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Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair

Author

Listed:
  • John R. Walker

    (Cellular Biochemistry and Biophysics Program)

  • Richard A. Corpina

    (Cellular Biochemistry and Biophysics Program)

  • Jonathan Goldberg

    (Cellular Biochemistry and Biophysics Program
    Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center)

Abstract

The Ku heterodimer (Ku70 and Ku80 subunits) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. The crystal structure of the human Ku heterodimer was determined both alone and bound to a 55-nucleotide DNA element at 2.7 and 2.5 Å resolution, respectively. Ku70 and Ku80 share a common topology and form a dyad-symmetrical molecule with a preformed ring that encircles duplex DNA. The binding site can cradle two full turns of DNA while encircling only the central 3–4 base pairs (bp). Ku makes no contacts with DNA bases and few with the sugar-phosphate backbone, but it fits sterically to major and minor groove contours so as to position the DNA helix in a defined path through the protein ring. These features seem well designed to structurally support broken DNA ends and to bring the DNA helix into phase across the junction during end processing and ligation.

Suggested Citation

  • John R. Walker & Richard A. Corpina & Jonathan Goldberg, 2001. "Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair," Nature, Nature, vol. 412(6847), pages 607-614, August.
    • Handle: RePEc:nat:nature:v:412:y:2001:i:6847:d:10.1038_35088000
    DOI: 10.1038/35088000
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    Cited by:

    1. Zhen Shu & Bhakti Dwivedi & Jeffrey M. Switchenko & David S. Yu & Xingming Deng, 2024. "PD-L1 deglycosylation promotes its nuclear translocation and accelerates DNA double-strand-break repair in cancer," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    2. Benjamin M. Stinson & Sean M. Carney & Johannes C. Walter & Joseph J. Loparo, 2024. "Structural role for DNA Ligase IV in promoting the fidelity of non-homologous end joining," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    3. Ida Friis & Ilia A Solov’yov, 2018. "Activation of the DNA-repair mechanism through NBS1 and MRE11 diffusion," PLOS Computational Biology, Public Library of Science, vol. 14(7), pages 1-16, July.
    4. Jun Huang & David Rowe & Pratima Subedi & Wei Zhang & Tyler Suelter & Barbara Valent & David E. Cook, 2022. "CRISPR-Cas12a induced DNA double-strand breaks are repaired by multiple pathways with different mutation profiles in Magnaporthe oryzae," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    5. Angel Rivera-Calzada & Raquel Arribas-Bosacoma & Alba Ruiz-Ramos & Paloma Escudero-Bravo & Jasminka Boskovic & Rafael Fernandez-Leiro & Antony W. Oliver & Laurence H. Pearl & Oscar Llorca, 2022. "Structural basis for the inactivation of cytosolic DNA sensing by the vaccinia virus," Nature Communications, Nature, vol. 13(1), pages 1-13, December.

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