skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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. As a result, the active site architecture shows clear evidence of having arisen by convergent evolution.

Authors:
 [1];  [2];  [2];  [1];  [1];  [1];  [1];  [1];  [3];  [3];  [3];  [3];  [3];  [3];  [3];  [3];  [4];  [3];  [5];  [5] more »;  [6];  [6];  [6];  [7];  [8];  [9];  [9];  [9];  [9];  [1] « less
+ Show Author Affiliations
  1. Trinity College Dublin, Dublin (Ireland)
  2. Univ. of Oxford, Oxford (United Kingdom)
  3. Arizona State Univ., Tempe, AZ (United States)
  4. Univ. of Southern California, Los Angeles, CA (United States)
  5. Univ. College Dublin, Dublin (Ireland)
  6. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)
  7. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Univ. of Hamburg, Hamburg (Germany)
  8. Univ. of Konstanz, Konstanz (Germany)
  9. SLAC National Accelerator Lab., Menlo Park, CA (United States)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1233178
Grant/Contract Number:  
AC03-76SF00515
Resource Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; biological sciences; biochemistry; biophysics

Citation Formats

Li, Dianfan, Stansfeld, Phillip J., Sansom, Mark S. P., Keogh, Aaron, Vogeley, Lutz, Howe, Nicole, Lyons, Joseph A., Aragao, David, Fromme, Petra, Fromme, Raimund, Basu, Shibom, Grotjohann, Ingo, Kupitz, Christopher, Rendek, Kimberley, Weierstall, Uwe, Zatsepin, Nadia A., Cherezov, Vadim, Liu, Wei, Bandaru, Sateesh, English, Niall J., Gati, Cornelius, Barty, Anton, Yefanov, Oleksandr, Chapman, Henry N., Diederichs, Kay, Messerschmidt, Marc, Boutet, Sébastien, Williams, Garth J., Marvin Seibert, M., and Caffrey, Martin. Ternary structure reveals mechanism of a membrane diacylglycerol kinase. United States: N. p., 2015. Web. doi:10.1038/ncomms10140.
Copy to clipboard
Li, Dianfan, Stansfeld, Phillip J., Sansom, Mark S. P., Keogh, Aaron, Vogeley, Lutz, Howe, Nicole, Lyons, Joseph A., Aragao, David, Fromme, Petra, Fromme, Raimund, Basu, Shibom, Grotjohann, Ingo, Kupitz, Christopher, Rendek, Kimberley, Weierstall, Uwe, Zatsepin, Nadia A., Cherezov, Vadim, Liu, Wei, Bandaru, Sateesh, English, Niall J., Gati, Cornelius, Barty, Anton, Yefanov, Oleksandr, Chapman, Henry N., Diederichs, Kay, Messerschmidt, Marc, Boutet, Sébastien, Williams, Garth J., Marvin Seibert, M., & Caffrey, Martin. Ternary structure reveals mechanism of a membrane diacylglycerol kinase. United States. doi:10.1038/ncomms10140.
Copy to clipboard
Li, Dianfan, Stansfeld, Phillip J., Sansom, Mark S. P., Keogh, Aaron, Vogeley, Lutz, Howe, Nicole, Lyons, Joseph A., Aragao, David, Fromme, Petra, Fromme, Raimund, Basu, Shibom, Grotjohann, Ingo, Kupitz, Christopher, Rendek, Kimberley, Weierstall, Uwe, Zatsepin, Nadia A., Cherezov, Vadim, Liu, Wei, Bandaru, Sateesh, English, Niall J., Gati, Cornelius, Barty, Anton, Yefanov, Oleksandr, Chapman, Henry N., Diederichs, Kay, Messerschmidt, Marc, Boutet, Sébastien, Williams, Garth J., Marvin Seibert, M., and Caffrey, Martin. Thu . "Ternary structure reveals mechanism of a membrane diacylglycerol kinase". United States. doi:10.1038/ncomms10140. https://www.osti.gov/servlets/purl/1233178.
Copy to clipboard
@article{osti_1233178,
title = {Ternary structure reveals mechanism of a membrane diacylglycerol kinase},
author = {Li, Dianfan and Stansfeld, Phillip J. and Sansom, Mark S. P. and Keogh, Aaron and Vogeley, Lutz and Howe, Nicole and Lyons, Joseph A. and Aragao, David and Fromme, Petra and Fromme, Raimund and Basu, Shibom and Grotjohann, Ingo and Kupitz, Christopher and Rendek, Kimberley and Weierstall, Uwe and Zatsepin, Nadia A. and Cherezov, Vadim and Liu, Wei and Bandaru, Sateesh and English, Niall J. and Gati, Cornelius and Barty, Anton and Yefanov, Oleksandr and Chapman, Henry N. and Diederichs, Kay and Messerschmidt, Marc and Boutet, Sébastien and Williams, Garth J. and Marvin Seibert, M. and Caffrey, Martin},
abstractNote = {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. As a result, the active site architecture shows clear evidence of having arisen by convergent evolution.},
doi = {10.1038/ncomms10140},
journal = {Nature Communications},
number = 1,
volume = 6,
place = {United States},
year = {2015},
month = {12}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI:  10.1038/ncomms10140
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Citation Metrics:
Cited by: 8 works
Citation information provided by
Web of Science

