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:

Evolution and mechanism from structures of an ADP-ribosylating toxin and NAD complex

Nature Structural Biology volume 6, pages 932–936 (1999)Cite this article

Abstract

A member of the Bacillus-produced vegetative insecticidal proteins (VIPs) possesses high specificity against the major insect pest, corn rootworms, and belongs to a class of binary toxins and regulators of biological pathways distinct from classical A-B toxins. The 1.5 Å resolution crystal structure of the enzymatic ADP-ribosyltransferase component, VIP2, from Bacillus cereus reveals structurally homologous N- and C-terminal α/β domains likely representing the entire class of binary toxins and implying evolutionary relationships between families of ADP-ribosylating toxins. The crystal structure of the kinetically trapped VIP2–NAD complex identifies the NAD binding cleft within the C-terminal enzymatic domain and provides a structural basis for understanding the targeting and catalysis of the medically and environmentally important binary toxins. These structures furthermore provide specific experimental results to help resolve paradoxes regarding the specific mechanism of ADP-ribosylation of actin by implicating ground state destabilization and nicotinamide product sequestration as the major driving forces for catalysis.

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: Overall fold, topology and hinge motion.
Figure 2: A structure-based sequence alignment of the Bacillus cereus VIP2-N-domain (VIP2-Ndom) with the C-domain (VIP2-Cdom) and with both N-terminal (IOTA-Ndom) and C-terminal (IOTA-Cdom) segments of the C. perfringens iota toxin (GeneBank accession number 2127361).
Figure 3: NAD interactions in the active site cleft of the C-domain.

Similar content being viewed by others

Accession codes

Accessions

Protein Data Bank

References

  1. Warren, G.W. In Advances in insect control: the role of transgenic plants. (eds Carozzi, N.B. & Koziel, M.G.) 109–121 (Gunpowder Square, London, United Kingdom; 1997).

    Google Scholar 

  2. Nishimatsu, T. & Jackson, J. J. J. Econ. Entomol. 91, 410–418 (1998).

    Article  CAS  Google Scholar 

  3. Madshus, I.H. & Stenmark, H. Curr. Top. Microbiol. Immunol. 175, 1–26 ( 1992).

    CAS  PubMed  Google Scholar 

  4. Warren, G.W. et al. Novel pesticidal proteins and strains. World Intellectual Property Organization. Patent WO 96/10083 (1996 ).

