Structural plasticity of an aminoacyl-tRNA synthetase active site

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

Volumn 103, Issue 17, 2006, Pages 6483-6488

  Turner, James M ^a   Graziano, James ^a   Spraggon, Glen ^b   Schultz, Peter G ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b GENOMICS INSTITUTE OF THE NOVARTIS RESEARCH FOUNDATION   (United States)

Author keywords

Expanded genetic code; Molecular evolution; Unnatural amino acids; X ray crystal structure

Indexed keywords

3 (2 NAPHTHYL)ALANINE; 4 ACETYLPHENYLALANINE; 4 BROMOPHENYLALANINE; AMINO ACID TRANSFER RNA LIGASE; AMINOACYL TRANSFER RNA; DNA; PHENYLALANINE; UNCLASSIFIED DRUG;

ALPHA HELIX; AMINO ACID ANALYSIS; ARTICLE; CHEMICAL INTERACTION; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; EUKARYOTE; HYDROGEN BOND; METHANOCOCCUS JANNASCHII; MOLECULAR RECOGNITION; NONHUMAN; PLASTICITY; PRIORITY JOURNAL; PROKARYOTE;

ALANINE; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; HYDROGEN BONDING; METHANOCOCCUS; MODELS, MOLECULAR; MUTAGENESIS; NAPHTHALENES; PHENYLALANINE; PROTEIN CONFORMATION; RECOMBINANT PROTEINS; SUBSTRATE SPECIFICITY; TYROSINE-TRNA LIGASE;

EUKARYOTA; METHANOCALDOCOCCUS JANNASCHII; PROKARYOTA;

EID: 33646256352     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0601756103     Document Type: Article

References (48)