Figures / Tables:

Table 1 Table 1: Crystallization conditions, data collection and refinement statistics.
All figures and tables (7 total)
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

Biomolecular cryocrystallography: Structural changes during flash-cooling
journal, March 2004

Cheetah : software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data
journal, May 2014

  • Barty, Anton; Kirian, Richard A.; Maia, Filipe R. N. C.
  • Journal of Applied Crystallography, Vol. 47, Issue 3
  • DOI: 10.1107/S1600576714007626

Linking Crystallographic Model and Data Quality
journal, May 2012

CrystFEL : a software suite for snapshot serial crystallography
journal, March 2012

  • White, Thomas A.; Kirian, Richard A.; Martin, Andrew V.
  • Journal of Applied Crystallography, Vol. 45, Issue 2
  • DOI: 10.1107/S0021889812002312

The Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS)
journal, March 2010

Active Sites of Diacylglycerol Kinase from Escherichia coli Are Shared between Subunits †
journal, April 1999

  • Lau, Francis W.; Chen, Xing; Bowie, James U.
  • Biochemistry, Vol. 38, Issue 17
  • DOI: 10.1021/bi982763t

Decision making in xia 2
journal, June 2013

  • Winter, Graeme; Lobley, Carina M. C.; Prince, Stephen M.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7
  • DOI: 10.1107/S0907444913015308

Irreversible Misfolding of Diacylglycerol Kinase Is Independent of Aggregation and Occurs Prior to Trimerization and Membrane Association †
journal, August 2006

  • Mi, Dehui; Kim, Hak Jun; Hadziselimovic, Arina
  • Biochemistry, Vol. 45, Issue 33
  • DOI: 10.1021/bi060887x

Crystal structure of the integral membrane diacylglycerol kinase
journal, May 2013

  • Li, Dianfan; Lyons, Joseph A.; Pye, Valerie E.
  • Nature, Vol. 497, Issue 7450
  • DOI: 10.1038/nature12179

Renaturing Membrane Proteins in the Lipid Cubic Phase, a Nanoporous Membrane Mimetic
journal, July 2014

  • Li, Dianfan; Caffrey, Martin
  • Scientific Reports, Vol. 4, Issue 1
  • DOI: 10.1038/srep05806

Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography
journal, February 2014

  • Weierstall, Uwe; James, Daniel; Wang, Chong
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms4309

Escherichia coli Diacylglycerol Kinase Is an Evolutionarily Optimized Membrane Enzyme and Catalyzes Direct Phosphoryl Transfer
journal, September 1997

  • Badola, Prakash; Sanders, Charles R.
  • Journal of Biological Chemistry, Vol. 272, Issue 39
  • DOI: 10.1074/jbc.272.39.24176

Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
journal, January 2004

  • Oostenbrink, Chris; Villa, Alessandra; Mark, Alan E.
  • Journal of Computational Chemistry, Vol. 25, Issue 13
  • DOI: 10.1002/jcc.20090

Prokaryotic Diacylglycerol Kinase and Undecaprenol Kinase
journal, June 2012

‘Hit and run’ serial femtosecond crystallography of a membrane kinase in the lipid cubic phase
journal, July 2014

  • Caffrey, Martin; Li, Dianfan; Howe, Nicole
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 369, Issue 1647
  • DOI: 10.1098/rstb.2013.0621

CSPAD-140k: A versatile detector for LCLS experiments
journal, August 2013

  • Herrmann, Sven; Boutet, Sébastien; Duda, Brian
  • Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Vol. 718
  • DOI: 10.1016/j.nima.2013.01.057

Quantum and Classical Dynamics Simulations of ATP Hydrolysis in Solution
journal, June 2012

  • Harrison, Christopher B.; Schulten, Klaus
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 7
  • DOI: 10.1021/ct200886j

Lipid cubic phase as a membrane mimetic for integral membrane protein enzymes
journal, May 2011

  • Li, D.; Caffrey, M.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 21
  • DOI: 10.1073/pnas.1101815108

Femtosecond X-ray protein nanocrystallography
journal, February 2011

  • Chapman, Henry N.; Fromme, Petra; Barty, Anton
  • Nature, Vol. 470, Issue 7332, p. 73-77
  • DOI: 10.1038/nature09750

Solution Nuclear Magnetic Resonance Structure of Membrane-Integral Diacylglycerol Kinase
journal, June 2009

