Kinetic mechanism of DNA polymerization catalyzed by human DNA polymerase ε

Biochemistry. 2013 Oct 8;52(40):7041-9. doi: 10.1021/bi400803v. Epub 2013 Sep 26.


Eukaryotes require highly accurate and processive DNA polymerases to ensure faithful and efficient replication of their genomes. DNA polymerase ε (Polε) has been shown to catalyze leading-strand DNA synthesis during replication in vivo, but little is known about the kinetic mechanism of polymerization catalyzed by this replicative enzyme. To elucidate this mechanism, we have generated a truncated, exonuclease-deficient mutant of the catalytic subunit of human Polε (Polε exo-) and carried out pre-steady-state kinetic analysis of this enzyme. Our results show that Polε exo-, as other DNA polymerases, follows an induced-fit mechanism when catalyzing correct nucleotide incorporation. Polε exo- binds DNA with a Kd(DNA) of 79 nM and dissociates from the E·DNA binary complex with a rate constant of 0.021 s(-1). Although Polε exo- binds a correct incoming nucleotide weakly with a Kd(dTTP) of 31 μM, it catalyzes correct nucleotide incorporation at a fast rate constant of 248 s(-1) at 20 °C. Both a large reaction amplitude difference (42%) between pulse-chase and pulse-quench assays and a small elemental effect (0.9) for correct dTTP incorporation suggest that a slow conformational change preceding the chemistry step limits the rate of correct nucleotide incorporation. In addition, our kinetic analysis shows that Polε exo- exhibits low processivity during polymerization. To catalyze leading-strand synthesis in vivo, Polε likely interacts with its three smaller subunits and additional replication factors in order to assemble a replication complex and significantly enhance its polymerization processivity.

Publication types

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

MeSH terms

  • Catalytic Domain
  • DNA / metabolism
  • DNA Polymerase II / genetics
  • DNA Polymerase II / metabolism*
  • DNA Replication*
  • DNA-Directed DNA Polymerase / metabolism
  • Exonucleases / metabolism
  • Humans
  • Kinetics
  • Poly-ADP-Ribose Binding Proteins


  • Poly-ADP-Ribose Binding Proteins
  • DNA
  • DNA Polymerase II
  • DNA-Directed DNA Polymerase
  • POLE protein, human
  • Exonucleases