Loop II of DNA polymerase beta is important for discrimination during substrate binding

DNA Repair (Amst). 2009 Feb 1;8(2):182-9. doi: 10.1016/j.dnarep.2008.10.006. Epub 2008 Dec 5.


Loop II of DNA polymerase beta (pol beta) consists of 14 amino acid residues and is highly flexible and solvent exposed. Previous research from our laboratory has shown that this loop is important for polymerase activity and fidelity. In the study presented here, we demonstrate that a shortened five amino acid residue loop compromises the fidelity of pol beta. This five-residue loop, termed ENEYP, induces one base frameshift errors and A-C transversions within a specific sequence context. We demonstrate that ENEYP misincorporates dGTP opposite template A at higher efficiencies than wild-type pol beta. The kinetic basis for misincorporation is a defect in discrimination of the correct from incorrect dNTP substrate at the level of ground-state binding. Our results are consistent with the idea that loop II of pol beta functions to maintain accurate DNA synthesis by a direct or indirect influence on the nucleotide binding pocket.

Publication types

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

MeSH terms

  • Adenosine / metabolism
  • Amino Acid Sequence
  • Animals
  • Base Pair Mismatch
  • Base Sequence
  • DNA / metabolism
  • DNA Polymerase beta / chemistry*
  • DNA Polymerase beta / metabolism*
  • Frameshift Mutation
  • Guanosine Triphosphate / metabolism
  • Herpesvirus 1, Human / enzymology
  • Kinetics
  • Molecular Sequence Data
  • Mutant Proteins / chemistry
  • Mutant Proteins / metabolism
  • Protein Binding
  • Protein Structure, Secondary
  • Rats
  • Sequence Deletion
  • Structure-Activity Relationship
  • Substrate Specificity
  • Thymidine Kinase / metabolism


  • Mutant Proteins
  • Guanosine Triphosphate
  • DNA
  • Thymidine Kinase
  • DNA Polymerase beta
  • Adenosine