Modelling and Engineering of Enzyme/Substrate Interactions in Subtilisin-Like Enzymes of Unknown 3-Dimensional Structure

  • Roland J. Siezen
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 379)

Abstract

Homology modelling was used to predict enzyme-substrate interactions in three entirely different subtilisin-like enzymes of unknown three-dimensional structure, i.e. (a) cell-envelope proteinase of Lactococcus lactis, (b) putative leader peptidase for pre-nisin from L. lactis, and (c) human furin. Models were based on known three-dimensional structures of subtilisins and thermitase in complex with inhibitors. Detailed analysis of interactions of the P1-P4 residues of model substrates with the S1-S4 binding sites in each enzyme suggest that electrostatic interactions at all four binding sites can contribute to binding and hence to specificity. In particular, one or more negative charges in the SI or S4 pockets can lead to a high selectivity for Arg residues in the substrate.

Many of the predicted interactions have been confirmed by engineering of either enzyme, substrate of both.

Keywords

Hydrolysis Serine Polypeptide Resi Lactis 

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References

  1. 1.
    R.J. Siezen, W.M. de Vos, and B.W. Dijkstra, Protein Eng. 4: 719 (1991).PubMedCrossRefGoogle Scholar
  2. S. Hirono, H. Akagawa, Y. Mitsui, and Y. Iitaka, J. Mol Biol178: 389 (1984).Google Scholar
  3. C.A. MePhalen, I. Svendsen, I. Jonassen, andM.N.G. James, Proc. Natl Acad. Sci. USA82: 7242 (1985).Google Scholar
  4. 4.
    C. Betzel, M. Belleman, G.P. Pal, J. Bajorath, W. Saenger, and K.S. Wilson, Proteins: Struct. Funct. Genet.4: 157 (1988).Google Scholar
  5. 5.
    C.A. MePhalen and M.N.G. James, Biochemistry27: 6582 (1988).CrossRefGoogle Scholar
  6. 6.
    P. Gros, C. Betzel, Z. Dauter, K.S. Wilson, and W.G.J. Hoi, J. Mol Biol210: 347 (1989).PubMedCrossRefGoogle Scholar
  7. 7.
    D.W. Heinz, J.P. Priestle, J. Rahuel, K.S. Wilson, and M.G. Grhtter, J. Mol Biol217: 353 (1991).PubMedCrossRefGoogle Scholar
  8. 8.
    Y. Takeuchi, S. Noguehi, Y. Satow, S. Kojima, I. Kumagai, K. Miura, K.T. Nakamura, and Y. Mitsui, Protein Eng. 4: 501 (1991).PubMedCrossRefGoogle Scholar
  9. 9.
    Y Takeuchi, Y. Satow, K.T. Nakamura, and Y. Mitsui, J. Mol Biol221: 309 (1991).PubMedGoogle Scholar
  10. J.A. Wells, B.C. Cunningham, T.P. Graycar, andD.A. Estell, Proc. Natl Acad. Sci. USA84: 5167 (1987).Google Scholar
  11. 11.
    D.A. Estell, T.P. Graycar, J.V. Miller, D.B. Powers, J.P. Rurnier, P.G. Ng, and J.A. Wells, Science233: 659 (1987)CrossRefGoogle Scholar
  12. 12.
    A.J. Russell and A.R. Fersht, Nature(London) 328: 496 (1987).Google Scholar
  13. 13.
    A.J. Russell, P.G. Thomas, and A.R. Fersht, J. Mol Biol193: 803 (1987).PubMedCrossRefGoogle Scholar
  14. 14.
    J.A. Wells, D.B. Powers, R.R. Bott, T.P. Graycar, and D.A. Estell, Proc. Natl Acad. Sci. USA84: 1219 (1987)PubMedCrossRefGoogle Scholar
  15. 15.
    P. Vos, G. Simons, R.J. Siezen, and W.M. de Vos, J. Biol Chem.264: 13579 (1989).PubMedGoogle Scholar
  16. 16.
    J.R. Van der Meer, J. Polman, M.M. Beerthuyzen, R.J. Siezen, O.P. Kuipers, and W.M. de Vos, J. Bacteriol.175: 2578 (1993).PubMedGoogle Scholar
  17. 17.
    A.M.W. Van den Ouweland, J.L.P. Van Duijnhoven, G.D. Keizer, L.C.J. Dorssers, and W.J.M. Van de Ven, Nucleic Acids Res. 18: 664 (1990).PubMedCrossRefGoogle Scholar
