Polymerization fidelity of a replicative DNA polymerase from the hyperthermophilic archaeon Sulfolobus solfataricus P2

Biochemistry. 2009 Aug 11;48(31):7492-501. doi: 10.1021/bi900532w.


Sulfolobus solfataricus P2 is an aerobic crenarchaeon which grows optimally at 80 degrees C and pH 2-4. This organism encodes a B-family DNA polymerase, DNA polymerase B1 (PolB1), which faithfully replicates its genome of 3 million base pairs. Using pre-steady-state kinetic methods, we estimated the fidelity of PolB1 to be in the range of 10(-6) to 10(-8), or one error per 10(6) to 10(8) nucleotide incorporations in vivo. To discern how the polymerase and 3' --> 5' exonuclease activities contribute to the high fidelity of PolB1, an exonuclease-deficient mutant of PolB1 was constructed by mutating three conserved residues at the exonuclease active site. The base substitution fidelity of this mutant was kinetically measured to be in the range of 10(-4) to 10(-6) at 37 degrees C and pH 7.5. PolB1 exhibited high fidelity due to large differences in both ground-state nucleotide binding affinity and nucleotide incorporation rates between correct and incorrect nucleotides. The kinetic partitioning between the slow mismatch extension catalyzed by the polymerase activity and the fast mismatch excision catalyzed by the 3' --> 5' exonuclease activity further lowers the error frequency of PolB1 by 14-fold. Furthermore, the base substitution error frequency of the exonuclease-deficient PolB1 increased by 5-fold as the reaction temperature increased. Interestingly, the fidelity of the exonuclease-deficient PolB1 mutant increased by 36-fold when the buffer pH was lowered from 8.5 to 6.0. A kinetic basis for these temperature and pH changes altering the fidelity of PolB1 was established. The faithful replication of genomic DNA catalyzed by PolB1 is discussed.

Publication types

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

MeSH terms

  • Archaeal Proteins / chemistry*
  • Archaeal Proteins / genetics
  • Archaeal Proteins / metabolism
  • Catalytic Domain / genetics
  • DNA Replication* / genetics
  • DNA-Directed DNA Polymerase / chemistry*
  • DNA-Directed DNA Polymerase / genetics
  • DNA-Directed DNA Polymerase / metabolism
  • Exonucleases / deficiency
  • Exonucleases / genetics
  • Exonucleases / metabolism
  • Kinetics
  • Mutagenesis, Site-Directed
  • Polymers / chemistry*
  • Polymers / metabolism
  • Sulfolobus solfataricus / enzymology*
  • Sulfolobus solfataricus / genetics


  • Archaeal Proteins
  • Polymers
  • DNA-Directed DNA Polymerase
  • Exonucleases