Thermodynamics and molecular simulation analysis of hydrophobic substrate recognition by aminotransferases

Journal of Biological Chemistry

Volumn 273, Issue 29, 1998, Pages 18353-18364

  Kawagxichi, Shin Ichi ^a   Kuramitsu, Seiki ^a  

^a OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; AMINOTRANSFERASE; ASPARTATE AMINOTRANSFERASE;

ARTICLE; BINDING AFFINITY; CONFORMATION; ENTHALPY; ENZYME ACTIVITY; ENZYME SPECIFICITY; ENZYME SUBSTRATE; HYDROPHOBICITY; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; SIMULATION; TEMPERATURE; THERMODYNAMICS;

ASPARTATE AMINOTRANSFERASES; CATALYSIS; COMPUTER SIMULATION; ESCHERICHIA COLI; KINETICS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PYRIDOXAL PHOSPHATE; PYRIDOXAMINE; SUBSTRATE SPECIFICITY; THERMODYNAMICS; TRANSAMINASES;

NEGIBACTERIA;

EID: 0032541164     PISSN: 00219258     EISSN: None     Source Type: Journal    
DOI: 10.1074/jbc.273.29.18353     Document Type: Article

References (71)

1. Fersht, A. (1985) Enzyme Structure and Mechanism, 2nd Ed., pp. 389-452, W. H. Freeman and Co., New York
2. Kuramitsu, S., Hiromi, K., Hayashi, H., Morino, Y., and Kagamiyama, H. (1990) Biochemistry 29, 5469-5476
3. Kawaguchi, S., Nobe, Y., Yasuoka, J., Wakamiya, T., Kusumoto, S., and Kuramitsu, S. (1997) J. Biochem. (Tokyo) 122, 55-63
4. Gillmor, S. A., Craik, C. S., and Fletterick, R. J. (1997) Protein Sci. 6, 1603-1611
5. Creighton, T. E. (1993) Proteins, 2nd Ed., pp. 217-238, W. H. Freeman and Co., New York
6. Hansch, C., and Coats, E. (1970) J. Pharm. Sci. 59, 731-743
7. Dorovska-Taran, V., Momtcheva, R., Gulubova, N., and Martinek, K. (1982) Biochim. Biophys. Acta 702, 37-53
8. Klyosov, A. A. (1996) Biochemistry 35, 4457-4467
9. Lu, W., Apostol, I., Qasim, M. A., Warne, N., Wynn, R., Zhang, W. L., Anderson, S., Chiang, Y. W., Ogin, E., Rothberg, I., Ryan, K., and Laskowski, M., Jr. (1997) J. Mol. Biol. 266, 441-461
10. Morton, A., Baase, W. A., and Matthews, B. W. (1995) Biochemistry 34, 8564-8575
11. Færgeman, N. J., Sigurskjold, B. W., Kragelund, B. B., Andersen, K. V., and Knudsen, J. (1996) Biochemistry 35, 14118-14126
12. Helms, V., Deprez, E., Gill, E., Barret, C., Hoa, G. H. B., and Wade, R. C. (1996) Biochemistry 35, 1485-1499
13. Jackson, S. E., Moracci, M., elMasry, N., Johnson, C. M., and Fersht, A. R. (1993) Biochemistry 32, 11259-11269
14. Yutani, K., Ogasahara, K., Tsujita, T., and Sugino, Y. (1987) Proc. Natl. Acad. Sci. U. S. A. 84, 4441-4444
15. Shortle, D., Stites, W. E., and Meeker, A. K. (1990) Biochemistry 29, 8033-8041
16. Sandberg, W. S., and Terwilliger, T. C. (1991) Proc. Natl. Acad. Sci. U. S. A. 88, 1706-1710
17. Serrano, L., Kellis, J. T., Jr., Cann, P., Matouschek, A., and Fersht, A. R. (1992) J. Mol. Biol. 224, 783-804
