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Title: Ternary structure reveals mechanism of a membrane diacylglycerol kinase

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
  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:
Grant/Contract Number:
AC03-76SF00515
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
Research Org:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; biological sciences; biochemistry; biophysics
OSTI Identifier:
1233178

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., Web. doi:10.1038/ncomms10140.
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.
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. 2015. "Ternary structure reveals mechanism of a membrane diacylglycerol kinase". United States. doi:10.1038/ncomms10140. https://www.osti.gov/servlets/purl/1233178.
@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}
}

Works referenced in this record:

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

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

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