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.

Molecular structure of the acyl-enzyme intermediate in β-lactam hydrolysis at 1.7 Å resolution

Nature volume 359, pages 700–705 (1992)Cite this article

Abstract

The X-ray crystal structure of the molecular complex of penicillin G with a deacylation-defective mutant of the RTEM-1 β-lactamase from Escherichia coli shows how these antibiotics are recognized and destroyed. Penicillin G is covalently bound to Ser 70 Oγ as an acyl-enzyme intermediate. The deduced catalytic mechanism uses Ser 70 Oγ as the attacking nucleophile during acylation. Lys 73 Nζ acts as a general base in abstracting a proton from Ser 70 and transferring it to the thiazolidine ring nitrogen atom via Ser 130 Oγ. Deacylation is accomplished by nucleophilic attack on the penicilloyl carbonyl carbon by a water molecule assisted by the general base, Glu 166.

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

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Get just this article for as long as you need it

$39.95

Learn more

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

References

  1. Herzberg, O. & Moult, J. Curr. Opin. struct. Biol. 1, 946–953 (1991).

    Article  CAS  Google Scholar 

  2. Frère, J.-M. & Joris, B. Crit. Rev. Microbiol. 11, 299–396 (1985).

    Article  Google Scholar 

  3. Ghuysen, J.-M. A. Rev. Microbiol. 45, 37–67 (1991).

    Article  CAS  Google Scholar 

  4. Herzberg, O. & Moult, J. Science 236, 694–701 (1987).

    Article  ADS  CAS  Google Scholar 

  5. Herzberg, O. J. molec. Biol. 217, 701–719 (1991).

    Article  CAS  Google Scholar 

  6. Moews, P. C., Knox, J. R., Dideberg, O., Charlier, P. & Frère, J.-M., Proteins Struct. Funct Genet. 7, 156–171 (1990).

    Article  CAS  Google Scholar 

  7. Knox, J. R. & Moews, P. C. J. molec. Biol. 220, 435–455 (1991).

    Article  CAS  Google Scholar 

  8. Jelsch, C., Lenfant, F., Masson, J. M. & Samama, J. P. FEBS Lett 299, 135–142 (1992).

    Article  CAS  Google Scholar 

  9. Knowles, J. R. Acct. Chem. Res. 18, 97–104 (1985).

    Article  CAS  Google Scholar 

  10. Christensen, H., Martin, M. T. & Waley, S. G. Biochem. J. 266, 853–861 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Gibson, R. M., Christensen, H. & Waley, S. G. Biochem. J. 272, 613–619 (1990).

