A 26 kDa yeast DNA topoisomerase I fragment: crystallographic structure and mechanistic implications

Neal Lue, Amit Sharma, Alfonso Mondragón*, James C. Wang

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

30 Scopus citations


Background: Type I DNA topoisomerases, divided mechanistically into two subfamilies, are ubiquitous enzymes that participate in replication and transcription. In addition to its role in these fundamental processes, the biological importance of eukaryotic DNA topoisomerase I is underscored by its identification as the target of the antitumor alkaloid camptothecin. An understanding of the mechanism of catalysis and interactions with camptothecin and other drugs has been hampered by a lack of detailed structural information. Results The three-dimensional structure of a 26 kDa fragment (residues 135 to about 363) of Saccharomyces cerevisiae DNA topoisomerase I has been determined at 1.9 å resolution. The fragment has a novel architecture comprising a concave platform and a pair of outlying V-shaped helices. Photocrosslinking and protein footprinting experiments show that the positively charged concave surface and the junction region of the V-shaped pair of helices contact DNA in the enzyme-DNA complex. Conclusion Crystallographic, biochemical and genetic data indicate that this 26 kDa fragment of yeast DNA topoisomerase I is involved in complex formation between the enzyme and DNA, and probably also in camptothecin-enzyme-DNA ternary complex formation. A molecular model for protein-DNA interaction based on these data is proposed. The bipartite DNA-binding regions of the 26 kDa fragment may enable eukaryotic DNA topoisomerase I to adapt to sequence-dependent structural variations in its DNA substrates.

Original languageEnglish (US)
Pages (from-to)1315-1322
Number of pages8
Issue number12
StatePublished - Dec 1995


  • DNA-protein interaction
  • X-ray structure
  • camptothecin
  • protein footprinting
  • topoisomerase I

ASJC Scopus subject areas

  • Molecular Biology
  • Structural Biology


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