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)

Volumn 70, Issue 6, 2005, Pages 672-684

  Zamolodchikova, T S ^a   Smirnova, E V ^a   Andrianov, A N ^a   Kashparov, I V ^a   Kotsareva, O D ^a   Sokolova, E A ^a   Ignatov, K B ^a   Pemberton, A D ^b  

^a SHEMYAKIN OVCHINNIKOV INSTITUTE OF BIOORGANIC CHEMISTRY   (Russian Federation)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

Chymotrypsin family; Duodenase cDNA; Granase; Molecular dynamic; Phylogeny; Substrate specificity

Indexed keywords

AMINO ACIDS; CATALYST SELECTIVITY; CHEMICAL BONDS; CONFORMATIONS; DNA; MOLECULAR DYNAMICS; SUBSTRATES; SULFUR;

CHYMOTRYPSIN FAMILY; DUODENASE CDNA; GRANASE; PHYLOGENY; SUBSTRATE SPECIFICITY;

ENZYMES;

BOS TAURUS; BOVINAE; HOMO SAPIENS; MAMMALIA; MUS MUSCULUS;

COMPLEMENTARY DNA; DISULFIDE; DUODENASE; SERINE PROTEINASE;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BINDING SITE; CATTLE; CHEMICAL STRUCTURE; CHEMISTRY; DNA SEQUENCE; ENZYME SPECIFICITY; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; BINDING SITES; CATTLE; DISULFIDES; DNA, COMPLEMENTARY; EVOLUTION, MOLECULAR; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SERINE ENDOPEPTIDASES; SUBSTRATE SPECIFICITY;

EID: 23744467729     PISSN: 00062979     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10541-005-0168-2     Document Type: Article

References (41)

1. Rawlings, N. D., and Barrett, A. J. (1993) Biochem. J., 290, 205-218.
2. Barrett, A. J., and Rawlings, N. D. (1998) in Handbook of Enzymes (Woessner, J. F., ed.) Academic Press, London, pp. 2-16.
3. Trapani, A. G. (2001) Genome Biol., 2, 3014.1-3014.7.
4. Zamolodchikova, T. S., Sokolova, E. A., and Smirnova, E. V. (2003) Biochemistry (Moscow), 68, 309-316.
5. Wouters, M. A., Liu, K., Riek, P., and Husain, A. (2003) Mol. Cell, 12, 343-354.
6. Zamolodchikova, T. S., Vorotyntseva, T. I., Nazimov, I. V., and Grishina, G. A. (1995) Eur. J. Biochem., 227, 873-879.
7. Zamolodchikova, T. S., Sokolova, E. A., Alexandrov, S. L., Mikhaleva, I. I., Pradchenko, 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.
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.
9. McAleese, S. M., Pemberton, A. D., McGrath, M. E., Huntley, J. F., and Miller, H. R. P. (1998) Biochem. J., 333, 801-809.
10. Zamolodchikova, T. S., Sokolova, E. A., Lu, D., and Sadler, E. (2000) FEBS Lett., 466, 295-299.
11. Shechter, I. V., and Berger, A. C. (1967) Biochem. Biophys. Res. Commun., 27, 157-162.
12. Pletnev, V. Z., Zamolodchikova, T. S., Pangborn, W. A., and Duax, W. L. (2000) Prot. Struct. Funct. Genet., 41, 8-16.
13. Chomezynski, P., and Sacchi, N. (1987) Analyt. Biochem., 162, 156-159.
14. Guex, N., and Peitsch, M. C. (1997) Electrophoresis, 18, 2714-2723.
15. Ruzheinikov, S. N., Popov, M. E., and Kashparov, I. V. (2002) Bioorg. Khim., 28, 28-37.
16. Marelius, J., Kolmodin, K., Feierberg, I., and Åqvist, J. Q. (1999) J. Mol. Graph. Model., 16, 213-225.
17. Ryckaert, J. P., Ciccotti, G., and Berendsen, H. J. C. (1977) J. Comp. Phyl., 23, 327-341.
18. Lee, F. S., and Warshel, A. (1992) J. Chem. Phys., 97, 3100-3107.
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.
20. Humphrey, W., Dalke, A., and Schulten, K. (1996) J. Mol. Graph., 14, 33-38.
21. Salvesen, G., and Enghild, J. J. (1990) Biochemistry, 29, 5304-5308.
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.
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.
24. Perona, J. J., Hedstrom, L., Rutter, W. J., and Fletterick, R. J. (1995) Biochemistry, 34, 1489-1499.
25. Waugh, S. M., Harris, J. L. Fletterick, R., and Craik, C. S. (2000) Nat. Struct. Biol., 7, 762-765.
26. Page, R. D. M., and Holmes, E. C. (2000) in Molecular Evolution: a Phylogenetic Approach, Blackwell Science, London, pp. 135-171.
27. Rypniewski, W. R., Perrakis, A., Vorgias, C. E., and Wilson, K. S. (1994) Protein. Eng., 7, 57-64.
28. Kam, C.-M., Hudig, D., and Powers, J. C. (2000) Biochim. Biophys. Acta, 1477, 307-323.
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.
30. Grigorenko, V. G., Yarovoi, S. V., Paulauskaite, R., and Amerik, A. Yu. (1994) FEBS Lett., 342, 278-280.
31. Edwards, K. M., Kam, Ch.-M., Powers, J. C., and Trapani, J. A. (1999) J. Biol. Chem., 274, 30468-30473.
32. Page, R. D. M., and Holmes, E. C. (2000) in Molecular Evolution: a Phylogenetic Approach, Blackwell Science, London, pp. 11-36.
33. Polanovska, J., Krokoszynska, I., Czapinska, H., Watorek, W., Dadlez, M., and Otlewski, J. (1998) Biochim. Biophys. Acta, 1386, 189-198.
34. Craik, Ch. S., Roczniak, S., Sprang, S., Fletterick, R., and Rutter, W. (1987) J. Cell. Biol., 33, 199-211.
35. Smith, M. J., O'Connor, M. D., Trapani, J. A., Kershaw, M. H., and Brinkworth, R. I. (1996) J. Immunol., 156, 4174-4181.
36. Bode, W., Meyer, E., and Powers, J. C. (1989) Biochemistry, 28, 1951-1963.
37. Kunori, Y., Koizumi, M., Masegi, T., Kasai, H., Kawabata, H., Yamazaki, Y., and Fukamizu, A. (2002) Eur. J. Biochem., 269, 5921-5930.
38. Perona, J. J., Tsu, C. A., McGrath, M. E., Craik, C. S., and Fletterick, R. J. (1993) J. Mol. Biol., 230, 934-939.
39. Remington, S. J., Wsodbury, R. G., Reynolds, R. A., Matthews, B. W., and Neurath, H. (1988) Biochemistry, 27, 8097-8105.
40. Pasternak, A., Ringe, D., and Hedstrom, L. (1999) Protein Sci., 8, 253-258.
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.