Coordinating the initial steps of base excision repair. Apurinic/apyrimidinic endonuclease 1 actively stimulates thymine DNA glycosylase by disrupting the product complex

J Biol Chem. 2008 Nov 21;283(47):32680-90. doi: 10.1074/jbc.M805504200. Epub 2008 Sep 19.

Abstract

DNA glycosylases initiate base excision repair by removing damaged or mismatched bases, producing apurinic/apyrimidinic (AP) DNA. For many glycosylases, the AP-DNA remains tightly bound, impeding enzymatic turnover. A prominent example is thymine DNA glycosylase (TDG), which removes T from G.T mispairs and recognizes other lesions, with specificity for damage at CpG dinucleotides. TDG turnover is very slow; its activity appears to reach a plateau as the [product]/[enzyme] ratio approaches unity. The follow-on base excision repair enzyme, AP endonuclease 1 (APE1), stimulates the turnover of TDG and other glycosylases, involving a mechanism that remains largely unknown. We examined the catalytic activity of human TDG (hTDG), alone and with human APE1 (hAPE1), using pre-steady-state kinetics and a coupled-enzyme (hTDG-hAPE1) fluorescence assay. hTDG turnover is exceedingly slow for G.T (k(cat)=0.00034 min(-1)) and G.U (k(cat)=0.005 min(-1)) substrates, much slower than k(max) from single turnover experiments, confirming that AP-DNA release is rate-limiting. We find unexpectedly large differences in k(cat) for G.T, G.U, and G.FU substrates, indicating the excised base remains trapped in the product complex by AP-DNA. hAPE1 increases hTDG turnover by 42- and 26-fold for G.T and G.U substrates, the first quantitative measure of the effect of hAPE1. hAPE1 stimulates hTDG by disrupting the product complex rather than merely depleting (endonucleolytically) the AP-DNA. The enhancement is greater for hTDG catalytic core (residues 111-308 of 410), indicating the N- and C-terminal domains are dispensable for stimulatory interactions with hAPE1. Potential mechanisms for hAPE1 disruption of the of hTDG product complex are discussed.

Publication types

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

MeSH terms

  • Base Pair Mismatch
  • Base Sequence
  • DNA Repair*
  • DNA-(Apurinic or Apyrimidinic Site) Lyase / chemistry
  • DNA-(Apurinic or Apyrimidinic Site) Lyase / physiology*
  • Humans
  • Kinetics
  • Models, Biological
  • Models, Chemical
  • Molecular Conformation
  • Molecular Sequence Data
  • Protein Structure, Tertiary
  • SUMO-1 Protein / metabolism
  • Thymine DNA Glycosylase / metabolism*
  • Time Factors

Substances

  • SUMO-1 Protein
  • SUMO1 protein, human
  • Thymine DNA Glycosylase
  • APEX1 protein, human
  • DNA-(Apurinic or Apyrimidinic Site) Lyase