the potential polβ-mediated cisplatin resistance.

Keywords: DNA Damage; DNA Polymerase; DNA Replication; Enzyme Catalysis; Enzyme Structure.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Antineoplastic Agents / chemistry
  • Catalysis
  • Catalytic Domain
  • Cisplatin / chemistry*
  • Cross-Linking Reagents / chemistry
  • Crystallization
  • Crystallography, X-Ray
  • Cytidine Triphosphate / chemistry
  • DNA / chemistry*
  • DNA Damage
  • DNA Polymerase beta / metabolism*
  • Drug Resistance, Neoplasm
  • Gene Expression Regulation*
  • Gene Expression Regulation, Neoplastic
  • Guanine / chemistry
  • Humans
  • Magnesium / chemistry
  • Manganese / chemistry
  • Neoplasms / drug therapy
  • Neoplasms / metabolism
  • Nucleotides / chemistry
  • Nucleotides / genetics
  • Protein Structure, Tertiary


  • Antineoplastic Agents
  • Cross-Linking Reagents
  • Nucleotides
  • Manganese
  • Guanine
  • Cytidine Triphosphate
  • DNA
  • DNA Polymerase beta
  • Magnesium
  • Cisplatin

Associated data

  • PDB/4TUP
  • PDB/4TUQ
  • PDB/4TUR
  • PDB/4TUS