1. Bock, A., Forchhammer, K., Heider, J., Leinfelder, W., Sawers, G., Veprek, B. & Zinoni, F. (1991) Mol. Microbiol. 5, 515-520.
2. Srinivasan, G., James, C. M. & Krzycki, J. A. (2002) Science 296, 1459-1462.
3. Polycarpo, C., Ambrogelly, A., Bérubé, A., Winbush, S. M., McCloskey, J. A., Crain, P. F., Wood, J. L. & Söll, D. (2004) Proc. Natl. Acad. Sci. USA 101, 12450-12454.
4. Wang, L. & Schultz, P. G. (2004) Angew. Chem. Int. Ed. 44, 34-66.
5. Wang, L., Xie, J. & Schultz, P. G. (2006) Annu. Rev. Biophys. Biomol. Struct. 35, 225-249.
6. Wang, L., Brock, A., Herberich, B. & Schultz, P. G. (2001) Science 292, 498-500.
7. Zhang, Z., Gildersleeve, J., Yang, Y.-Y., Xu, R., Loo, J. A., Uryu, S., Wong, C.-H. & Schultz, P. G. (2004) Science 303, 371-373.
8. Chin, J. W., Martin, A. B., King, D. S., Wang, L. & Schultz, P. G. (2002) Proc. Natl. Acad. Sci. USA 99, 11020-11024.
9. Wang, L., Zhang, Z., Brock, A. & Schultz, P. G. (2003) Proc. Natl. Acad. Sci. USA 100, 56-61.
10. Chin, J. W., Santoro, S. W., Martin, A. B., King, D. S., Wang, L. & Schultz, P. G. (2002) J. Am. Chem. Soc. 124, 9026-9027.
11. Xie, J., Wang, L., Wu, N., Brock, A., Spraggon, G. & Schultz, P. G. (2004) Nat. Biotechnol. 22, 1297-1301.
12. Turner, J. M., Graziano, J., Spraggon, G. & Schultz, P. G. (2005) J. Am. Chem. Soc. 127, 14976-14977.
13. Wang, L., Brock, A. & Schultz, P. G. (2002) J. Am. Chem. Soc. 124, 1836-1837.
14. Brick, P., Bhat, T. N. & Blow, D. M. (1989) J. Mol. Biol. 208, 83-98.
15. Zhang, Y., Wang, L., Schultz, P. G. & Wilson, I. A. (2005) Protein Sci. 14, 1340-1349.
16. Kobayashi, T., Nureki, O., Ishitani, R., Yaremchuk, A., Tukalo, M., Cusack, S., Sakamoto, K. & Yokoyama, S. (2003) Nat. Struct. Biol. 10, 425-432.
17. Richardson, J. S. & Richardson, D. C. (1988) Science 240, 1648-1652.
18. Zhou, H. X., Lyu, P., Wemmer, D. E. & Kallenbach, N. R. (1994) Proteins Struct. Funct. Genet. 18, 1-7.
19. Lyu, P. C., Wemmer, D. E., Zhou, H. X., Pinker, R. J. & Kallenbach, N. R. (1993) Biochemistry 32, 421-425.
20. Presta, L. G. & Rose, G. D. (1988) Science 240, 1632-1641.
21. Pal, L. & Basu, G. (1999) Protein Eng. 12, 811-814.
22. Vasseur, C., Blouquit, Y., Kister, J., Promé, D., Kavanaugh, J. S., Rogers, P. H., Guillemin, C., Arnone, A., Galacteros, F., Poyart, C., et al. (1992)J. Biol. Chem. 267, 12682-12691.
23. Fukuyama, K., Kunishima, N., Amada, F., Kubota, T. & Matsubara, H. (1995) J. Biol. Chem. 270, 21884-21892.
24. Saraogi, I., Vijay, V. G., Das, S., Sekar, K. & Row, T. N. G. (2003) Crystal Eng. 6, 69-77.
25. Nagaraj, B., Narasimhamurthy, T., Yathirajan, H. S., Nagaraja, P., Narasegowda, R. S. & Rathore, R. S. (2005) Acta Crystallogr. C 61, o177-o180.
26. Prusiner, P. & Sundaralingam, M. (1973) Acta Crystallogr. B 29, 2328-2334.
27. Kobayashi, T., Sakamoto, K., Takimura, T., Sekine, R., Vincent, K., Kamata. K., Nishimura, S. & Yokoyama, S. (2005) Proc. Natl Acad. Sci. USA 102, 1366-1371.
28. Buddha, M. R. & Crane, B. R. (2005) Nat. Struct. Mol. Biol. 12, 274-275.
29. Hurley, J. H., Chen, R. & Dean, A. M. (1996) Biochemistry 35, 5670-5678.
30. Chen, R., Greer, A. & Dean, A. M. (1996) Proc. Natl. Acad. Sci. USA 93, 12171-12176.
31. Oue, S., Okamoto, A., Yano, T. & Kagamiyama, H. (1999) J. Biol. Chem. 274, 2344-2349.
32. Lin, K., Rath, V. L., Dai, S. C., Fletterick, R. J. & Hwang, P. K. A. (1996) Science 273, 1539-1541.
33. Willis, M. A., Bishop, B., Regan, L. & Brunger, A. T. (2000) Structure (London) 8, 1319-1328.
34. Glykos, N. M., Cesareni, G. & Kokkinidis, M. (1999) Structure (London) 7, 597-603.
35. Yin, J., Beuscher, A. E., IV, Andryski, S. E., Stevens, R. C. & Schultz, P. G. (2003) J. Mol. Biol. 330, 651-656.
36. Wedemayer, G. J., Patten, P. A., Wang, L. H., Schultz, P. G. & Stevens, R. C. (1997) Science 276, 1665-1669.
37. Cordes, M. H. J., Walsh, N. P., McKnight, C. J. & Sauer, R. T. (2003) J. Mol. Biol. 326, 899-909.
38. Otwinowski, Z. & Minor, W. (1997) Methods Enzymol. 276, 307-326.
39. Vagin, A. & Teplyakov, A. (1997) J. Appl. Cryst. 30, 1022-1025.
40. Read, R. J. (1986) Acta Crystallogr. A 42, 140-149.
41. Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991) Acta Crystallogr. A 47, 110-119.
42. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997) Acta Crystallogr. D 53, 240-255.
43. Lamzin, V. S. & Wilson, K. S. (1993) Acta Crystallogr. D 49, 129-147.
44. Project, C. C. (1994) Acta Crystallogr. D 50, 760-763.
45. Esnouf, R. M. (1997) J. Mol. Graphics Model. 15, 132-134.
46. Kraulis, P. J. (1991) J. Appl. Crystallogr. 24, 946-950.
47. Merritt, E. A. & Murphy, M. E. P. (1994) Acta Crystallogr. D 50, 869-873.
48. DeLano, W. L. (2002) The PYMOL User's Manual (DeLano Scientific, San Carlos, CA).