Structural insights into DNA polymerase beta deterrents for misincorporation support an induced-fit mechanism for fidelity

Structure. 2004 Oct;12(10):1823-32. doi: 10.1016/j.str.2004.08.001.


DNA polymerases generally select the correct nucleotide from a pool of structurally similar molecules to preserve Watson-Crick base-pairing rules. We report the structure of DNA polymerase beta with DNA mismatches situated in the polymerase active site. This was achieved by using nicked product DNA that traps the mispair (template-primer, A-C or T-C) in the nascent base pair binding pocket. The structure of each mispair complex indicates that the bases do not form hydrogen bonds with one another, but form a staggered arrangement where the bases of the mispair partially overlap. This prevents closure/opening of the N subdomain that is believed to be required for catalytic cycling. The partially open conformation of the N subdomain results in distinct hydrogen bonding networks that are unique for each mispair. These structures define diverse molecular aspects of misinsertion that are consistent with the induced-fit model for substrate specificity.

MeSH terms

  • Base Pair Mismatch*
  • Base Pairing
  • Base Sequence
  • Binding Sites
  • Crystallography
  • DNA / chemistry*
  • DNA Polymerase beta / chemistry*
  • DNA Polymerase beta / metabolism
  • Hydrogen Bonding
  • Models, Molecular
  • Molecular Structure
  • Nucleic Acid Conformation
  • Nucleotides / chemistry
  • Nucleotides / metabolism
  • Protein Conformation


  • Nucleotides
  • DNA
  • DNA Polymerase beta

Associated data

  • PDB/1TV9
  • PDB/1TVA