    Article  CAS  Google Scholar 

  12. Adachi, H., Ohta, T. & Matsuzawa, H. J. biol. Chem. 266, 3186–3191 (1991).

    CAS  PubMed  Google Scholar 

  13. Escobar, W. A., Tan, A. K. & Fink, A. L. Biochemistry 30, 10783–10787 (1991).

    Article  CAS  Google Scholar 

  14. Ellerby, L. M., Escobar, W. A., Fink, A. L., Mitchinson, C. & Wells, J. A. Biochemistry 29, 5797–5800 (1990).

    Article  CAS  Google Scholar 

  15. Dalbadie-McFarland, G., Neitzel, J. J. & Richards, J. H. Biochemistry 25, 332–338 (1986).

    Article  CAS  Google Scholar 

  16. Martin, M. T. & Waley, S. G. Biochem. J. 254, 923–925 (1988).

    Article  CAS  Google Scholar 

  17. Virden, R., Tan, A. K. & Fink, A. L. Biochemistry 29, 145–153 (1990).

    Article  CAS  Google Scholar 

  18. Healey, W. J., Labgold, M. R. & Richards, J. H. Proteins Struct. Funct. Genet. 6, 275–283 (1989).

    Article  CAS  Google Scholar 

  19. Fisher, J., Belsaco, J. G., Khosla, S. & Knowles, J. R. Biochemistry 19, 2895–2901 (1980).

    Article  CAS  Google Scholar 

  20. Jacob, F. et al. Protein Engng 4, 79–86 (1990).

    Article  CAS  Google Scholar 

  21. Jacob, F., Joris, B., Lepage, S., Dusart, J. & Frére, J.-M. Biochem. J. 271, 399–406 (1990).

    Article  CAS  Google Scholar 

  22. Cartwright, S. J., Tan, A. K. & Fink, A. L. Biochem. J. 263, 905–912 (1989).

    Article  CAS  Google Scholar 

  23. Abraham, E. P. & Chain, E. Nature 146, 837 (1940).

    Article  ADS  CAS  Google Scholar 

  24. Matthew, M. & Hedges, R. W. J. Bact. 125, 713–718 (1976).

    CAS  PubMed  Google Scholar 

  25. Green, D. W., Ingram, V. M. & Perutz, M. F. Proc. R. Soc. A225, 287–307 (1954).

    ADS  CAS  Google Scholar 

  26. Rossman, M. G. The Molecular Replacement Method. Int. Sci. Rev. Vol. 13 (Gordon & Breach, New York, 1972).

    Google Scholar 

  27. Bernstein, F. C. et al. J. molec. Biol. 112, 535–542 (1977).

    Article  CAS  Google Scholar 

  28. Ambler, R. P. et al. Biochem. J. 276, 269–272 (1991).

    Article  CAS  Google Scholar 

  29. Henderson, R. J. molec. Biol. 54, 341–354 (1970).

    Article  CAS  Google Scholar 

  30. Robertus, J. D., Kraut, J., Alden, R. A. & Birktoft, J. J. Biochemistry 11, 4293–4303 (1972).

    Article  CAS  Google Scholar 

  31. Crowfoot, D., Bunn, C. W., Rogers-Low, B. W. & Turner-Jones, A. in The Chemistry of Penicillin (eds Clarke, H. T., Johnson, J. R. & Robinson, R.) 310–367 (Princeton Univ, Press, 1949).

    Google Scholar 

  32. Dexter, D. D. & van der Veen, J. M. J. chem. Soc. 185, 110–115 (1978).

    Google Scholar 

  33. Oefner, G. et al. Nature 343, 284–288 (1990).

    Article  ADS  CAS  Google Scholar 

  34. Zafaralla, G., Manavathu, E. K., Lerner, S. A. & Mobashery, S. Biochemistry 31, 3847–3852 (1992).

    Article  CAS  Google Scholar 

  35. Kraut, J. A. Rev. Biochem. 46, 331–358 (1977).

    Article  CAS  Google Scholar 

  36. Knap, A. K. & Pratt, R. F. Biochem. J. 273, 85–91 (1991).

    Article  CAS  Google Scholar 

  37. James, M. N. G., Hall, D. & Hodgkin, D. C. Nature 220, 168–170 (1968).

    Article  ADS  CAS  Google Scholar 

  38. Sweet, R. M. & Dahl, L. F. J. Am. chem. Soc. 92, 5489–5507 (1970).

    Article  CAS  Google Scholar 

  39. Viera, J. & Messing, J. Meth. Enzym 153, 3–11 (1987).

    Article  Google Scholar 

  40. Hamlin, R. Meth. Enzym. 114, 416–452 (1985).

    Article  CAS  Google Scholar 

  41. Howard, A. J., Nielson, C. & Xuong, N. H. Meth. Enzym. 114, 452–472 (1985).

    Article  CAS  Google Scholar 

  42. Otwinowski, Z. Am. Crystallogr. Ass. Ann. Meeting, New Orleans, Abstr. CO4 (1990).

  43. Navaza, J. Acta crystallogr. A46, 619–620 (1990).

    Article  Google Scholar 

  44. Read, R. J. & Schierbeek, A. J. J. appl. Crystallogr. 21, 490–495 (1988).

    Article  CAS  Google Scholar 

  45. Read, R. J. Acta crystallogr. A42, 140–149 (1986).

    Article  Google Scholar 

  46. Jones, T. A. J. Appl. Crystallogr. 11, 268–272 (1978).

    Article  CAS  Google Scholar 

  47. Leslie, A. G. W., Brick, P. & Wonacott, A. J. CCP4 Newsletter 18, 33–39 (1986).

    Google Scholar 

  48. Brünger, A. J. J. molec. Biol. 203, 803–816 (1988).

    Article  Google Scholar 

  49. Hendrickson, W. A. & Konnert, J. H. in Computing in Crystallography (eds Diamond, R., Ramaseshan, S. & Venkatesan, K.) 1301–1323 (Indian Institute of Sciences, Bangalore 1980).

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. MRC Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada

    Natalie C. J. Strynadka, Kathy Johns, Anita Sielecki & Michael N. G. James

  2. Department of Pure and Applied Sciences, College of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153, Japan

    Hiroyuki Adachi & Kazuo Sutoh

  3. Department of Microbiology, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada

    Susan E. Jensen

  4. European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, Hamburg, Germany

    Christian Betzel

Authors
  1. Natalie C. J. Strynadka
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hiroyuki Adachi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Susan E. Jensen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Kathy Johns
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Anita Sielecki
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Christian Betzel
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Kazuo Sutoh
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Michael N. G. James
    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

Strynadka, N., Adachi, H., Jensen, S. et al. Molecular structure of the acyl-enzyme intermediate in β-lactam hydrolysis at 1.7 Å resolution. Nature 359, 700–705 (1992). https://doi.org/10.1038/359700a0

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/359700a0

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