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Structural basis for gate-DNA recognition and bending by type IIA topoisomerases

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  • Ken C. Dong

    (Chemical Biology Graduate Program, College of Chemistry, University of California, Berkeley, California 94720-3220, USA
    QB3 Institute, Stanley Hall 3220, University of California at Berkeley, Berkeley, California 94720-3220, USA)

  • James M. Berger

    (QB3 Institute, Stanley Hall 3220, University of California at Berkeley, Berkeley, California 94720-3220, USA)

Abstract

Type II topoisomerases disentangle DNA to facilitate chromosome segregation, and represent a major class of therapeutic targets. Although these enzymes have been studied extensively, a molecular understanding of DNA binding has been lacking. Here we present the structure of a complex between the DNA-binding and cleavage core of Saccharomyces cerevisiae Topo II (also known as Top2) and a gate-DNA segment. The structure reveals that the enzyme enforces a 150° DNA bend through a mechanism similar to that of remodelling proteins such as integration host factor. Large protein conformational changes accompany DNA deformation, creating a bipartite catalytic site that positions the DNA backbone near a reactive tyrosine and a coordinated magnesium ion. This configuration closely resembles the catalytic site of type IA topoisomerases, reinforcing an evolutionary link between these structurally and functionally distinct enzymes. Binding of DNA facilitates opening of an enzyme dimerization interface, providing visual evidence for a key step in DNA transport.

Suggested Citation

  • Ken C. Dong & James M. Berger, 2007. "Structural basis for gate-DNA recognition and bending by type IIA topoisomerases," Nature, Nature, vol. 450(7173), pages 1201-1205, December.
    • Handle: RePEc:nat:nature:v:450:y:2007:i:7173:d:10.1038_nature06396
    DOI: 10.1038/nature06396
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    Cited by:

    1. Jaeyoon Lee & Meiling Wu & James T. Inman & Gundeep Singh & Seong ha Park & Joyce H. Lee & Robert M. Fulbright & Yifeng Hong & Joshua Jeong & James M. Berger & Michelle D. Wang, 2023. "Chromatinization modulates topoisomerase II processivity," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    2. Yuhui Xin & Runqi Xian & Yunge Yang & Jingyuan Cong & Zihe Rao & Xuemei Li & Yutao Chen, 2024. "Structural and functional insights into the T-even type bacteriophage topoisomerase II," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    3. Jingyuan Cong & Yuhui Xin & Huiling Kang & Yunge Yang & Chenlong Wang & Dongming Zhao & Xuemei Li & Zihe Rao & Yutao Chen, 2024. "Structural insights into the DNA topoisomerase II of the African swine fever virus," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

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