Modulation of the 5'-deoxyribose-5-phosphate lyase and DNA synthesis activities of mammalian DNA polymerase beta by apurinic/apyrimidinic endonuclease 1

J Biol Chem. 2004 Jun 11;279(24):25268-75. doi: 10.1074/jbc.M400804200. Epub 2004 Apr 11.


The Ape1 protein initiates the repair of apurinic/apyrimidinic sites during mammalian base excision repair (BER) of DNA. Ape1 catalyzes hydrolysis of the 5'-phosphodiester bond of abasic DNA to create nicks flanked by 3'-hydroxyl and 5'-deoxyribose 5-phosphate (dRP) termini. DNA polymerase (pol) beta catalyzes both DNA synthesis at the 3'-hydroxyl terminus and excision of the 5'-dRP moiety prior to completion of BER by DNA ligase. During BER, Ape1 recruits pol beta to the incised apurinic/apyrimidinic site and stimulates 5'-dRP excision by pol beta. The activities of these two enzymes are thus coordinated during BER. To examine further the coordination of BER, we investigated the ability of Ape1 to modulate the deoxynucleotidyltransferase and 5'-dRP lyase activities of pol beta. We report here that Ape1 stimulates 5'-dRP excision by a mechanism independent of its apurinic/apyrimidinic endonuclease activity. We also demonstrate a second mechanism, independent of Ape1, in which conditions that support DNA synthesis by pol beta also enhance 5'-dRP excision. Ape1 modulates the gap-filling activity of pol beta by specifically inhibiting synthesis on an incised abasic substrate but not on single-nucleotide gapped DNA. In contrast to the wild-type Ape1 protein, a catalytically impaired mutant form of Ape1 did not affect DNA synthesis by pol beta. However, this mutant protein retained the ability to stimulate 5'-dRP excision by pol beta. Simultaneous monitoring of 5'-dRP excision and DNA synthesis by pol beta demonstrated that the 5'-dRP lyase activity lags behind the polymerase activity despite the coordination of these two steps by Ape1 during BER.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Animals
  • Base Sequence
  • DNA / biosynthesis*
  • DNA Polymerase beta / metabolism*
  • DNA Repair*
  • DNA-(Apurinic or Apyrimidinic Site) Lyase / physiology*
  • Deoxycytosine Nucleotides / pharmacology
  • Deoxyribonuclease IV (Phage T4-Induced) / physiology
  • Humans
  • Molecular Sequence Data
  • Phosphorus-Oxygen Lyases / metabolism*


  • Deoxycytosine Nucleotides
  • 2'-deoxycytidine 5'-triphosphate
  • DNA
  • 5'-deoxyribose phosphate lyase
  • DNA Polymerase beta
  • Deoxyribonuclease IV (Phage T4-Induced)
  • APEX1 protein, human
  • DNA-(Apurinic or Apyrimidinic Site) Lyase
  • Phosphorus-Oxygen Lyases