Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1

  1. Fahad Rashid
  2. Paul D Harris
  3. Manal S Zaher
  4. Mohamed A Sobhy
  5. Luay I Joudeh
  6. Chunli Yan
  7. Hubert Piwonski
  8. Susan E Tsutakawa
  9. Ivaylo Ivanov
  10. John A Tainer
  11. Satoshi Habuchi
  12. Samir M Hamdan  Is a corresponding author
  1. King Abdullah University of Science and Technology, Saudi Arabia
  2. Georgia State University, United States
  3. Lawrence Berkeley National Laboratory, United States

Abstract

Human flap endonuclease 1 (FEN1) and related structure-specific 5'nucleases precisely identify and incise aberrant DNA structures during replication, repair and recombination to avoid genomic instability. Yet, it is unclear how the 5'nuclease mechanisms of DNA distortion and protein ordering robustly mediate efficient and accurate substrate recognition and catalytic selectivity. Here, single-molecule sub-millisecond and millisecond analyses of FEN1 reveal a protein-DNA induced-fit mechanism that efficiently verifies substrate and suppresses off-target cleavage. FEN1 sculpts DNA with diffusion-limited kinetics to test DNA substrate. This DNA distortion mutually 'locks' protein and DNA conformation and enables substrate verification with extreme precision. Strikingly, FEN1 never misses cleavage of its cognate substrate while blocking probable formation of catalytically competent interactions with noncognate substrates and fostering their pre-incision dissociation. These findings establish FEN1 has practically perfect precision and that separate control of induced-fit substrate recognition sets up the catalytic selectivity of the nuclease active site for genome stability.

Article and author information

Author details

  1. Fahad Rashid

    Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
    Competing interests
    The authors declare that no competing interests exist.
  2. Paul D Harris

    Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
    Competing interests
    The authors declare that no competing interests exist.
  3. Manal S Zaher

    Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
    Competing interests
    The authors declare that no competing interests exist.
  4. Mohamed A Sobhy

    Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
    Competing interests
    The authors declare that no competing interests exist.
  5. Luay I Joudeh

    Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
    Competing interests
    The authors declare that no competing interests exist.
  6. Chunli Yan

    Department of Chemistry, Georgia State University, Atlanta, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Hubert Piwonski

    Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8666-3945
  8. Susan E Tsutakawa

    Lawrence Berkeley National Laboratory, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Ivaylo Ivanov

    Department of Chemistry, Georgia State University, Atlanta, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. John A Tainer

    Lawrence Berkeley National Laboratory, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Satoshi Habuchi

    Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
    Competing interests
    The authors declare that no competing interests exist.
  12. Samir M Hamdan

    Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
    For correspondence
    samir.hamdan@kaust.edu.sa
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5192-1852

Funding

King Abdullah University of Science and Technology (2201 CRG3)

  • Fahad Rashid
  • Paul D Harris
  • Manal S Zaher
  • Mohamed A Sobhy
  • Luay I Joudeh
  • Hubert Piwonski
  • John A Tainer
  • Satoshi Habuchi
  • Samir M Hamdan

National Science Foundation (MCB-1149521)

  • Chunli Yan
  • Ivaylo Ivanov

NIH Clinical Center (R01GM110387)

  • Chunli Yan
  • Ivaylo Ivanov

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. James M Berger, Johns Hopkins University School of Medicine, United States

Publication history

  1. Received: September 27, 2016
  2. Accepted: February 20, 2017
  3. Accepted Manuscript published: February 23, 2017 (version 1)
  4. Version of Record published: March 20, 2017 (version 2)

Copyright

© 2017, Rashid et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Fahad Rashid
  2. Paul D Harris
  3. Manal S Zaher
  4. Mohamed A Sobhy
  5. Luay I Joudeh
  6. Chunli Yan
  7. Hubert Piwonski
  8. Susan E Tsutakawa
  9. Ivaylo Ivanov
  10. John A Tainer
  11. Satoshi Habuchi
  12. Samir M Hamdan
(2017)
Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1
eLife 6:e21884.
https://doi.org/10.7554/eLife.21884

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