1. Biochemistry and Chemical Biology
  2. Structural Biology and Molecular Biophysics

Structure of protein O-mannose kinase reveals a unique active site architecture

  1. Qinyu Zhu
  2. David Venzke
  3. Ameya S Walimbe
  4. Mary E Anderson
  5. Qiuyu Fu
  6. Lisa N Kinch
  7. Wei Wang
  8. Xing Chen
  9. Nick V Grishin
  10. Niu Huang
  11. Liping Yu
  12. Jack E Dixon
  13. Kevin P Campbell  Is a corresponding author
  14. Junyu Xiao  Is a corresponding author
  1. School of Life Sciences, Peking University, China
  2. Howard Hughes Medical Institute, University of Iowa Roy J. and Lucille A. Carver College of Medicine, United States
  3. National Institute of Biological Sciences, China
  4. University of Texas Southwestern Medical Center, United States
  5. Peking University, China
  6. University of Iowa, United States
  7. University of California, San Diego, United States
https://doi.org/10.7554/eLife.22238
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Cite this article
  1. Qinyu Zhu
  2. David Venzke
  3. Ameya S Walimbe
  4. Mary E Anderson
  5. Qiuyu Fu
  6. Lisa N Kinch
  7. Wei Wang
  8. Xing Chen
  9. Nick V Grishin
  10. Niu Huang
  11. Liping Yu
  12. Jack E Dixon
  13. Kevin P Campbell
  14. Junyu Xiao
(2016)
Structure of protein O-mannose kinase reveals a unique active site architecture
eLife 5:e22238.
https://doi.org/10.7554/eLife.22238
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Abstract

The 'pseudokinase' SgK196 is a protein O-mannose kinase (POMK) that catalyzes an essential phosphorylation step during biosynthesis of the laminin-binding glycan on α-dystroglycan. However, the catalytic mechanism underlying this activity remains elusive. Here we present the crystal structure of Danio rerio POMK in complex with Mg2+ ions, ADP, aluminum fluoride, and the GalNAc-β3-GlcNAc-β4-Man trisaccharide substrate, thereby providing a snapshot of the catalytic transition state of this unusual kinase. The active site of POMK is established by residues located in non-canonical positions and is stabilized by a disulfide bridge. GalNAc-β3-GlcNAc-β4-Man is recognized by a surface groove, and the GalNAc-β3-GlcNAc moiety mediates the majority of interactions with POMK. Expression of various POMK mutants in POMK knockout cells further validated the functional requirements of critical residues. Our results provide important insights into the ability of POMK to function specifically as a glycan kinase, and highlight the structural diversity of the human kinome.

Article and author information

Author details

  1. Qinyu Zhu

    The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.

  2. David Venzke

    Department of Molecular Physiology and Biophysics, Howard Hughes Medical Institute, University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, United States
    Competing interests
    The authors declare that no competing interests exist.

  3. Ameya S Walimbe

    Department of Molecular Physiology and Biophysics, Howard Hughes Medical Institute, University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, United States
    Competing interests
    The authors declare that no competing interests exist.

  4. Mary E Anderson

    Department of Molecular Physiology and Biophysics, Howard Hughes Medical Institute, University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, United States
    Competing interests
    The authors declare that no competing interests exist.

  5. Qiuyu Fu

    National Institute of Biological Sciences, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.

  6. Lisa N Kinch

    Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    The authors declare that no competing interests exist.

  7. Wei Wang

    Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.

  8. Xing Chen

    Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.

  9. Nick V Grishin

    Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    The authors declare that no competing interests exist.

  10. Niu Huang

    National Institute of Biological Sciences, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.

  11. Liping Yu

    University of Iowa Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, United States
    Competing interests
    The authors declare that no competing interests exist.

  12. Jack E Dixon

    Department of Pharmacology, University of California, San Diego, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.

  13. Kevin P Campbell

    Department of Molecular Physiology and Biophysics, Howard Hughes Medical Institute, University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, United States
    For correspondence
    kevin-campbell@uiowa.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2066-5889

  14. Junyu Xiao

    The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
    For correspondence
    junyuxiao@pku.edu.cn
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1822-1701

Funding

National Natural Science Foundation of China (31570735)

  • Junyu Xiao

National Key Research & Development Plan of China (2016YFC0906000)

  • Junyu Xiao

National Institute of Diabetes and Digestive and Kidney Diseases (DK18849, DK18024)

  • Jack E Dixon

Paul D. Wellstone Muscular Dystrophy Cooperative Research Center (1U54NS053672)

  • Kevin P Campbell

Howard Hughes Medical Institute

  • Jack E Dixon
  • Kevin P Campbell

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

Reviewing Editor

  1. Reid Gilmore, University of Massachusetts Medical School, United States

Version history

  1. Received: October 10, 2016
  2. Accepted: November 22, 2016
  3. Accepted Manuscript published: November 23, 2016 (version 1)
  4. Version of Record published: December 7, 2016 (version 2)

Copyright

© 2016, Zhu 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. Qinyu Zhu
  2. David Venzke
  3. Ameya S Walimbe
  4. Mary E Anderson
  5. Qiuyu Fu
  6. Lisa N Kinch
  7. Wei Wang
  8. Xing Chen
  9. Nick V Grishin
  10. Niu Huang
  11. Liping Yu
  12. Jack E Dixon
  13. Kevin P Campbell
  14. Junyu Xiao
(2016)
Structure of protein O-mannose kinase reveals a unique active site architecture
eLife 5:e22238.
https://doi.org/10.7554/eLife.22238

Share this article

https://doi.org/10.7554/eLife.22238

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