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints
journal, April 2003

  • Vreven, Thom; Morokuma, Keiji; Farkas, Ödön
  • Journal of Computational Chemistry, Vol. 24, Issue 6
  • DOI: 10.1002/jcc.10156

Building a Thermostable Membrane Protein
journal, March 2000

Structural changes in a cryo-cooled protein crystal owing to radiation damage
journal, March 2000

  • Burmeister, Wilhelm Pascal
  • Acta Crystallographica Section D Biological Crystallography, Vol. 56, Issue 3
  • DOI: 10.1107/S0907444999016261

Exploring the allowed sequence space of a membrane protein
journal, February 1996

  • Wen, Juan; Chen, Xing; Bowie, James U.
  • Nature Structural Biology, Vol. 3, Issue 2
  • DOI: 10.1038/nsb0296-141

2.2 Å refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MnATP and a peptide inhibitor
journal, May 1993

  • Zheng, J.; Trafny, E. A.; Knighton, D. R.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 49, Issue 3
  • DOI: 10.1107/S0907444993000423

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
journal, February 2013

From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations
journal, March 2011

  • Stansfeld, Phillip J.; Sansom, Mark S. P.
  • Journal of Chemical Theory and Computation, Vol. 7, Issue 4
  • DOI: 10.1021/ct100569y

Changing single side-chains can greatly enhance the resistance of a membrane protein to irreversible inactivation
journal, July 1999

  • Lau, Francis W.; Nauli, Sehat; Zhou, Yufeng
  • Journal of Molecular Biology, Vol. 290, Issue 2
  • DOI: 10.1006/jmbi.1999.2905

Membrane topology of Escherichia coli diacylglycerol kinase.
journal, September 1994

Protein structural ensembles are revealed by redefining X-ray electron density noise
journal, December 2013

  • Lang, P. T.; Holton, J. M.; Fraser, J. S.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 1
  • DOI: 10.1073/pnas.1302823110

Preparation of microcrystals in lipidic cubic phase for serial femtosecond crystallography
journal, August 2014

Escherichia coli Diacylglycerol Kinase Is an α-Helical Polytopic Membrane Protein and Can Spontaneously Insert into Preformed Lipid Vesicles †
journal, January 1996

  • Sanders, Charles R.; Czerski, Lech; Vinogradova, Olga
  • Biochemistry, Vol. 35, Issue 26
  • DOI: 10.1021/bi9604892

FEM: feature-enhanced map
journal, February 2015

  • Afonine, Pavel V.; Moriarty, Nigel W.; Mustyakimov, Marat
  • Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 3
  • DOI: 10.1107/S1399004714028132

Multiscale Simulations Reveal Conserved Patterns of Lipid Interactions with Aquaporins
journal, May 2013

  • Stansfeld, Phillip J.; Jefferys, Elizabeth E.; Sansom, Mark S. P.
  • Structure, Vol. 21, Issue 5
  • DOI: 10.1016/j.str.2013.03.005

XDS
journal, January 2010

  • Kabsch, Wolfgang
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
  • DOI: 10.1107/S0907444909047337

X-ray lasers for structural and dynamic biology
journal, September 2012

The Structural Basis for Control of Eukaryotic Protein Kinases
journal, July 2012

Cell-free expression and in meso crystallisation of an integral membrane kinase for structure determination
journal, July 2014

  • Boland, Coilín; Li, Dianfan; Shah, Syed Tasadaque Ali
  • Cellular and Molecular Life Sciences, Vol. 71, Issue 24
  • DOI: 10.1007/s00018-014-1655-7

Diffraction before destruction
journal, July 2014

  • Chapman, Henry N.; Caleman, Carl; Timneanu, Nicusor
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 369, Issue 1647
  • DOI: 10.1098/rstb.2013.0313

Accessing protein conformational ensembles using room-temperature X-ray crystallography
journal, September 2011

  • Fraser, J. S.; van den Bedem, H.; Samelson, A. J.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 39
  • DOI: 10.1073/pnas.1111325108

Mapping the Oligomeric Interface of Diacylglycerol Kinase by Engineered Thiol Cross-Linking: Homologous Sites in the Transmembrane Domain †
journal, April 2000

  • Nagy, Joanna K.; Lau, Francis W.; Bowie, James U.
  • Biochemistry, Vol. 39, Issue 14
  • DOI: 10.1021/bi991781n

Serial Femtosecond Crystallography of G Protein-Coupled Receptors
journal, December 2013

Phaser crystallographic software
journal, July 2007

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 40, Issue 4
  • DOI: 10.1107/S0021889807021206
    [ × clear filter / sort ]

    Figures / Tables found in this record:

    Table 1(p. 3)table
    Figure 1(p. 4)figure
    Figure 2(p. 5)figure
    Figure 3(p. 6)figure
    Figure 4(p. 7)figure
    Figure 5(p. 8)figure
    Figure 6(p. 9)figure
      [ × clear filter / sort ]
      Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.

      Similar records in OSTI.GOV collections: