Abstract
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 language | English (US) |
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Pages (from-to) | 1315-1322 |
Number of pages | 8 |
Journal | Structure |
Volume | 3 |
Issue number | 12 |
DOIs | |
State | Published - Dec 1995 |
Funding
We thank J Berger, T Ellenberger, S Garman, T Jardetzky, C Lima, V Tokars and J Widom for their help, comments, and suggestions. We also thank the staff at SSRL for their help with synchrotron data collection; all other diffraction data were collected at Northwestern University. This work was supported by NIH grants. NL was supported in part by a Life Technologies postdoctoral fellowship from the Life Sciences Research Foundation.
Keywords
- DNA-protein interaction
- X-ray structure
- camptothecin
- protein footprinting
- topoisomerase I
ASJC Scopus subject areas
- Structural Biology
- Molecular Biology
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YEAST DNA TOPOISOMERASE I, N-TERMINAL FRAGMENT
Lue, N. (Contributor), Sharma, A. (Contributor), Mondragón, A. (Contributor) & Wang, J. C. (Contributor), Protein Data Bank (PDB), Mar 12 1997
DOI: 10.2210/pdb1OIS/pdb, https://www.wwpdb.org/pdb?id=pdb_00001ois
Dataset