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Cloning and Molecular Modeling of Duodenase with Respect to Evolution of Substrate Specificity within Mammalian Serine Proteases That Have Lost a Conserved Active-Site Disulfide Bond

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Abstract

Mammalian serine proteases such as the chromosome 14 (Homo sapiens, Mus musculus) located granzymes, chymases, cathepsin G, and related enzymes including duodenase collectively represent a special group within the chymotrypsin family which we refer to here as “granases”. Enzymes of this group have lost the ancient active-site disulfide bond Cys191-Cys220 (bovine chymotrypsinogen A numbering) which is strongly conserved in classic serine proteases such as pancreatic, blood coagulation, and fibrinolysis proteases and others (granzymes A, M, K and leukocyte elastases). We sequenced the cDNA encoding bovine (Bos taurus) duodenase, a granase with unusual dual trypsin-like and chymotrypsin-like specificity. The sequence revealed a 17-residue signal peptide and two-residue (GlyLys) activation peptide typical for granases. Production of the mature enzyme is apparently accompanied by further proteolytic processing of the C-terminal pentapeptide extension of duodenase. Similar C-terminal processing is known for another dual-specific granase, human cathepsin G. Using phylogenetic analysis based on 39 granases we retraced the evolution of residues 189 and 226 crucial for serine protease primary specificity. The analysis revealed that while there is no obvious link between mutability of residue 189 and the appearance of novel catalytic properties in granases, the mutability of residue 226 evidently gives rise to different specificity subgroups within this enzyme group. The architecture of the extended substrate-binding site of granases and structural basis of duodenase dual specificity based on molecular dynamic method are discussed. We conclude that the marked selectivity of granases that is crucial to their role as regulatory proteases has evolved through the fine-tuning of specificity at three levels— primary, secondary, and conformational.

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Abbreviations

MCP:

mast cell protease

GLP:

granzyme-like protein

NKP:

natural killer protease

HLE:

human leukocyte elastase (medullasin)

PRN:

human leukocyte protease 3 (myeloblastin)

ChlP:

chymase-like protease

REFERENCES

  1. Rawlings, N. D., and Barrett, A. J. (1993) Biochem. J., 290, 205–218.

    Google Scholar 

  2. Barrett, A. J., and Rawlings, N. D. (1998) in Handbook of Enzymes (Woessner, J. F., ed.) Academic Press, London, pp. 2–16.

    Google Scholar 

  3. Trapani, A. G. (2001) Genome Biol., 2, 3014.1–3014.7.

    Google Scholar 

  4. Zamolodchikova, T. S., Sokolova, E. A., and Smirnova, E. V. (2003) Biochemistry (Moscow), 68, 309–316.

    Google Scholar 

  5. Wouters, M. A., Liu, K., Riek, P., and Husain, A. (2003) Mol. Cell, 12, 343–354.

    Google Scholar 

  6. Zamolodchikova, T. S., Vorotyntseva, T. I., Nazimov, I. V., and Grishina, G. A. (1995) Eur. J. Biochem., 227, 873–879.

    Google Scholar 

  7. Zamolodchikova, T. S., Sokolova, E. A., Alexandrov, S. L., Mikhaleva, I. I., Prudchenko, I. A., Morozov, I. A., Kononenko, N. V., Mirgorodskaya, O. A., Da, U., Larionova, N. I., Pozdnev, V. F., Ghosh, D., Duax, W. L., and Vorotyntseva, T. I. (1997) Eur. J. Biochem., 249, 612–621.

    Google Scholar 

  8. Pemberton, A. D., Zamolodchikova, T. S., Scudamore, C. L., Chilvers, E. R., Miller, H. R., and Walker, T. R. (2002) Eur. J. Biochem., 269, 1171–1180.

    Google Scholar 

  9. McAleese, S. M., Pemberton, A. D., McGrath, M. E., Huntley, J. F., and Miller, H. R. P. (1998) Biochem. J., 333, 801–809.

