Identification of active sites in amidase: Evolutionary relationship between amide bond- and peptide bond-cleaving enzymes

Proceedings of the National Academy of Sciences of the United States of America

Volumn 94, Issue 22, 1997, Pages 11986-11991

  Kobayashi, Michihiko ^a   Fujiwara, Yoshie ^a   Goda, Masahiko ^a   Komeda, Hidenobu ^a   Shimizu, Sakayu ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

Aspartic acid; Hydrolase; Nitrile; Rhodococcus; Serine

Indexed keywords

AMIDASE; AMIDE; ASPARTIC ACID; CYSTEINE; NITRILE; PEPTIDE; SERINE;

AMINO ACID SUBSTITUTION; ARTICLE; BACTERIAL METABOLISM; CELL INCLUSION; CHEMICAL BINDING; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ESCHERICHIA COLI; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DEGRADATION; RHODOCOCCUS; SITE DIRECTED MUTAGENESIS;

AMIDES; AMIDOHYDROLASES; AMINO ACID SEQUENCE; ASPARTIC ENDOPEPTIDASES; BINDING SITES; ESCHERICHIA COLI; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; MUTAGENESIS, SITE-DIRECTED; NITRILES; PEPTIDES; RECOMBINANT PROTEINS; RHODOCOCCUS; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY, AMINO ACID;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; RHODOCOCCUS; RHODOCOCCUS RHODOCHROUS;

EID: 0030700490     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.94.22.11986     Document Type: Article

References (50)

