title: Ternary structure reveals mechanism of a membrane diacylglycerol kinase.
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.
authors.affiliation: School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland.
authors.forename: Dianfan
authors.initials: D
authors.lastname: Li
authors.affiliation: Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
authors.forename: Phillip J
authors.initials: PJ
authors.lastname: Stansfeld
authors.affiliation: Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
authors.forename: Mark S P
authors.initials: MSP
authors.lastname: Sansom
authors.affiliation: School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland.
authors.forename: Aaron
authors.initials: A
authors.lastname: Keogh
authors.affiliation: School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland.
authors.forename: Lutz
authors.initials: L
authors.lastname: Vogeley
authors.affiliation: School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland.
authors.forename: Nicole
authors.initials: N
authors.lastname: Howe
authors.affiliation: School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland.
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Lyons
authors.affiliation: School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland.
authors.forename: David
authors.initials: D
authors.lastname: Aragao
authors.affiliation: School of Molecular Sciences and Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA.
authors.forename: Petra
authors.initials: P
authors.lastname: Fromme
authors.affiliation: School of Molecular Sciences and Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA.
authors.forename: Raimund
authors.initials: R
authors.lastname: Fromme
authors.affiliation: School of Molecular Sciences and Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA.
authors.forename: Shibom
authors.initials: S
authors.lastname: Basu
authors.affiliation: School of Molecular Sciences and Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA.
authors.forename: Ingo
authors.initials: I
authors.lastname: Grotjohann
authors.affiliation: School of Molecular Sciences and Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Kupitz
authors.affiliation: School of Molecular Sciences and Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA.
authors.forename: Kimberley
authors.initials: K
authors.lastname: Rendek
authors.affiliation: Department of Physics, Arizona State University, Tempe, Arizona 85287, USA.
authors.forename: Uwe
authors.initials: U
authors.lastname: Weierstall
authors.affiliation: Department of Physics, Arizona State University, Tempe, Arizona 85287, USA.
authors.forename: Nadia A
authors.initials: NA
authors.lastname: Zatsepin
authors.affiliation: Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA.
authors.forename: Vadim
authors.initials: V
authors.lastname: Cherezov
authors.affiliation: School of Molecular Sciences and Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Liu
authors.affiliation: SFI Strategic Research Cluster in Solar Energy Conversion, School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: Sateesh
authors.initials: S
authors.lastname: Bandaru
authors.affiliation: SFI Strategic Research Cluster in Solar Energy Conversion, School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: Niall J
authors.initials: NJ
authors.lastname: English
authors.affiliation: Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany.
authors.forename: Cornelius
authors.initials: C
authors.lastname: Gati
authors.affiliation: Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany.
authors.forename: Anton
authors.initials: A
authors.lastname: Barty
authors.affiliation: Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany.
authors.forename: Oleksandr
authors.initials: O
authors.lastname: Yefanov
authors.affiliation: Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany.|Department of Physics, University of Hamburg, 22761 Hamburg, Germany.
authors.forename: Henry N
authors.initials: HN
authors.lastname: Chapman
authors.affiliation: Department of Biology, University of Konstanz, Box 647, D-78457 Konstanz, Germany.
authors.forename: Kay
authors.initials: K
authors.lastname: Diederichs
authors.affiliation: Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA.
authors.forename: Marc
authors.initials: M
authors.lastname: Messerschmidt
authors.affiliation: Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Boutet
authors.affiliation: Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA.
authors.forename: Garth J
authors.initials: GJ
authors.lastname: Williams
authors.affiliation: Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA.
authors.forename: M
authors.initials: M
authors.lastname: Marvin Seibert
authors.affiliation: School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland.
authors.forename: Martin
authors.initials: M
authors.lastname: Caffrey
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D020134:Catalytic Domain; D002462:Cell Membrane / Q000737:chemistry / Q000201:enzymology*; D018360:Crystallography, X-Ray; D019852:Diacylglycerol Kinase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000737:chemistry / Q000201:enzymology* / Q000235:genetics; D008958:Models, Molecular; D011487:Protein Conformation
chemical_list: D000255:Adenosine Triphosphate; D019852:Diacylglycerol Kinase