    Google Scholar 

  10. Zamolodchikova, T. S., Sokolova, E. A., Lu, D., and Sadler, E. (2000) FEBS Lett., 466, 295–299.

    Google Scholar 

  11. Shechter, I. V., and Berger, A. C. (1967) Biochem. Biophys. Res. Commun., 27, 157–162.

    Google Scholar 

  12. Pletnev, V. Z., Zamolodchikova, T. S., Pangborn, W. A., and Duax, W. L. (2000) Prot. Struct. Funct. Genet., 41, 8–16.

    Google Scholar 

  13. Chomezynski, P., and Sacchi, N. (1987) Analyt. Biochem., 162, 156–159.

    Google Scholar 

  14. Guex, N., and Peitsch, M. C. (1997) Electrophoresis, 18, 2714–2723.

    Google Scholar 

  15. Ruzheinikov, S. N., Popov, M. E., and Kashparov, I. V. (2002) Bioorg. Khim., 28, 28–37.

    Google Scholar 

  16. Marelius, J., Kolmodin, K., Feierberg, I., and Aqvist, J. Q. (1999) J. Mol. Graph. Model., 16, 213–225.

    Google Scholar 

  17. Ryckaert, J. P., Ciccotti, G., and Berendsen, H. J. C. (1977) J. Comp. Phyl., 23, 327–341.

    Google Scholar 

  18. Lee, F. S., and Warshel, A. (1992) J. Chem. Phys., 97, 3100–3107.

    Google Scholar 

  19. Berendsen, H. J. C., Postma, J. P. M., Gunsteren, W. F., DiNola, A., and Haak, J. R. (1984) J. Chem. Phys., 81, 3684–3690.

    Google Scholar 

  20. Humphrey, W., Dalke, A., and Schulten, K. (1996) J. Mol. Graph., 14, 33–38.

    Google Scholar 

  21. Salvesen, G., and Enghild, J. J. (1990) Biochemistry, 29, 5304–5308.

    Google Scholar 

  22. Hof, P., Mayr, I., Huber, R., Korzus, E., Potemba, J., Travis, J., Powers, J. C., and Bode, W. (1996) EMBO J., 15, 5481–5491.

    Google Scholar 

  23. Pereira, P. J. B., Wang, Z. M., Rubin, H., Huber, R., Bode, W., Schechter, N. M., and Strobl, S. (1999) J. Mol. Biol., 286, 163–173.

    Google Scholar 

  24. Perona, J. J., Hedstrom, L., Rutter, W. J., and Fletterick, R. J. (1995) Biochemistry, 34, 1489–1499.

    Google Scholar 

  25. Waugh, S. M., Harris, J. L. Fletterick, R., and Craik, C. S. (2000) Nat. Struct. Biol., 7, 762–765.

    Google Scholar 

  26. Page, R. D. M., and Holmes, E. C. (2000) in Molecular Evolution: a Phylogenetic Approach, Blackwell Science, London, pp. 135–171.

    Google Scholar 

  27. Rypniewski, W. R., Perrakis, A., Vorgias, C. E., and Wilson, K. S. (1994) Protein. Eng., 7, 57–64.

    Google Scholar 

  28. Kam, C. M., Hudig, D., and Powers, J. C. (2000) Biochim. Biophys. Acta, 1477, 307–323.

    Google Scholar 

  29. Ewoldt, G. R., Smyth, M. J., Darcy, P. K., Harris, H. L., Craik, C. S., Horowitz, B., Woodard, S. L., Powers, J. C., and Hudig, D. (1997) J. Immunol., 158, 4574–4583.

