Crystal structure of human tryptophanyl-tRNA synthetase catalytic fragment: Insights into substrate recognition, tRNA binding, and angiogenesis activity

Journal of Biological Chemistry

Volumn 279, Issue 9, 2004, Pages 8378-8388

  Yu, Yadong ^a   Liu, Yunqing ^a   Shen, Ning ^a   Xu, Xiang ^a   Xu, Feng ^a   Jia, Jie ^a   Jin, Youxin ^a   Arnold, Eddy ^b   Ding, Jianping ^a,b  

^a Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^b RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; CONFORMATIONS; CRYSTAL STRUCTURE; ENZYMES; RNA;

CATALYTIC FRAGMENTS; DIMERIC ENZYMES;

BIOCHEMISTRY;

CYTOKINE; TRYPTOPHAN TRANSFER RNA LIGASE;

ALPHA HELIX; ALTERNATIVE RNA SPLICING; AMINOACYLATION; ANGIOGENESIS; ARTICLE; CATALYSIS; CRYSTAL STRUCTURE; ENZYME INACTIVATION; ENZYME STRUCTURE; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DEGRADATION; PROTEIN DOMAIN; RNA BINDING;

ADENOSINE TRIPHOSPHATE; AMINO ACID SEQUENCE; BACILLUS STEAROTHERMOPHILUS; BINDING SITES; CATALYSIS; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; ELECTROPHORESIS, POLYACRYLAMIDE GEL; ENDOPEPTIDASES; HUMANS; HYDROGEN BONDING; HYDROLYSIS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; NEOVASCULARIZATION, PHYSIOLOGIC; PEPTIDE FRAGMENTS; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; RNA, TRANSFER; SEQUENCE ALIGNMENT; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY; TRYPTOPHAN; TRYPTOPHAN-TRNA LIGASE;

BACTERIA (MICROORGANISMS); GEOBACILLUS STEAROTHERMOPHILUS; MAMMALIA;

EID: 1542349274     PISSN: 00219258     EISSN: None     Source Type: Journal    
DOI: 10.1074/jbc.M311284200     Document Type: Article

References (53)

1. Schimmel, P. (1987) Annu. Rev. Biochem. 56, 125-158
2. Webster, T., Tsai, H., Kula, M., Mackie, G. A., and Schimmel, P. (1984) Science 226, 1315-1317
3. Eriani, G., Delarue, M., Poch, O., Gangloff, J., and Moras, D. (1990) Nature 347, 203-206
4. Carter, C. W. (1993) Annu. Rev. Biochem. 62, 715-748
5. Nagel, G., and Doolittle, R. (1995) J. Mol. Evol. 40, 487-498
6. Hountondji, C., Dessen, P., and Blanquet, S. (1986) Biochimie (Paris) 68, 1071-1078
7. Mirande, M. (1991) Prog. Nucleic Acids Res. Mol. Biol. 40, 95-142
8. Kisselev, L. L., and Wilfson, A. D. (1994) Prog. Nucleic Acids Res. Mol. Biol. 48, 83-142
9. Shiba, K. (2002) J. Mol. Evol. 55, 727-733
10. Tolstrup, A. B., Bejder, A., Fleckner, J., and Justesen, J. (1995) J. Biol. Chem. 270, 397-403
11. Turpaev, K. T., Zakhariev, V. M., Sokolova, I. V., Narovlyansky A. N., Amchenkova, A. M., Justesen, J., and Frolova, L. Y. (1996) Eur. J. Biochem. 240, 732-737
12. Xu, F., Chen, X., Xin, L., Chen, L., Jin, Y., and Wang, D. (2001) Nucleic Acids Res. 29, 4125-4133
13. Wakasugi, K., Slike, B. M., Hood, J., Otani, A., Ewalt, K. L., Friedlander, M., Cheresh, D. A., and Schimmel, P. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 173-177
14. Otani, A., Slike, B. M., Dorrell, M. I., Hood, J., Kinder, K., Ewalt, K. L., Cheresh, D., Schimmel, P., and Friedlander, M. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 178-183
15. Kleeman, T. A., Wei, B. B., Simpson, K. L., and First, E. A. (1997) J. Biol. Chem. 272, 14420-14425
16. Wakasugi, K., and Schimmel, P. (1999) Science 284, 147-151
17. Yang, X. L., Skene, R. J., McRee, D. E., and Schimmel, P. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 15369-15374
18. Yang, X.-L., Liu, J., Skene, R. J., Mcree, D. E., and Schimmel, P. (2003) Helv. Chim. Acta 86, 1246
19. Doublie, S., Bricogne, G., Gilmore, C., and Carter, C. W., Jr. (1995) Structure 3, 17-31
20. Ilyin, V., Temple, B., Hu, M., Li, G., Yin, Y., Vachette, P., and Carter, C. W., Jr. (2000) Protein Sci. 9, 218-231
21. Retailleau, P., Huang, X., Yin, Y., Hu, M., Weinreb, V., Vachette, P., Vonrhein, C., Bricogne, G., Roversi, P., Ilyin, V., and Carter, C. W. (2003) J. Mol. Biol. 325, 39-63
22. Xu, F., Jia, J., Jin, Y., and Wang, D. T. (2001) Protein Expression Purif. 23, 296-300
23. Otwinowski, Z., and Minor, W. (1997) Methods Enzymol. 276, 307-326
24. Matthews, B. W. (1968) J. Mol. Biol. 33, 491-497
25. Terwilliger, T. C., and Berendzen, J. (1999) Acta Crystallogr. Sect. D Biol. Crystallogr. 55, 849-861
26. Terwilliger, T. C. (2001) Acta Crystallogr. Sect. D Biol. Crystallogr. 57, 1755-1762
27. Brunger, A. T., Adams, P. D., Clore, G. M., Delano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Acta Crystallogr. Sect. D Biol. Crystallogr. 54, 905-921
28. Pannu, N. S., Murshudov, G. N., Dodson, E. J., and Read, R. J. (1998) Acta Crystallogr. Sect. D Biol. Crystallogr. 54, 1285-1294
29. Jones, T. A., Zou, J. Y., Cowan, S. W., and Keldgaard, M. (1991) Acta Crystallographica A47, 110-119
30. Starzyk, R. M., Webster, T. A., and P., S. (1937) Science 237, 1614-1618
31. Hou, Y. M., Shiba, K., Mottes, C., and Schimmel, P. (1991) Proc. Natl. Acad. Sci. U. S. A. 88, 976-980
32. Zuniga, R., Salazar, J., Canales, M., and Orellana, O. (2002) FEBS Lett. 532, 387-390
33. Rould, M. A., Perona, J. J., Soll, D., and Steitz, T. A. (1989) Science 246, 1135-1142
34. Wakasugi, K., Quinn, C. L., Tao, N., and Schimmel, P. (1998) EMBO J. 17, 297-305
35. Jia, J., Xu, F., Chen, X., Chen, L., Jin, Y., and Wang, D. T. (2002) Biochem. J. 365, 749-756
36. Nureki, O., Vassylyev, D. G., Tateno, M., Shimada, A., Nakama, T., Fukai, S., Konno, M., Hendrickson, T. L., Schimmel, P., and Yokoyama, S. (1998) Science 280, 578-582
37. Silvian, L. F., Wang, J., and Steitz, T. A. (1999) Science 285, 1074-1077
38. Mursinna, R. S., Lincecum, T. L. J., and Martinis, S. A. (2001) Biochemistry 40, 5376-5381
39. Fersht, A. R., Knill-Jones, J. W., Bedouelle, H., and Winter, G. (1988) Biochemistry 27, 1581-1587
40. Praetorius-Ibba, M., Stange-Thomann, N., Kitabatake, M., Ali, K., Soll, I., Carter, C. W., Jr., Ibba, M., and Soll, D. (2000) Biochemistry 39, 13136-13143
41. Yaremchuk, A., Kriklivyi, I., Tukalo, M., and Cusack, S. (2002) EMBO J. 21, 3829-3840
42. Himeno, H., Hasegawa, T., Asahara, H., Tamura, K., and Shimizu, M. (1991) Nucleic Acids Res. 19, 6379-6382
43. Wakasugi, K., Slike, B. M., Hood, J., Otani, A., Ewalt, K., Cheresh, D., and Schimmel, P. (2002) J. Biol. Chem. 277, 20124-20126
44. Otani, A., Kinder, K., Ewalt, K., Otero, F. J., Schimmel, P., and Friedlander, M. (2002) Nat. Med. 8, 1004-1010
45. Hebert, C. A., Vitangcol, R. V., and Baker, J. B. (1991) J. Biol. Chem. 266, 18989-18994
46. Clark-Lewis, I., Schumacher, C., Baggiolini, M., and Moser, B. (1991) J. Biol. Chem. 266, 23128-23134
47. Arai, K. I., Lee, F., Miyajima, S., Arai, N., and Takashi, Y. (1990) Annu. Rev. Biochem. 59, 783-836
48. Sprang, S. R., and Bazan, J. F. (1993) Cur. Opin. Struct. Biol. 3, 815-827
49. Grotzinger, J. (2002) Biochim. Biophys. Acta 1592, 215-223
50. Mueller, T. D., Zhang, J. L., Sebald, W., and Duschl, A. (2002) Biochim. Biophys. Acta 1592, 237-250
51. Higgins, D., Thompson, J., Gibson, T., Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) Nucleic Acids Res. 22, 4673-6480
52. Kabsch, W., and Sander, C. (1983) Biopolymers 22, 2577-2637
53. Gouet, P., Courcelle, E., Stuart, D. I., and Metoz, F. (1999) Bioinformatics 15, 305-308