1. Bradbury, A. F. & Smyth, D. G. (1991) Trends Biochem. Sci. 16, 112-115.
2. Schomburg, D. & Salzmann, M., eds. (1991) Enzyme Handbook 4 (Springer, Berlin).
3. Cravatt, B. F., Giang, D. K., Mayfield, S. P., Boger, D. L., Lerner, R. A. & Gilula, N. B. (1996) Nature (London) 384, 83-87.
4. Yamada, T., Palm, C. J., Brooks, B. & Kosuge, T. (1985) Proc. Natl. Acad. Sci. USA 82, 6522-6526.
5. Klee, H., Montoya, A., Horodyski, F., Lichtenstein, C., Garfinkel, D., Fuller, S., Flores, C., Peschon, J., Nester, E. & Gordon, M. (1984) Proc. Natl. Acad. Sci. USA 81, 1728-1732.
6. Kobayashi, M., Nagasawa, T. & Yamada, H. (1992) Trends Biotechnol. 10, 402-408.
7. Yamada, H. & Kobayashi, M. (1996) Biosci. Biotech. Biochem. 60, 1391-1400.
8. Hayashi, T., Yamamoto, K., Matsuo, A., Otsubo, K., Muramatsu, S., Matsuda, A. & Komatsu, K.-I. (1997) J. Ferment. Bioeng. 83, 139-145.
9. Zambryski, P., Tempe, J. & Schell, J. (1989) Cell 56, 193-201.
10. Kobayashi, M., Komeda, H., Nagasawa, T., Nishiyama, M., Horinouchi, S., Beppu, T., Yamada, H. & Shimizu, S. (1993) Eur. J. Biochem. 217, 327-336.
11. Komeda, H., Kobayashi, M. & Shimizu, S. (1997) Proc. Natl. Acad. Sci. USA 94, 36-41.
12. Komeda, H. Kobayashi, M. & Shimizu, S. (1996) J. Biol. Chem. 271, 15796-15802.
13. Ettinger, R. A. & DeLuca, H. F. (1995) Arch. Biochem. Biophys. 316, 14-19.
14. Ettinger, R. A., Ismail, R. & DeLuca, H. F. (1994) J. Biol. Chem. 269, 176-182.
15. Tsuchiya, K., Fukuyama, S., Kanzaki, N., Kanagawa, K., Negoro, S. & Okada, H. (1989) J. Bacteriol. 171, 3187-3191.
16. Okada, H., Negoro, S., Kimura, H. & Nakamura, S. (1983) Nature (London) 306, 203-206.
17. Mayaux, J.-F. Cerbelaud, E., Soubrier, F., Yeh, P., Blanche, F. & Petre, D. (1991) J. Bacteriol. 173, 6694-6704.
18. Ciskanik, L. M., Wilczek, J. M. & Fallon, R. D. (1995) Appl. Environ. Microbiol. 61, 998-1003.
19. Hashimoto, Y., Nishiyama, M., Ikehata, O., Horinouchi, S. & Beppu, T. (1991) Biochim. Biophys. Acta 1088, 225-233.
20. Mayaux, J.-F., Cerbelaud, E., Soubrier, F., Faucher, D. & Petre, D. (1990) J. Bacteriol. 172, 6764-6773.
21. Nishiyama, M., Horinouchi, S., Kobayashi, M., Nagasawa, T., Yamada, H. & Beppu, T. (1991) J. Bacteriol. 173, 2465-2472.
22. Silva, A. M., Cachau, R. E., Sham, H. L. & Erickson, J. W. (1996) J. Mol. Biol. 255, 321-346.
23. Beppu, T. (1988) in Recombinant DNA and Bacterial Fermentation, ed. Thomson, J. A. (CRC, Boca Raton, FL), pp. 11-21.
24. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Lab. Press, Plainview, NY), 2nd Ed.
25. Sanger, F., Nicklen, S. & Coulson, A. R. (1977) Proc. Natl. Acad. Sci. USA 74, 5463-5467.
26. Taylor, J. W., Ott, J. & Eckstein, F. (1985) Nucleic Acids Res. 13, 8764-8785.
27. Carter, P. & Wells, J. A. (1988) Nature (London) 332, 564-568.
28. Paetzel, M. & Dalbey, R. E. (1997) Trends Biochem. Sci. 22, 28-31.
29. Toh, H., Ono, M., Saigo, K. & Miyata, T. (1985) Nature (London) 315, 691.
30. Veerapandian, B., Cooper, J. B., Sali, A., Blundell, T. L., Rosati, R. L., Dominy, B. W., Damon, D. B. & Hoover, D. J. (1992) Protein Sci. 1, 322-328.
31. Tang, J., James, M. N. G., Hsu, I. N., Jenkins, J. A. & Blundell, T. L. (1978) Nature (London) 271, 618-621.
32. Jakoby, W. B. & Fredericks, J. (1964) J. Biol. Chem. 239, 1978-1982.
33. Negoro, S., Mitamura, T., Oka, K., Kanagawa, K. & Okada, H. (1989) Eur. J. Biochem. 185, 521-524.
34. Nishiya, Y. & Imanaka, T. (1993) J. Ferment. Bioeng. 75, 245-253.
35. Brammar, W. J., Charles, I. G., Matfield, M., Liu, C. P., Drew, R. E. & Clarke, P. H. (1987) FEBS Lett. 215, 291-294.
36. Bork, P. & Koonin, E. V. (1994) Protein Sci. 3, 1344-1346.
37. Novo, C., Tata, R., Clemente, A. & Brown, P. R. (1995) FEBS Lett. 367, 275-279.
38. Kobayashi, M., Izui. H., Nagasawa, T. & Yamada, H. (1993) Proc. Natl. Acad. Sci. USA 90, 247-251.
39. Komeda, H., Hori, Y., Kobayashi, M. & Shimizu, S. (1996) Proc. Natl. Acad. Sci. USA 93, 10572-10577.
40. Brown, D. T., Turner, P. D. & O'Reilly, C. (1995) FEMS Microbiol. Lett. 134, 143-146.
41. Wang, P. & Van Etten, H. D. (1992) Biochem. Biophys. Res. Commun. 187, 1048-1054.
42. Kobayashi, M. & Shimizu, S. (1994) FEMS Microbiol. Lett. 120, 217-224.
43. Nishimori, K., Kawaguchi, Y., Hidaka, M., Uozumi, T. & Beppu, T. (1982) J. Biochem. (Tokyo) 91, 1085-1088.
44. Harris, T. J. R., Lowe, P. A., Lyons, A., Thomas, P. G., Eaton, M. A. W., Millican, T. A., Patel, T. P., Bose, C. C., Carey, N. H. & Doel, M. T. (1982) Nucleic Acids Res. 10, 2177-2187.
45. Lin, X., Wong, R. N. S. & Tang, J. (1989) J. Biol. Chem. 264, 4482-4489.
46. Chang, T. H. & Abelson, J. (1990) Nucleic Adds Res. 18, 7180.
47. Sekine, M., Watanabe, K. & Syono, K. (1989) Nucleic Acids Res. 17, 6400.
48. Gomi, K., Kitamoto, K. & Kumagai, C. (1991) Gene 108, 91-98.
49. Corrick, C. M., Twomey, A. P. & Hynes, M. J. (1987) Gene 53, 63-71.
50. Barrie, K. A., Perez, E. E., Lamers, S. L., Farmerie, W. G., Dunn, B. M., Sleasman, J. W. & Goodenow, M. M. (1996) Virology 219, 407-416.