    Google Scholar 

  30. Grigorenko, V. G., Yarovoi, S. V., Paulauskaite, R., and Amerik, A. Yu. (1994) FEBS Lett., 342, 278–280.

    Google Scholar 

  31. Edwards, K. M., Kam, Ch.-M., Powers, J. C., and Trapani, J. A. (1999) J. Biol. Chem., 274, 30468–30473.

    Google Scholar 

  32. Page, R. D. M., and Holmes, E. C. (2000) in Molecular Evolution: a Phylogenetic Approach, Blackwell Science, London, pp. 11–36.

    Google Scholar 

  33. Polanovska, J., Krokoszynska, I., Czapinska, H., Watorek, W., Dadlez, M., and Otlewski, J. (1998) Biochim. Biophys. Acta, 1386, 189–198.

    Google Scholar 

  34. Craik, Ch. S., Roczniak, S., Sprang, S., Fletterick, R., and Rutter, W. (1987) J. Cell. Biol., 33, 199–211.

    Google Scholar 

  35. Smith, M. J., O’Connor, M. D., Trapani, J. A., Kershaw, M. H., and Brinkworth, R. I. (1996) J. Immunol., 156, 4174–4181.

    Google Scholar 

  36. Bode, W., Meyer, E., and Powers, J. C. (1989) Biochemistry, 28, 1951–1963.

    Google Scholar 

  37. Kunori, Y., Koizumi, M., Masegi, T., Kasai, H., Kawabata, H., Yamazaki, Y., and Fukamizu, A. (2002) Eur. J. Biochem., 269, 5921–5930.

    Google Scholar 

  38. Perona, J. J., Tsu, C. A., McGrath, M. E., Craik, C. S., and Fletterick, R. J. (1993) J. Mol. Biol., 230, 934–939.

    Google Scholar 

  39. Remington, S. J., Woodbury, R. G., Reynolds, R. A., Matthews, B. W., and Neurath, H. (1988) Biochemistry, 27, 8097–8105.

    Google Scholar 

  40. Pasternak, A., Ringe, D., and Hedstrom, L. (1999) Protein Sci., 8, 253–258.

    Google Scholar 

  41. Frigerio, F., Coda, A., Pugliese, L., Lionetti, C., Menagatti, E., Amiconi, G., Schnebli, H. P., Ascenzi, P., and Bolognesi, M. (1992) J. Mol. Biol., 225, 107–123.

    Google Scholar 

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Authors and Affiliations

  1. Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997, Moscow, Russia

    T. S. Zamolodchikova, E. V. Smirnova, A. N. Andrianov, I. V. Kashparov, O. D. Kotsareva, E. A. Sokolova & K. B. Ignatov

  2. Department of Veterinary Clinical Studies, Welcome Trust Centre for Research in Comparative Respiratory Medicine, University of Edinburgh, Easter-Bush Veterinary Centre, Roslin, Midlothian, EH25 9RG, UK

    A. D. Pemberton

Authors
  1. T. S. Zamolodchikova
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  2. E. V. Smirnova
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  3. A. N. Andrianov
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  4. I. V. Kashparov
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  5. O. D. Kotsareva
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  6. E. A. Sokolova
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  7. K. B. Ignatov
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  8. A. D. Pemberton
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Correspondence to T. S. Zamolodchikova.

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__________

Translated from Biokhimiya, Vol. 70, No. 6, 2005, pp. 814–828.

Original Russian Text Copyright © 2005 by Zamolodchikova, Smirnova, Andrianov, Kashparov, Kotsareva, Sokolova, Ignatov, Pemberton.

Originally published in Biochemistry (Moscow) On-Line Papers in Press, as Manuscript BM04-127, September 12, 2004.

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Zamolodchikova, T.S., Smirnova, E.V., Andrianov, A.N. et al. Cloning and Molecular Modeling of Duodenase with Respect to Evolution of Substrate Specificity within Mammalian Serine Proteases That Have Lost a Conserved Active-Site Disulfide Bond. Biochemistry (Moscow) 70, 672–684 (2005). https://doi.org/10.1007/s10541-005-0168-2

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