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Molecular snapshots of APE1 proofreading mismatches and removing DNA damage

Author

Listed:
  • Amy M. Whitaker

    (University of Kansas Medical Center)

  • Tony S. Flynn

    (University of Kansas Medical Center)

  • Bret D. Freudenthal

    (University of Kansas Medical Center)

Abstract

Human apurinic/apyrimidinic (AP) endonuclease 1 (APE1) is an essential DNA repair enzyme which uses a single active site to process DNA damage via two distinct activities: (1) AP-endonuclease and (2) 3′ to 5′ exonuclease. The AP-endonuclease activity cleaves at AP-sites, while the exonuclease activity excises bulkier 3′ mismatches and DNA damage to generate clean DNA ends suitable for downstream repair. Molecular details of the exonuclease reaction and how one active site can accommodate various toxic DNA repair intermediates remains elusive despite being biologically important. Here, we report multiple high-resolution APE1–DNA structural snapshots revealing how APE1 removes 3′ mismatches and DNA damage by placing the 3′ group within the intra-helical DNA cavity via a non-base flipping mechanism. This process is facilitated by a DNA nick, instability of a mismatched/damaged base, and bending of the DNA. These results illustrate how APE1 cleanses DNA dirty-ends to generate suitable substrates for downstream repair enzymes.

Suggested Citation

  • Amy M. Whitaker & Tony S. Flynn & Bret D. Freudenthal, 2018. "Molecular snapshots of APE1 proofreading mismatches and removing DNA damage," Nature Communications, Nature, vol. 9(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-017-02175-y
    DOI: 10.1038/s41467-017-02175-y
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    Cited by:

    1. Haichao Zhao & Jia Li & Zhongsheng You & Howard D. Lindsay & Shan Yan, 2024. "Distinct regulation of ATM signaling by DNA single-strand breaks and APE1," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. Renye Yue & Zhe Li & Huiyi Liu & Youjuan Wang & Yuhang Li & Rui Yin & Baoli Yin & Haisheng Qian & Heemin Kang & Xiaobing Zhang & Guosheng Song, 2024. "Imaging-guided companion diagnostics in radiotherapy by monitoring APE1 activity with afterglow and MRI imaging," Nature Communications, Nature, vol. 15(1), pages 1-23, December.

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