  5. Carlier, M.-F. Int. Rev. Cytol. 115, 139–170 (1989).

    Article  CAS  Google Scholar 

  6. Aktories, K. et al. Nature 322, 390–392 (1986).

    Article  CAS  Google Scholar 

  7. Stiles, B.G. & Wilkens, T.D. Infect. Immunol. 54 , 683–688 (1986).

    CAS  Google Scholar 

  8. Simpson, L.L., Stiles, B.G., Zepeda, H. & Wilkins, T.D. Infect. Immunol. 57, 255–261 ( 1989).

    CAS  Google Scholar 

  9. Popoff, M.R., Rubin, E.J., Gill, D.M. & Boquet, P. Infect. Immunol. 56, 2299–2306 ( 1988).

    CAS  Google Scholar 

  10. Sixma, T.K. et al. Nature 351, 371–377 (1991).

    Article  CAS  Google Scholar 

  11. Bell, C.E. & Eisenberg, D. Biochemistry 36, 481–488 (1997).

    Article  CAS  Google Scholar 

  12. Li, M., Dyda, F., Benhar, I., Pastan, I. & Davies, D.R. Proc. Natl. Acad. Sci. USA 93, 6902–6906 (1996).

    Article  CAS  Google Scholar 

  13. Aktories, K., Weller, U. & Chhatwal, G.S. FEBS Lett. 212, 109– 113 (1987).

    Article  CAS  Google Scholar 

  14. Barth, H., Hofmann, F., Olenik, C., Just, I. & Aktories, K. Infect. Immunol. 66, 1364– 1369 (1998).

    CAS  Google Scholar 

  15. Bull, H.G., Ferraz, J.P., Cordes, E.H., Ribbi, A. & Apitz–Castro, R. J. Biol. Chem. 253, 5186–5192 (1978).

    CAS  PubMed  Google Scholar 

  16. Oppenheimer, N.J. Mol. Cell. Biochem. 138, 245–251 (1994).

    Article  CAS  Google Scholar 

  17. Rising, K.A. & Schramm, V.L. J. Am. Chem. Soc. 119, 27–37 (1997).

    Article  CAS  Google Scholar 

  18. Berti, P.J., Blanke, S.R. & Schramm, V.L. J. Am. Chem. Soc. 119, 12079 –12088 (1997).

    Article  CAS  Google Scholar 

  19. Scheuring, J. & Schramm, V.L. Biochemistry 36, 8215–8223 (1997).

    Article  CAS  Google Scholar 

  20. Scheuring, J. & Schramm, V.L. Biochemistry 36, 4526–4534 (1997).

    Article  CAS  Google Scholar 

  21. Scheuring, J., Berti, P.J. & Schramm V.L. Biochemistry 37, 2748– 2758 (1998).

    Article  CAS  Google Scholar 

  22. Banait, N.S. & Jencks, W.P. J. Am. Chem. Soc. 113 , 7958–7963 (1991).

    Article  CAS  Google Scholar 

  23. Cherian, X.M., Van Arman, S.A. & Czarnik, A.W. J. Am. Chem. Soc. 112, 4490 –4498 (1990).

    Article  CAS  Google Scholar 

  24. Bell, C.E. & Eisenberg, D. Biochemistry 35, 1137–1149 (1996).

    Article  CAS  Google Scholar 

  25. Buckley, N., Handlon, A.L., Maltby, D., Burlingame, A.L. & Oppenheimer, N.J. J. Org. Chem. 59, 3609–3615 (1994).

    Article  CAS  Google Scholar 

  26. Johnson, R.W., Marschner, T.M. & Oppenheimer, N.J. J. Am. Chem. Soc. 110, 2257 –2263 (1988).

    Article  CAS  Google Scholar 

  27. Perelle, S., Domenighini, M. & Popoff, M.R. FEBS Lett. 395, 191– 194 (1996).

    Article  CAS  Google Scholar 

  28. Barth, H., Preiss, J.C., Hofmann, F. & Aktories, K. J. Biol. Chem. 273, 29506–29511 (1998).

    Article  CAS  Google Scholar 

  29. Bell, C.E., Yeates, T.O. & Eisenberg, D. Protein Sci. 6, 2084– 2096 (1997).

    Article  CAS  Google Scholar 

  30. Berti, P.J. & Schramm, V.L. J. Am. Chem. Soc. 119, 12069–12078 (1997).

    Article  CAS  Google Scholar 

  31. Otwinowski, Z. & Minor, W. Methods Enzymol. 276, 307–326 ( 1997).

    Article  CAS  Google Scholar 

  32. Collaborative Computational Project, Number 4. Acta Crystallogr. D 50, 760– 763 (1994).

  33. Jones, T.A., Zhou, J.-Y., Cowan, S.W. & Kjeldgaard, M. Acta Crystallogr. A 47, 110–119 ( 1991).

    Article  Google Scholar 

  34. Brünger, A.T. et al. Acta Crystallogr. D 54, 905–921 (1998).

    Article  Google Scholar 

  35. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. J. Appl. Crystallogr. 26, 283–291 (1993).

    Article  CAS  Google Scholar 

  36. Navaza, J. Acta Crystallogr. A 50, 157–163 (1994).

    Article  Google Scholar 

  37. Kraulis, P.J. J. Appl. Crystallogr. 24, 946–950 (1991).

    Article  Google Scholar 

Download references

Acknowledgements

We thank D.S. Daniels, J.L. Pellequer, T.P. Lo and C.M. Bruns for insightful discussions, and facilities at ALS and CHESS. Work on VIP2 was supported in part by the Skaggs Institute for Research and by Novartis Agribusiness Biotechnology Research Inc. C.D.P. was supported by a Howard Hughes Predoctoral Fellowship and J.A.T. by the NSF.

Author information

Authors and Affiliations

  1. Department of Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, , 92037, California, USA

    Seungil Han, Christopher D. Putnam & John A. Tainer

  2. Novartis Agribusiness Biotechnology Research, Inc.,

    Joyce A. Craig & Nadine B. Carozzi

  3. P.O. Box 12257, 3054 Cornwallis Road, Research Triangle Park, 27709-2257, North Carolina, USA

    Joyce A. Craig & Nadine B. Carozzi

Authors
  1. Seungil Han
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Joyce A. Craig
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Christopher D. Putnam
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Nadine B. Carozzi
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. John A. Tainer
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to John A. Tainer.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Han, S., Craig, J., Putnam, C. et al. Evolution and mechanism from structures of an ADP-ribosylating toxin and NAD complex. Nat Struct Mol Biol 6, 932–936 (1999). https://doi.org/10.1038/13300

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/13300

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