Ternary structure reveals mechanism of a membrane diacylglycerol kinase

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, Christopher Kupitz, Kimberley Rendek, Uwe Weierstall, Nadia A. Zatsepin, Vadim Cherezov, Wei Liu, Sateesh Bandaru, Niall J. English, Cornelius Gati, Anton Barty, Oleksandr Yefanov, Henry N. Chapman, Kay Diederichs, Marc Messerschmidt, Sébastien Boutet, Garth J. Williams, M. Marvin Seibert and Martin Caffrey ()
Additional contact information
Dianfan Li: School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin
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
David Aragao: School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin
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
Kay Diederichs: University of Konstanz
Marc Messerschmidt: Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory
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
Martin Caffrey: School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin

Nature Communications, 2015, vol. 6, issue 1, 1-12

Abstract: 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.

Date: 2015
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/ncomms10140 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms10140

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/ncomms10140

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().