18. Eriksson, A. E., Baase, W. A., and Matthews, B. W. (1993) J. Mol. Biol. 229, 747-769
19. Akasako, A., Haruki, M., Oobatake, M., and Kanaya, S. (1997) J. Biol. Chem. 272, 18686-18693
20. Wangikar, P. P., Rich, J. O., Clark, D. S., and Dordick, J. S. (1995) Biochemistry 34, 12302-12310
21. Kiick, D. M., and Cook, P. F. (1983) Biochemistry 22, 375-382
22. Jenkins, W. T., and Fonda, M. L. (1985) in Transaminases (Christen, P., and Metzler, D. E., eds), pp. 216-234, John Wiley & Sons, New York
23. Mehta, P. K., Hale, T. I., and Christen, P. (1993) Eur. J. Biochem. 214, 549-561
24. Jensen, R. A., and Gu, W. (1996) J. Bacteriol. 178, 2161-2171
25. Hayashi, H., Inoue, K., Nagata, T., Kuramitsu, S., and Kagamiyama, H. (1993) Biochemistry 32, 12229-12239
26. John, R. A. (1995) Biochim. Biophys. Acta 1248, 81-96
27. Hayashi, H. (1995) J. Biochem. (Tokyo) 118, 463-473
28. Smith, D. L., Almo, S. C., Toney, M. D., and Ringe, D. (1989) Biochemistry 28, 8161-8167
29. Okamoto, A., Higuchi, T., Hirotsu, K., Kuramitsu, S., and Kagamiyama, H. (1994) J. Biochem. (Tokyo) 116, 95-107
30. Rhee, S., Silva, M. M., Hyde, C. C., Rogers, P. H., Metzler, C. M., Metzler, D. E., and Arnone, A. (1997) J. Biol. Chem. 272, 17293-17302
31. Kuramitsu, S., Inoue, K., Ogawa, T., Ogawa, H., and Kagamiyama, H. (1985) Biochem. Biophys. Res. Commun. 133, 134-139
32. Kuramitsu, S., Okuno, S., Ogawa, T., Ogawa, H., and Kagamiyama, H. (1985) J. Biochem. (Tokyo) 97, 1259-1262
33. Miyazawa, K., Kawaguchi, S., Okamoto, A., Kato, R., Ogawa, T., and Kuramitsu, S. (1994) J. Biochem. (Tokyo) 115, 568-577
34. Seville, M., Vincent, M. G., and Hahn, K. (1988) Biochemistry 27, 8344-8349
35. Jäger, J., Solmajer, T., and Jansonius, J. N. (1992) FEBS Lett. 306, 234-238
36. Malashkevich, V. N., Onuffer, J. J., Kirsch, J. F., and Jansonius, J. N. (1995) Nat. Struct. Biol. 2, 548-553
37. Karplus, M., and McCammon, J. A. (1983) Annu. Rev. Biochem. 52, 263-300
38. Yano, T., Kuramitsu, S., Tanase, S., Morino, Y., Hiromi, K., and Kagamiyama, H. (1991) J. Biol. Chem. 266, 6079-6085
39. Messing, J., Crea, R., and Seeburg, P. H. (1981) Nucleic Acids Res. 9, 309-321
40. Jenkins, W. T., and D'Ari, L. (1966) J. Biol. Chem. 241, 5667-5674
41. Iwasaki, M., Hayashi, H., and Kagamiyama, H. (1994) J. Biochem. (Tokyo) 115, 156-161
42. Kasper, P., Sterk, M., Christen, P., and Gehring, H. (1996) Eur. J. Biochem. 240, 751-755
43. Fersht, A. (1985) Enzyme Structure and Mechanism, 2nd Ed., pp. 311-346, W. H. Freeman and Co., New York
44. Onuffer, J. J., Ton, B. T., Klement, I., and Kirsch, J. F. (1995) Protein Sci. 4, 1743-1749
45. Murphy, K. P., and Freire, E. (1992) Adv. Protein Chem. 43, 313-361
46. Miyahara, I., Hirotsu, K., Hayashi, H., and Kagamiyama, H. (1994) J. Biochem. (Tokyo) 116, 1001-1012