  18. 18.
    R.J. Siezen, P.G. Bruinenberg, P.Vos, I. van Alen-Boerrigter, M. Nijhuis, A.C. Alting, F.A. Exterkate, and W.M. de Vos, Protein Eng. 6: 927 (1993).PubMedCrossRefGoogle Scholar
  19. R.J. Siezen, J.W.M. Creemers, and W.J.M. van de Ven, Eur. J. Biochem. 222:255(1994).PubMedCrossRefGoogle Scholar
  20. 20.
    G.W. Buchman, S. Banerjee, and J.N. Hansen, J. Biol Chem. 263:16260 (1988).CrossRefGoogle Scholar
  21. 21.
    I. Schechter and A. Berger, Biochem. Biophys. Res. Commun.27: 157 (1967).Google Scholar
  22. 22.
    H. Gron, M. Meldal, and K. Breddam, Biochemistry31: 6011 (1992).PubMedCrossRefGoogle Scholar
  23. 23.
    S. Visser, A.J.P.M. Robben, and C.J. Slangen, Appl. Microbiol Biotechnol35: 477 (1991).PubMedCrossRefGoogle Scholar
  24. 24.
    J.R. Reid, C.H. Moore, G.G. Midwinter, and G.G. Pritchard, Appl Microbiol Biotechnol35: 222 (1991).PubMedCrossRefGoogle Scholar
  25. 25.
    V. Monnet, J.P. Ley, and S. Gonzalez, Int. J. Biochem, 24: 707 (1992).PubMedCrossRefGoogle Scholar
  26. 26.
    F.A. Exterkate, Appl Microbiol Biotechnol33: 401 (1990).PubMedCrossRefGoogle Scholar
  27. 27.
    F.A. Exterkate, A.C. Alting, and C.J. Slangen, Biochem. J.273: 135 (1991).PubMedGoogle Scholar
  28. 28.
    F.A. Exterkate, A.C. Alting, and P.G. Bruinenberg, J. Environ. Microbiol59: 3640 (1993).Google Scholar
  29. 29.
    P. Vos, I.J. Boerrigter, G. Buist, A.J. Haandrikman, M. Nijhuis, M.B. de Reuver, R.J. Siezen, G. Venema, W.M. de Vos, and J. Kok, Protein Eng. 4: 479 (1991).PubMedCrossRefGoogle Scholar
  30. 30.
    N. Schnell, G. Engelke, J. Augustin, R. Rosenstein, V. Ungermann, F. G’tz, and K.-D. Entian, Eur. J. Biochem.204: 57 (1992).PubMedCrossRefGoogle Scholar
  31. 31.
    O.P. Kuipers, M.M. Beerthuyzen, R.J. Siezen, and W.M. de Vos, Eur. J. Biochem.216: 281 (1993).PubMedCrossRefGoogle Scholar
  32. 32.
    J.C. Hutton, Curr. Opin. Cell Biol2: 1131 (1990).PubMedCrossRefGoogle Scholar
  33. 33.
    M. Hosaka, M. Nagahama, W.-S. Kim, T. Watanabe, K. Hatsuzawa, J. Ikemizu, K. Murakami, and K. Nakayama, J. Biol Chem.266: 12127 (1991).PubMedGoogle Scholar
  34. 34.
    W.J.M. Van de Ven, J. Voorberg, R. Fontijn, H. Pannekoek, A.M.W. van den Ouweland, H.L.P. van Duijnhoven, A.J.M. Roebroek, and R.J. Siezen, Mol Biol Rep. 14: 265 (1990).PubMedCrossRefGoogle Scholar
  35. 35.
    W.J.M. Van de Ven, H.L.P. van Duijnhoven, and A.J.M. Roebroek, Crit. Rev. Oncogenesis4: 115 (1993).PubMedGoogle Scholar
  36. 36.
    T. Watanabe, T. Nakagawa, J. Ikemizu, M. Nagahama, K. Murakami, and K. Nakayama, J. Biol Chem.267: 8270 (1992).PubMedGoogle Scholar
  37. 37.
    R. Leduc, S.S. Molloy, B.A. Thorne, and G. Thomas, J. Biol Chem.267: 14304 (1992).PubMedGoogle Scholar
  38. 38.
    R.J. Wise, P.J. Barr, P.A. Wong, M.C. Kiefer, A.J. Brake, and R.J. Kaufman, Proc. Natl Acad. Sci. USA87: 9378 (1990).PubMedCrossRefGoogle Scholar
  39. 39.
    A. Rehemtulla and R.J. Kaufman, Blood79: 2349 (1992).PubMedGoogle Scholar
  40. 40.
    J.W.M. Creemers, R.J. Siezen, A.J.M. Roebroek, T.A.Y. Ayoubi, D. Huylebroeck, and W.J.M. van de Ven, J. Biol Chem.268: 21826 (1993).PubMedGoogle Scholar

Copyright information

© Plenum Press, New York 1996

Authors and Affiliations

  • Roland J. Siezen
    • 1
  1. 1.Department of Biophysical ChemistryNIZOEdeNetherlands

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