Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Structural evidence for dimerization-regulated activation of an integral membrane phospholipase

Nature volume 401, pages 717–721 (1999)Cite this article

Abstract

Dimerization is a biological regulatory mechanism employed by both soluble and membrane proteins1. However, there are few structural data on the factors that govern dimerization of membrane proteins. Outer membrane phospholipase A (OMPLA) is an integral membrane enzyme which participates in secretion of colicins in Escherichia coli. In Campilobacter2 and Helicobacter pylori strains3, OMPLA is implied in virulence. Its activity is regulated by reversible dimerization4,5. Here we report X-ray structures of monomeric and dimeric OMPLA from E. coli. Dimer interactions occur almost exclusively in the apolar membrane-embedded parts, with two hydrogen bonds within the hydrophobic membrane area being key interactions. Dimerization results in functional oxyanion holes and substrate-binding pockets, which are absent in monomeric OMPLA. These results provide a detailed view of activation by dimerization of a membrane protein.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Structure of outer membrane phosopholipase A.
Figure 2: Dimer covalently inhibited with hexadecanesulphonylfluoride.
Figure 3: Comparison of the catalytic machinery of OMPLA and Streptomyces scabies esterase.

Similar content being viewed by others

References

  1. Klemm, J. D., Schreiber, S. L. & Crabtree, G. R. Dimerization as a regulatory mechanism in signal transduction. Annu. Rev. Immunol. 16, 569–592 (1998).

    Article  CAS  Google Scholar 

  2. Grant, K. A., Ubarretxena-Belandia, I., Dekker, N., Richardson, P. T. & Park, S. F. Molecular characterization of pldA, the structural gene for a phospholipase A from Campylobacter coli, and its contribution to cell-associated hemolysis. Infect. Immun. 65, 569–592 (1997).

    Google Scholar 

  3. Bukholm, G. et al. Colony variation of Helicobacter pylori: pathogenic potential is correlated to cell wall lipid composition. Scan. J. Gastroenterol. 32, 569–592 (1997).

    Article  Google Scholar 

  4. Dekker, N., Tommassen, J., Lustig, A., Rosenbusch, J. P. & Verheij, H. M. Dimerization regulates the enzymatic activity of Escherichia coli outer membrane phospholipase A. J. Biol. Chem. 272, 569–592 (1997).

    Google Scholar 

  5. Dekker, N., Tommassen, J. & Verheij, H. M. Bacteriocin release protein triggers dimerization of outer membrane phospholipase A in vivo. J. Bacteriol. 181, 569–592 (1999).

    Google Scholar 

  6. Merck, K. B., de Cock, H., Verheij, H. M. & Tommassen, J. Topology of the outer membrane phospholipase A of Salmonella typhimurium. J. Bacteriol. 179, 569–592 (1997).

    Article  Google Scholar 

  7. Weiss, M. S. et al. Molecular architecture and electrostatic properties of a bacterial porin. Science 254, 569–592 (1991).

    Google Scholar 

  8. Schirmer, T., Keller, T. A., Wang, Y.-F. & Rosenbusch, J. P. Structural basis for sugar translocation through maltoporin channels at 3.1 Å resolution. Science 267, 569–592 (1995).

    Article  Google Scholar 

  9. Pautsch, A. & Schulz, G. E. Structure of the outer membrane protein A transmembrane domain. Nature Struct. Biol. 5, 569–592 (1998).

    Article  Google Scholar 

  10. Locher, K. P. et al. Transmembrane signaling across the ligand-gated FhuA receptor: Crystal structures of free and ferrichrome-bound states reveal allosteric changes. Cell 95, 569–592 (1998).

    Article  Google Scholar 

  11. Buchanan, S. K. et al. Crystal structure of the outer membrane active transporter FepA from Escherichia coli. Nature Struct. Biol. 6, 569–592 (1999).

    Article  Google Scholar 

  12. Horrevoets, A. J., Verheij, H. M. & de Haas, G. H. Inactivation of Escherichia coli outer-membrane phospholipase A by the affinity label hexadecanesulfonyl fluoride. Evidence for an active-site serine. Eur. J. Biochem. 198, 569–592 (1991).

    Google Scholar 

  13. Brok, R. G. P. M., Dekker, N., Gerrits, N., Verheij, H. M. & Tommassen, J. A conserved histidine residue of Escherichia coli outer-membrane phospholipase A is important for activity. Eur. J. Biochem. 234, 569–592 (1995).