47. Kabsch, W., and Sander, C. (1983) Biopolymers 22, 2577-2637
48. Nishikawa, K., Ooi, T., Isogai, Y., and Saito, N. (1972) J. Phys. Soc. 32, 1331-1337
49. Inoue, Y., Kuramitsu, S., Inoue, K., Kagamiyama, H., Hiromi, K., Tanase, S., and Morino, Y. (1989) J. Biol. Chem. 264, 9673-9681
50. Vacca, R. A., Giannattasio, S., Graber, R., Sandmeier, E., Marra, E., and Christen, P. (1997) J. Biol. Chem. 272, 21932-21937
51. Pfister, K., Sandmeier, E., Berchtold, W., and Christen, P. (1985) J. Biol. Chem. 260, 11414-11421
52. Pfister, K., Kagi, J. H. R., and Christen, P. (1978) Proc. Natl. Acad. Sci. U. S. A. 75, 145-148
53. Tanford, C. (1980) The Hydrophobie Effect: Formation of Micelles and Biological Membranes, 2nd Ed., John Wiley & Sons, New York
54. Wynn, R., Harkins, P. C., Richards, F. M., and Fox, R. O. (1997) Protein Sci. 6, 1621-1626
55. Dunker, A. K., Garner, E., Guilliot, S., Romero, P., Albrecht, K., Hart, Z., Obradovic, Z., Kissinger, C., and Villafranca, J. E. (1998) Pac. Symp. Biocomp. 3, 471-482
56. Bigler, T. L., Lu, W., Park, S. J., Tashiro, M., Wieczorek, M., Wynn, R., and Laskowski, M., Jr. (1993) Protein Sci. 2, 786-799
57. Huang, K., Lu, W., Anderson, S., Laskowski, M., Jr., and James, M. N. G. (1995) Protein Sci. 4, 1985-1997
58. Oue, S., Okamoto, A., Nakai, Y., Nakahira, M., Shibatani, T., Hayashi, H., and Kagamiyama, H. (1997) J. Biochem. (Tokyo) 121, 161-171
59. Dorovska, V. N., Varfolomeyev, S. D., Kazanskaya, N. F., Klyosov, A. A., and Martinek, K. (1972) FEBS Lett. 23, 122-124
60. Hedstrom, L., Szilagyi, L., and Rutter, W. J. (1992) Science 255, 1249-1253
61. Perona, J. J., Hedstrom, L., Rutter, W. J., and Fletterick, R. J. (1995) Biochemistry 34, 1489-1499
62. Mace, J. E., and Agard, D. A. (1995) J. Mol. Biol. 254, 720-736
63. Mace, J. E., Wilk, B. J., and Agard, D. A. (1995) J. Mol. Biol. 251, 116-134
64. Rader, S. D., and Agard, D. A. (1997) Protein Sci. 6, 1375-1386
65. Onuffer, J. J., and Kirsch, J. F. (1995) Protein Sci. 4, 1750-1757
66. Suginohara, K., Hamasaki, N., Tanase, S., Fukumoto, Y., and Morino, Y. (1991) in Enzymes Dependent on Pyridoxal Phosphate and Other Carbonyl Compounds as Cofactors (Fukui, T., Kagamiyama, H., Soda, K., and Wada, H., eds) pp. 195-197, Pergamon Press, New York
67. Winter, N. S., Bratt, J. M., and Banaszak, L. J. (1993) J. Mol. Biol. 230, 1247-1259
68. Mehta, P. K., Hale, T. I., and Christen, P. (1989) Eur. J. Biochem. 186, 249-253
69. McPhalen, C. A., Vincent, M. G., and Jansonius, J. N. ( 1992) J. Mol. Biol. 225, 495-517
70. McPhalen, C. A., Vincent, M. G., Picot, D., Jansonius, J. N., Lesk, A. K., and Chothia, C. (1992) J. Mol. Biol. 227, 197-213
71. Malashkevich, V. N., Strokopytov, B. V., Borisov, V. V., Dauter, Z., Wilson, K. S., and Torchinsky, Y. M. (1995) J. Mol. Biol. 247, 111-124