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.

  • Article
  • Published:

X-ray structure of Streptococcus pneumoniae PBP2x, a primary penicillin target enzyme

Nature Structural Biology volume 3, pages 284–289 (1996)Cite this article

Abstract

All β-lactam antibiotics exert their biological effects by interacting with a unique class of proteins, the penicillin-binding proteins (PBPs). These membrane proteins are involved in the biosynthesis of the murein or peptidoglycan, a mesh-like structure which completely surrounds the bacterial cell. Sequence similarities indicate that one domain of these proteins belongs to a large family of β-lactam-recognizing proteins, which includes the active-site serine β-lactamases. We here report the first three-dimensional crystal structure of a high molecular weight penicillin-binding protein, PBP2x of Streptococcus pneumoniae, at 3.5 Å resolution. The molecule has three domains, the central domain being a transpeptidase, which is a suitable target for antibiotic development.

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

Similar content being viewed by others

References

  1. Hakenbeck, R., Briese, T. & Ellerbrok, H. Antibodies against the benzylpenicilloyl moiety as a probe for penicillin-binding proteins. Eur. J. Biochem. 157, 101–106 (1986).

    Article  CAS  Google Scholar 

  2. Hakenbeck, R. & Kohiyama, M. Purification of penicillin-binding protein 3 from Streptococcus pneumoniae. Eur. J. Biochem. 127, 231–236 (1982).

    Article  CAS  Google Scholar 

  3. Waxman, D.J. & Strominger, J.L. Penicillin-binding proteins and the mechanism of action of β-lactam antibiotics. Annu. Rev. Biochem. 52, 825–865 (1983).

    Article  CAS  Google Scholar 

  4. Matsuhashi, M. in New Comprehensive Biochemistry. Bacterial Cell Wall Vol. 27, (eds J.-M. Ghuysen & R. Hakenbeck) 55–71 (Elsevier Science Publishers, Amsterdam 1994).

    Book  Google Scholar 

  5. Spratt, B.G. Resistance to antibiotics mediated by target alterations. Science 264, 388–393 (1994).

    Article  CAS  Google Scholar 

  6. Laible, G., Spratt, B.G. & Hakenbeck, R. Interspecies recombinational events during the evolution of altered PBP 2x genes in penicillin-resistant clinical isolates of Streptococcus pneumoniae. Mol. Microbiol. 5, 1993–2002 (1991).

    Article  CAS  Google Scholar 

  7. Laible, G. & Hakenbeck, R. Penicillin-binding proteins in β-lactam-resistant laboratory mutants of Streptococcus pneumoniae. Mol. Microbiol. 1, 355–363 (1987).

    Article  CAS  Google Scholar 

  8. Charlier, P. et al. Crystallization of a genetically engineered water-soluble primary penicillin target enzyme. The high molecular mass PBP2x of Streptococcus pneumoniae. J. Mol. Biol. 232, 1007–1009 (1993).

    Article  CAS  Google Scholar 

  9. Lobkovsky, E. et al. Evolution of an enzyme activity: Crystallographic structure at 2- Å resolution of cephalosporinase from the ampCgene of Enterobacter cloacae P99 and comparison with a class A penicillinase. Proc. Natl. Acad. Sci. USA 90, 11257–11261 (1993).

    Article  CAS  Google Scholar 

  10. Kelly, J.A. & Kuzin, A.P. The refined Crystallographic structure of a DD-peptidase penicillin-target enzyme at 1.6 Å resolution. J. Mol. Biol. 254, 223–236 (1995).

    Article  CAS  Google Scholar 

  11. Jamin, M., Damblon, C., Miller, S., Hakenbeck, R. & Frère, J.-M. Penicillin-binding protein 2x of Streptococcus pneumoniae: enzymic activities and interactions with β-lactams. Biochem. J. 292, 735–741 (1993).

    Article  CAS  Google Scholar 

  12. Adachi, H., Ohta, T. & Matsuzawa, H. Site-directed mutants, at position 166, of RTEM-1 β-lactamase that form a stable acyl-enzyme intermediate with penicillin. J. Biol. Chem. 266, 3186–3191 (1991).

    CAS  Google Scholar 

  13. Bustos, J.F., Chait, B.T. & Tomasz, A. Structure of the peptide network of pneumococcal peptidoglycan. J. Biol. Chem. 262, 15400–15405 (1987).

    Google Scholar 

  14. Kuroki, R., Weaver, L.H. & Matthews, B.W. A covalent enzyme-substrate intermediate with saccharide distortion in a mutant T4 lysozyme. Science 262, 2030–2033 (1993).

    Article  CAS  Google Scholar 

  15. Messerschmidt, A. & Pflugrath, J.W. Crystal orientation and X-ray pattern prediction routines for area-detector diffractometer systems in Macromolecular Crystallography. J. Appl. Crystallogr. 20, 306–315 (1987).

    Article  CAS  Google Scholar 

  16. Kabsch, W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 26, 795–800 (1993).

    Article  CAS  Google Scholar 

  17. CCP4, Collaborative Computing Project No.4, Acta Crystallogr. D50, 760–763 (1993).

  18. Otwinowski, W. Isomorphous Replacement and Anomalous Scattering, Proceedings of the CCP4 Study Weekend. (eds Wolf, W., Evans, P.R. & Leslie, A.G.W.) 80–86 (SERC Daresbury Laboratory, Warrington, 1991).

    Google Scholar 

  19. Zhang, K.Y.J. & Main, P. The use of Sayre's equation with solvent flattening and histogram matching for phase extension and refinement of protein structures. Acta Crystallogr. A46, 377–381 (1990).

    Article  CAS  Google Scholar 

  20. 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. A47, 110–119 (1991).

    Article  CAS  Google Scholar 

  21. Read, R.J., Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr. A42, 140–149 (1986).

    Article  CAS  Google Scholar 

  22. Brünger, A.T. A system for X-ray Crystallography and NMR. X-PLOR Version 3.0. Yale Univ. Press, New Haven (1992).

    Google Scholar 

  23. Kraulis, P.J. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946–950 (1991).

    Article  Google Scholar 

  24. Nicholls, A., Sharp, K.A. & Honig, B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281–286 (1991).

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institut de Biologie Structure Jean-Pierre Ebel (CEA-CNRS), Laboratoire de Cristallographie Macromoléculaire, 41, avenue des Martyrs, F-38027, Grenoble, Cedex 1, France

    S. Pares, N. Mouz & O. Dideberg

  2. Institut de Biologie Structure Jean-Pierre Ebel (CEA-CNRS), Laboratoire de Spectrométrie de Masse des Protéines, 41, avenue des Martyrs, F-38027, Grenoble, Cedex 1, France

    Y. Pétillot

  3. Max-Planck Institut fur Molekülare Genetik, Ihnestrasse 73, D-14195, Berlin, Germany

    R. Hakenbeck

Authors
  1. S. Pares
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. N. Mouz
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Y. Pétillot
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. R. Hakenbeck
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. O. Dideberg
    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

Pares, S., Mouz, N., Pétillot, Y. et al. X-ray structure of Streptococcus pneumoniae PBP2x, a primary penicillin target enzyme. Nat Struct Mol Biol 3, 284–289 (1996). https://doi.org/10.1038/nsb0396-284

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsb0396-284

This article is cited by

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