Guarding the genome: Electrostatic repulsion of water by DNA suppresses a potent nuclease activity of topoisomerase IB

Ligeng Tian, Christopher D. Claeboe, Sidney M. Hecht, Stewart Shuman

Research output: Contribution to journalArticle

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Type IB topoisomerases cleave and rejoin DNA strands through a stable covalent DNA-(3′-phosphotyrosyl)-enzyme intermediate. The stability of the intermediate is a two-edged sword; it preserves genome integrity during supercoil relaxation, but it also reinforces the toxicity of drugs and lesions that interfere with the DNA rejoining step. Here, we identify a key determinant of the stability of the complex by showing that introduction of an Sp or Rp methylphosphonate linkage at the cleavage site transforms topoisomerase IB into a potent endonuclease. The nuclease reaction entails formation and surprisingly rapid hydrolysis of a covalent enzyme-DNA methylphosphonate intermediate. The ∼30,000-fold acceleration in the rate of hydrolysis of a methylphosphonate versus phosphodiester suggests that repulsion of water by the DNA phosphate anion suppresses the latent nuclease function of topoisomerase IB. These findings expose an Achilles' heel of topoisomerases as guardians of the genome, and they have broad implications for understanding enzymatic phosphoryl transfer.

Original languageEnglish (US)
Pages (from-to)199-208
Number of pages10
JournalMolecular Cell
Issue number1
StatePublished - Jul 1 2003


ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

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