Eukaryotic DNA polymerase amino acid sequence required for 3'----5' exonuclease activity

Proc Natl Acad Sci U S A. 1991 Nov 1;88(21):9473-7. doi: 10.1073/pnas.88.21.9473.


We have identified an amino-proximal sequence motif, Phe-Asp-Ile-Glu-Thr, in Saccharomyces cerevisiae DNA polymerase II that is almost identical to a sequence comprising part of the 3'----5' exonuclease active site of Escherichia coli DNA polymerase I. Similar motifs were identified by amino acid sequence alignment in related, aphidicolin-sensitive DNA polymerases possessing 3'----5' proofreading exonuclease activity. Substitution of Ala for the Asp and Glu residues in the motif reduced the exonuclease activity of partially purified DNA polymerase II at least 100-fold while preserving the polymerase activity. Yeast strains expressing the exonuclease-deficient DNA polymerase II had on average about a 22-fold increase in spontaneous mutation rate, consistent with a presumed proofreading role in vivo. In multiple amino acid sequence alignments of this and two other conserved motifs described previously, five residues of the 3'----5' exonuclease active site of E. coli DNA polymerase I appeared to be invariant in aphidicolin-sensitive DNA polymerases known to possess 3'----5' proofreading exonuclease activity. None of these residues, however, appeared to be identifiable in the catalytic subunits of human, yeast, or Drosophila alpha DNA polymerases.

Publication types

  • Comparative Study

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • DNA Mutational Analysis
  • DNA Polymerase II / chemistry*
  • DNA Polymerase II / metabolism
  • Exonucleases / chemistry
  • Exonucleases / metabolism
  • Genes, Fungal
  • Molecular Sequence Data
  • Oligonucleotides / chemistry
  • Polymerase Chain Reaction
  • Saccharomyces cerevisiae / enzymology*
  • Sequence Alignment
  • Structure-Activity Relationship


  • Oligonucleotides
  • DNA Polymerase II
  • Exonucleases