    Article  Google Scholar 

  14. Brok, R. G. P. M., Ubarretxena-Belandia, I., Dekker, N., Tommassen, J. & Verheij, H. M. Escherichia coli outer membrane phospholipase A: Role of two serines in enzymatic activity. Biochemistry 35, 569–592 (1996).

    Article  Google Scholar 

  15. Dodson, G. & Wlodawer, A. Catalytic triads and their relatives. Trends Biochem. Sci. 23, 569–592 (1998).

    Article  Google Scholar 

  16. Ubarretxena-Belandia, I., Boots, J. W. P., Verheij, H. M. & Dekker, N. Role of the cofactor calcium in the activation of outer membrane phosphilipase A. Biochemistry 37, 569–592 (1998).

    Article  Google Scholar 

  17. Horrevoets, A. J. G., Hackeng, T. M., Verheij, H. M., Dijkman, R. & De Haas, G. H. Kinetic characterization of Escherichia coli outer membrane phospholipase A using mixed detergent-lipid micelles. Biochemistry 28, 569–592 (1989).

    Article  Google Scholar 

  18. Wei, Y. et al. A novel variant of the catalytic triad in the Streptomyces scabies esterase. Nature Struct. Biol. 2, 569–592 (1995).

    Article  Google Scholar 

  19. Ubarretxena-Belandia, I. et al. Outer membrane phospholipase A is dimeric in phospholipid bilayers: A cross-linking and fluorescence resonance energy transfer study. Biochemistry 38, 569–592 (1999).

    Article  Google Scholar 

  20. Blaauw, M., Dekker, N., Verheij, H. M., Kalk, K. H. & Dijkstra, B. W. Crystallization and preliminary X-ray analysis of outer membrane phospholipase A from Escherichia coli. FEBS Lett. 373, 569–592 (1995).

    Article  Google Scholar 

  21. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 569–592 (1997).

    Google Scholar 

  22. Kabsch, W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 26, 569–592 (1993).

    Article  Google Scholar 

  23. Collaborative Computational Project Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 569–592 (1994).

  24. Brünger, A. T. Free R value: a novel statistical quantity for assessing the accuracy of structures. Nature 355, 569–592 (1992).

    Article  Google Scholar 

  25. Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 569–592 (1991).

    Google Scholar 

  26. Kraulis, P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 569–592 (1991).

    Article  Google Scholar 

  27. Merritt, E. A. & Bacon, J. A. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 569–592 (1997).

    Google Scholar 

  28. Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 569–592 (1991).

    Article  Google Scholar 

  29. Esnouf, R. M. An extensively modified version of Molscript that includes greatly enhanced coloring capabilities. J. Mol. Graphics 15, 569–592 (1997).

    Google Scholar 

Download references

Acknowledgements

We thank the staff at the EMBL-outstation at DESY in Hamburg, and at the D2AM and the ID2B beam lines at ESRF Grenoble, for assistance with data collection. We thank R. L. Kingma for her enthusiastic collaboration and discussions. We thank the ESRF for supporting the work at the ESRF. These investigations were supported by the Netherlands Foundation for Chemical Research (CW) with financial aid from the Netherlands Organization for Scientific Research (NWO). We thank the EU for supporting the work at EMBL Hamburg through the HCMP Access to Large Installations Project.

Author information

Author notes

  1. I. Ubarretxena-Belandia

    Present address: Molecular Biophysics and Biochemistry, Yale University, 429 Bass Center, 266 Whitney Avenue, New Haven, Connecticut, 06520, USA

  2. M. Blaauw

    Present address: Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands

  3. H.M.V. died in an accident on 1 August 1998.

Authors and Affiliations

  1. Laboratory of Biophysical Chemistry, BIOSON Research Institute, University of Groningen, Nijenborgh 4, Groningen, 9747 AG, The Netherlands

    H. J. Snijder, M. Blaauw, K. H. Kalk & B. W. Dijkstra

  2. Department of Enzymology and Protein Engineering, Centre for Biomembranes and Lipid Enzymology, Institute of Biomembranes, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands

    I. Ubarretxena-Belandia, H. M. Verheij, M. R. Egmond & N. Dekker

Authors
  1. H. J. Snijder
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. I. Ubarretxena-Belandia
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. M. Blaauw
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. K. H. Kalk
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. H. M. Verheij
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. M. R. Egmond
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. N. Dekker
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. B. W. Dijkstra
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Snijder, H., Ubarretxena-Belandia, I., Blaauw, M. et al. Structural evidence for dimerization-regulated activation of an integral membrane phospholipase. Nature 401, 717–721 (1999). https://doi.org/10.1038/401717a0

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/401717a0

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing