Ammonium scanning in an enzyme active site: The chiral specificity of aspartyl-tRNA synthetase

Journal of Biological Chemistry

Volumn 282, Issue 42, 2007, Pages 30856-30868

  Thompson, Damien ^a,b   Lazennec, Christine ^a   Plateau, Pierre ^a   Simonson, Thomas ^a  

^a LABORATOIRE DE BIOCHIMIE   (France)

^b UNIVERSITY COLLEGE CORK   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIUM COMPOUNDS; BIOTECHNOLOGY; COULOMB INTERACTIONS; MOLECULAR DYNAMICS; MOLECULAR ORIENTATION; RNA;

AMMONIUM SCANNING; ENZYME ACTIVE SITES; MISACYLATE; MOLECULAR DYNAMICS SIMULATIONS;

ENZYME ACTIVITY;

ASPARTATE TRANSFER RNA LIGASE;

ARTICLE; CHIRALITY; CONFORMATIONAL TRANSITION; ELECTRICITY; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME ENGINEERING; ENZYME KINETICS; ENZYME SPECIFICITY; ENZYME STRUCTURE; ENZYME SUBSTRATE; LIGAND BINDING; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; PREDICTION; PRIORITY JOURNAL; SIMULATION; STRUCTURE ANALYSIS;

ASPARTATE-TRNA LIGASE; BINDING SITES; COMPUTER SIMULATION; D-ASPARTIC ACID; KINETICS; LIGANDS; MODELS, CHEMICAL; MODELS, MOLECULAR; MUTATION, MISSENSE; PROTEIN BINDING; QUATERNARY AMMONIUM COMPOUNDS; RNA, TRANSFER, ASP; STEREOISOMERISM; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY; SUCCINIC ACID; TRANSFER RNA AMINOACYLATION;

EID: 35648937527     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M704788200     Document Type: Article

References (69)

1. Berg, J. M., Tymoczko, J. L., and Stryer, L. (2002) Biochemistry, 5th Ed., W. H. Freeman, New York
2. Ibba, M., Francklyn, C., and Cusack, S. (eds) (2005) Aminoacyl-tRNA Synthetases, Landes Bioscience, Georgetown, TX
3. Arnez, J. G., and Moras, D. (1994) in RNA-Protein Interactions (Nagai, K., Mattaj, I., eds) pp. 52-81, Oxford University Press, Oxford, UK
4. Meinnel, T., Mechulam, Y., and Blanquet, S. (1995) in tRNA: Structure, Biosynthesis, and Function (Soll, D., and Raj Bhandary, T. L., eds) pp. 251-291, ASM Press, Washington, D. C.
5. Schimmel, P., and Ribas de Pouplana, L. (2000) Trends Biochem. Sci. 25, 207-209
6. Pallanck, L., Pak, M., and Schulman, L. H. (1995) in tRNA: Structure, Biosynthesis and Function (Soll, D., and Raj Bhandary, T. L., eds) pp. 371-393, ASM Press, Washington, D. C.
7. Arnez, J. G., and Moras, D. (1997) Trends Biochem. Sci. 22, 211-216
8. Francklyn, C. S. (2003) Proc. Natl. Acad. Sci. U. S. A. 100, 9650-9652
9. Ruff, M., Krishnaswamy, S., Boeglin, M., Poterszman, A., Mitschler, A., Podjarny, A., Rees, B., Thierry, J. C., and Moras, D. (1991) Science 252, 1682-1689
10. Cavarelli, J., Eriani, B., Rees, B., Ruff, M., Boeglin, M., Mitschler, A., Martin, F., Gangloff, J., Thierry, J. C., and Moras, D. (1994) EMBO J. 13, 327-337
11. Poterzman, A., Delarue, M., Thierry, J. C., and Moras, D. (1994) J. Mol. Biol. 244, 158-167
12. Schmitt, E., Moulinier, L., Fujiwara, S., Imanaka, T., Thierry, J. C., and Moras, D. (1998) EMBO J. 17, 5227-5237
13. Eiler, S., Dock-Bregeon, A. C., Moulinier, L., Thierry, J. C., and Moras, D. (1999) EMBO J. 18, 6532-6541
14. Briand, C., Poterszman, A., Eiler, S., Webster, G., Thierry, J. C., and Moras, D. (2000) J. Mol. Biol. 299, 1051-1060
15. Moulinier, L., Eiler, S., Eriani, G., Gangloff, J., Thierry, J. C., Gabriel, K., McClain, W. H., and Moras, D. (2001) EMBO J. 20, 5290-5301
16. Ador, L., Jaeger, S., Geslain, R., Martin, F., Cavarelli, J., and Eriani, G. (2004) Biochemistry 43, 7028-7037
17. Berthet-Colominas, C., Seignovert, L., Hartlein, M., Grotli, M., Cusack, S., and Leberman, R. (1998) EMBO J. 17, 2947-2960
18. Onesti, S., Desogus, G., Brevet, A., Chen, J., Plateau, P., Blanquet, S., and Brick, P. (2000) Biochemistry 39, 12853-12861
19. Desogus, G., Todone, F., Brick, P., and Onesti, S. (2000) Biochemistry 39, 8418-8425
20. Ataide, S. F., and Ibba, M. (2004) Biochemistry 43, 11836-11841
21. Archontis, G., Simonson, T., Moras, D., and Karplus, M. (1998) J. Mol. Biol. 275, 823-846
22. Archontis, G., and Simonson, T. (2001) J. Am. Chem. Soc. 123, 11047-11056
23. Archontis, G., Simonson, T., and Karplus, M. (2001) J. Mol. Biol. 306, 307-327
24. Thompson, D., Plateau, P., and Simonson, T. (2006) ChemBioChem 7, 337-344
25. Thompson, D., and Simonson, T. (2006) J. Biol. Chem. 281, 23792-24803
26. Soutourina, J., Plateau, P., and Blanquet, S. (2000) J. Biol. Chem. 275, 32535-32542
27. Hopfield, J. J. (1974) Proc. Natl. Acad. Sci. U. S. A. 71, 4135-4139
28. Baldwin, A. N., and Berg, P. (1966) J. Biol. Chem. 241, 839-845
29. Fischer, P. M. (2003) Curr. Protein Pept. Sci. 4, 339-356
30. Tugyi, R., Uray, K., Iván, D., Fellinger, E., Perkins, A., and Hudecz, F. (2005) Proc. Natl. Acad. Sci. U. S. A. 102, 413-418
31. Nakatsu, T., Kato, H., and Oda, J. (1998) Nat. Struct. Biol. 5, 15-19
32. Wong, C., and McCammon, J. (1986) J. Am. Chem. Soc. 108, 3830-3832
33. Warshel, A., Sussman, F., and King, G. (1986) Biochemistry 25, 8368-8372
34. Kollman, P. (1993) Chem. Rev. 93, 2395
35. van Gunsteren, W., Beutler, T., Fraternali, F., King, P., Mark, A., and Smith, P. (1993) in Computer Simulation of Biomolecular Systems (van Gunsteren, W., Weiner, P., and Wilkinson, A., eds) pp. 315-348, Escom Science Publishers, Leiden, The Netherlands
36. Lamb, M. L., and Jorgensen, W. (1997) Curr. Opin. Chem. Biol. 1, 449-457
37. Warshel, A. (1991) Computer Modelling of Chemical Reactions in Enzymes and Solutions, Wiley, New York
38. Simonson, T. (2001) in Computational Biochemistry and Biophysics (Becker, O. M., MacKerell, A. D., Roux, B., and Watanabe, M., eds) pp. 169-197, Marcel Dekker Inc., New York
39. Simonson, T., Archontis, G., and Karplus, M. (2002) Acc. Chem. Res. 35, 430-437
40. Cleland, W. W., and Kreevoy, M. M. (1994) Science 264, 1887-1890
41. Warshel, A., Papazyan, A., and Kollman, P. (1995) Science 269, 102-106
42. Warshel, A. (1998) J. Biol. Chem. 273, 27035-27038
43. Simonson, T. (2003) Rep. Prog. Phys. 66, 737-787
44. Zeng, J., Fridman, H., Maruta, H., Treutlein, H., and Simonson, T. (1999) Protein Sci. 8, 50-64
45. Simonson, T., Carlsson, J., and Case, D. A. (2004) J. Am. Chem. Soc. 126, 4167-4180
46. Thompson, D., and Larson, J. A. (2006) J. Phys. Chem. B 110, 16640-16645
47. Wang, J., Deng, Y., and Roux, B. (2006) Biophys. J. 91, 2798-2814
48. Burkhard, P., Meier, M., and Lustig, A. (2001) Protein Sci. 9, 2294-2301
49. Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Montgomery, J. A., Jr., Vreven, T., Kudin, K. N., Burant, J. C., Millam, J. M., Lyengar, S. S., Tomasi, J., Barone, V., Mennucci, B., Cossi, M., Scalmani, G., Rega, N., Petersson, G. A., Nakatsuji, H., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Klene, M., Li, X., Knox, J. E., Hratchian, H. P., Cross, J. B., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R. E., Yazyev, O., Austin, A. J., Camml, R., Pomelli, C., Ochterski, J. W., Ayala, P. Y., Morokuma, K., Voth, G. A., Salvador, P., Dannenberg, J. J., Zakrzewski, V. G., Dapprich, S., Daniels, A. D., Strain, M. C., Farkas, O., Malick, D. K., Rabuck, A. D., Raghavachari, K., Foresman, J. B., Ortiz, J. V., Cui, Q., Baboul, A. G., Clifford, S., Cioslowski, J., Stefanov, B. B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Martin, R. L., Fox, D. J., Keith, T., Al-Laham, M. A., Peng, C. Y., Nanayakkara, A., Challacombe, M., Gill, P. M. W., Johnson, B., Chen, W., Wong, M. W., Gonzalez, C., and Pople, J. A. (2003) Gaussian 03, revision B.04, Gaussian, Inc., Pittsburgh, PA
50. Becke, A. D. (1993) J. Chem. Phys. 98, 5648-5652
51. Reed, A. E., Weinhold, F. J., and Curtiss, L. A. (1988) Chem. Rev. 88, 899-926
52. MacKerrell, A. D., Bashford, D., Bellott, M., Dunbrack, D. L., Evanseck, J. D., and Field, M. J. (1998) J. Phys. Chem. B 102, 3586-3616
53. Archontis, G., and Simonson, T. (2005) Biophys. J. 88, 3888-3904
54. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaninathan, S., and Karplus, M. (1983) J. Comp. Chem. 4, 187-217
55. Kobayashi, T., Takimura, T., Sekine, R., Vinvent, K., Kamata, K., Sakamoto, K., Nishimura, S., and Yokoyama, S. (2005) J. Mol. Biol. 346, 105-117
56. Simonson, T. (2000) J. Phys. Chem. B 104, 6509-6513
57. Beglov, D., and Roux, B. (1994) J. Chem. Phys. 100, 9050-9063
58. Stote, R. H., States, D. J., and Karplus, M. (1991) J. Chim. Phys. 88, 2419-2433
59. Kraulis, P. J. (1991) Appl. Crystallogr. 24, 946-950
60. Merritt, E. A., and Murphy, M. E. P. (1994) Acta Crystallogr. Sect. D 50, 869-873
61. Boresch, S., Archontis, G., and Karplus, M. (1994) Proteins Struct. Funct. Genet. 20, 25-33
62. Yang, A.-S., and Honig, B. (1993) J. Mol. Biol. 231, 459-474
63. Alexov, E. G., and Gunner, M. R. (1997) Biophys. J. 72, 2075-2093
64. Takita, T., Nakagoshi, M., Inouye, K., and Tonomura, B. (2003) J. Mol. Biol. 325, 677-695
65. Giege, R., and Rees, B. (2005) in Aminoacyl-tRNA Synthetases (Ibba, M., Francklyn, C., Cusack, S., eds) pp. 210-226, Landes Bioscience, Georgetown, TX
66. McQuarrie, D. (1975) Statistical Mechanics, Harper and Row, New York
67. Tajkhorshid, E., Baudry, J., Schulten, K., and Suhai, S. (2000) Biophys. J. 78, 683-693
68. Strajbl, M., Shurki, A., and Warshel, A. (2003) Proc. Natl. Acad. Sci. U. S. A. 100, 14834-14839
69. Warshel, A. (2003) Annu. Rev. Biophys. Biomol. Struct. 32, 425-443