IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v6y2015i1d10.1038_ncomms10140.html
   My bibliography  Save this article

Ternary structure reveals mechanism of a membrane diacylglycerol kinase

Author

Listed:
  • Dianfan Li

    (School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin
    Present address: National Center for Protein Sciences, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201210, China)

  • Phillip J. Stansfeld

    (University of Oxford)

  • Mark S. P. Sansom

    (University of Oxford)

  • Aaron Keogh

    (School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin)

  • Lutz Vogeley

    (School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin)

  • Nicole Howe

    (School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin)

  • Joseph A. Lyons

    (School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin
    Present address: Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000, Denmark)

  • David Aragao

    (School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin
    Present address: Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria VIC 3168, Australia)

  • Petra Fromme

    (School of Molecular Sciences and Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University)

  • Raimund Fromme

    (School of Molecular Sciences and Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University)

  • Shibom Basu

    (School of Molecular Sciences and Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University)

  • Ingo Grotjohann

    (School of Molecular Sciences and Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University)

  • Christopher Kupitz

    (School of Molecular Sciences and Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University)

  • Kimberley Rendek

    (School of Molecular Sciences and Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University)

  • Uwe Weierstall

    (Arizona State University)

  • Nadia A. Zatsepin

    (Arizona State University)

  • Vadim Cherezov

    (Bridge Institute, University of Southern California)

  • Wei Liu

    (School of Molecular Sciences and Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University)

  • Sateesh Bandaru

    (SFI Strategic Research Cluster in Solar Energy Conversion, School of Chemical and Bioprocess Engineering, University College Dublin)

  • Niall J. English

    (SFI Strategic Research Cluster in Solar Energy Conversion, School of Chemical and Bioprocess Engineering, University College Dublin)

  • Cornelius Gati

    (Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron)

  • Anton Barty

    (Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron)

  • Oleksandr Yefanov

    (Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron)

  • Henry N. Chapman

    (Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron
    University of Hamburg)

  • Kay Diederichs

    (University of Konstanz)

  • Marc Messerschmidt

    (Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory
    Present address: BioXFEL STC, 700 Ellicott Street, Buffalo, New York 14203, USA)

  • Sébastien Boutet

    (Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory)

  • Garth J. Williams

    (Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory)

  • M. Marvin Seibert

    (Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory
    Present address: Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-751 24 Uppsala, Sweden)

  • Martin Caffrey

    (School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin)

Abstract

Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the membrane/cytosol interface. How nature has accomplished this extraordinary feat is revealed here in a crystal structure of the kinase captured as a ternary complex with bound lipid substrate and an ATP analogue. Residues, identified as essential for activity by mutagenesis, decorate the active site and are rationalized by the ternary structure. The γ-phosphate of the ATP analogue is positioned for direct transfer to the primary hydroxyl of the lipid whose acyl chain is in the membrane. A catalytic mechanism for this unique enzyme is proposed. The active site architecture shows clear evidence of having arisen by convergent evolution.

Suggested Citation

  • Dianfan Li & Phillip J. Stansfeld & Mark S. P. Sansom & Aaron Keogh & Lutz Vogeley & Nicole Howe & Joseph A. Lyons & David Aragao & Petra Fromme & Raimund Fromme & Shibom Basu & Ingo Grotjohann & Chri, 2015. "Ternary structure reveals mechanism of a membrane diacylglycerol kinase," Nature Communications, Nature, vol. 6(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms10140
    DOI: 10.1038/ncomms10140
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/ncomms10140
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/ncomms10140?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms10140. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.