Human DNA polymerase beta deoxyribose phosphate lyase. Substrate specificity and catalytic mechanism

J Biol Chem. 1998 Jun 12;273(24):15263-70. doi: 10.1074/jbc.273.24.15263.


DNA polymerase beta (beta-pol) cleaves the sugar-phosphate bond 3' to an intact apurinic/apyrimidinic (AP) site (i.e. AP lyase activity). The same bond is cleaved even if the AP site has been previously 5'-incised by AP endonuclease, resulting in a 5' 2-deoxyribose 5-phosphate (i.e. dRP lyase activity). We characterized these lyase reactions by steady-state kinetics with the amino-terminal 8-kDa domain of beta-pol and with the entire 39-kDa polymerase. Steady-state kinetic analyses show that the Michaelis constants for both the dRP and AP lyase activities of beta-pol are similar. However, kcat is approximately 200-fold lower for the AP lyase activity on an intact AP site than for an AP endonuclease-preincised site. The 8-kDa domain was also less efficient with an intact AP site than on a preincised site. The full-length enzyme and the 8-kDa domain efficiently remove the 5' dRP from a preincised AP site in the absence of Mg2+, and the pH profiles of beta-pol and 8-kDa domain dRP lyase catalytic efficiency exhibit a broad alkaline pH optimum. An inhibitory effect of pyridoxal 5'-phosphate on the dRP lyase activity is consistent with involvement of a primary amine (Lys72) as the Schiff base nucleophile during lyase chemistry.

MeSH terms

  • Carbon-Oxygen Lyases / metabolism*
  • DNA / metabolism
  • DNA Glycosylases*
  • DNA Polymerase beta / chemistry*
  • DNA-(Apurinic or Apyrimidinic Site) Lyase
  • Deoxyribonuclease IV (Phage T4-Induced)
  • Humans
  • Hydrogen-Ion Concentration
  • Kinetics
  • Molecular Structure
  • N-Glycosyl Hydrolases / metabolism
  • Peptide Fragments / metabolism
  • Pyridoxal Phosphate / pharmacology
  • Uracil-DNA Glycosidase


  • Peptide Fragments
  • Pyridoxal Phosphate
  • DNA
  • DNA Polymerase beta
  • Deoxyribonuclease IV (Phage T4-Induced)
  • DNA Glycosylases
  • N-Glycosyl Hydrolases
  • Uracil-DNA Glycosidase
  • Carbon-Oxygen Lyases
  • DNA-(Apurinic or Apyrimidinic Site) Lyase