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Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate

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  • Shin-Fu Chen

    (College of Medicine, National Taiwan University)

  • Nan-Lan Huang

    (Research Center for Applied Sciences and Institute of Biomedical Sciences, Academia Sinica
    University of California, San Diego)

  • Jung-Hsin Lin

    (Research Center for Applied Sciences and Institute of Biomedical Sciences, Academia Sinica)

  • Chyuan-Chuan Wu

    (College of Medicine, National Taiwan University
    Institute of Molecular Biology, Academia Sinica)

  • Ying-Ren Wang

    (College of Medicine, National Taiwan University)

  • Yu-Jen Yu

    (College of Medicine, National Taiwan University)

  • Michael K. Gilson

    (University of California, San Diego)

  • Nei-Li Chan

    (College of Medicine, National Taiwan University
    National Chung Hsing University
    Scientific Research Division, National Synchrotron Radiation Research Center)

Abstract

Type IIA topoisomerases (Top2s) manipulate the handedness of DNA crossovers by introducing a transient and protein-linked double-strand break in one DNA duplex, termed the DNA-gate, whose opening allows another DNA segment to be transported through to change the DNA topology. Despite the central importance of this gate-opening event to Top2 function, the DNA-gate in all reported structures of Top2-DNA complexes is in the closed state. Here we present the crystal structure of a human Top2 DNA-gate in an open conformation, which not only reveals structural characteristics of its DNA-conducting path, but also uncovers unexpected yet functionally significant conformational changes associated with gate-opening. This structure further implicates Top2’s preference for a left-handed DNA braid and allows the construction of a model representing the initial entry of another DNA duplex into the DNA-gate. Steered molecular dynamics calculations suggests the Top2-catalyzed DNA passage may be achieved by a rocker-switch-type movement of the DNA-gate.

Suggested Citation

  • Shin-Fu Chen & Nan-Lan Huang & Jung-Hsin Lin & Chyuan-Chuan Wu & Ying-Ren Wang & Yu-Jen Yu & Michael K. Gilson & Nei-Li Chan, 2018. "Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate," Nature Communications, Nature, vol. 9(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-05406-y
    DOI: 10.1038/s41467-018-05406-y
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    Cited by:

    1. Heeyoun Bunch & Deukyeong Kim & Masahiro Naganuma & Reiko Nakagawa & Anh Cong & Jaehyeon Jeong & Haruhiko Ehara & Hongha Vu & Jeong Ho Chang & Matthew J. Schellenberg & Shun-ichi Sekine, 2023. "ERK2-topoisomerase II regulatory axis is important for gene activation in immediate early genes," Nature Communications, Nature, vol. 14(1), pages 1-16, 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.

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