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


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.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.


  1. 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).

  2. 2

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

  3. 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).

  4. 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).

  5. 5

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

  6. 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).

  7. 7

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

  8. 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).

  9. 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).

  10. 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).

  11. 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).

  12. 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).

  13. 13

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

  14. 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).

  15. 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).

  16. 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).

  17. 17

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

  18. 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).

  19. 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).

  20. 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).

  21. 21

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

  22. 22

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

  23. 23

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

  24. 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).

Download references

Author information

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) doi:10.1038/nsb0396-284

Download citation

Further reading