Ternary Structure Reveals Mechanism of a Membrane Diacylglycerol Kinase.Li, D., Stansfeld, P.J., Sansom, M.S.P., Keogh, A., Vogeley, L., Howe, N., Lyons, J.A., Aragao, D., Fromme, P., Fromme, R., Basu, S., Grotjohann, I., Kupitz, C., Rendek, K., Weierstall, U., Zatsepin, N.A., Cherezov, V., Liu, W., Bandaru, S., English, N.J., Gati, C., Barty, A., Yefanov, O., Chapman, H.N., Diederichs, K., Messerschmidt, M., Boutet, S., Williams, G.J., Marvin Seibert, M., Caffrey, M.
(2015) Nat.Commun. 6: 10140
- PubMed: 26673816
- DOI: 10.1038/ncomms10140
- Primary Citation of Related Structures:
- PubMed 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 ...
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.
SFI Strategic Research Cluster in Solar Energy Conversion, School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland.,School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland.,Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA.,Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA.,Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany.,Department of Biology, University of Konstanz, Box 647, D-78457 Konstanz, Germany.,School of Molecular Sciences and Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA.,Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.,Department of Physics, Arizona State University, Tempe, Arizona 85287, USA.,Department of Physics, University of Hamburg, 22761 Hamburg, Germany.