Structure of human tryptophanyl-tRNA synthetase in complex with tRNA Trp reveals the molecular basis of tRNA recognition and specificity

Nucleic Acids Research

Volumn 34, Issue 11, 2006, Pages 3246-3258

  Shen, Ning ^a,b   Guo, Litao ^a,b   Yang, Bei ^a,b   Jin, Youxin ^a   Ding, Jianping ^a  

^a INSTITUTE OF BIOCHEMISTRY AND CELL BIOLOGY   (China)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

TRYPTOPHAN; TRYPTOPHAN TRANSFER RNA; TRYPTOPHAN TRANSFER RNA LIGASE; WARS PROTEIN, HUMAN;

AMINO ACID SEQUENCE; ANIMAL; ANTICODON; ARTICLE; CATTLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; ENZYME SPECIFICITY; HUMAN; METABOLISM; MOLECULAR GENETICS; PROTEIN BINDING; PROTEIN TERTIARY STRUCTURE; SPECIES DIFFERENCE; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; ANIMALS; ANTICODON; CATTLE; CRYSTALLOGRAPHY, X-RAY; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; RNA, TRANSFER, TRP; SPECIES SPECIFICITY; SUBSTRATE SPECIFICITY; TRYPTOPHAN; TRYPTOPHAN-TRNA LIGASE;

EID: 33745794737     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl441     Document Type: Article

References (33)

1. O'Donoghue,P. and Luthey-Schulten,Z. (2003) On the evolution of structure in aminoacyl-tRNA synthetases. Microbiol. Mol. Biol. Rev., 67, 550-573.
2. Woese,C., Olsen,G.J., Ibba,M. and Söll,D. (2000) Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol. Mol. Biol. Rev., 64, 202-236. (Pubitemid 30143846)
3. Arnez,J.G. and Moras,D. (1997) Structural and functional considerations of the aminoacylation reaction. Trends Biochem. Sci., 22, 211-216. (Pubitemid 27246637)
4. Cusack,S. (1997) Aminoacyl-tRNA synthetases. Curr. Opin. Struct. Biol., 7, 881-889.
5. Eriani,G., Delarue,M., Poch,O., Gangloff,J. and Moras,D. (1990) Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature, 347, 203-206.
6. Brick,P., Bhat,T.N. and Blow,D.M. (1989) Structure of tyrosyl-tRNA synthetase refined at 2.3 Å resolution: interaction of the enzyme with the tyrosyl adenylate intermediate. J. Mol. Biol., 208, 83-98. (Pubitemid 19191519)
7. Brown,J.R., Robb,F.T., Weiss,R. and Doolittle,W.F. (1997) Evidence for the early divergence of tryptophanyl- and tyrosyl-tRNA synthetases. J. Mol. Evol., 45, 9-16. (Pubitemid 27284333)
8. Cusack,S. (1995) Eleven down and nine to go. Nature Struct. Biol., 2, 824-831.
9. Doublie,S., Bricogne,G., Gilmore,C. and Carter,C.W.,Jr (1995) Tryptophanyl-tRNA synthetase crystal structure reveals an unexpected homology to tyrosyl-tRNA synthetase. Structure, 3, 17-31.
10. Yang,X.L., Otero,F.J., Skene,R., McRee,D.E., Schimmel,P. and de Pouplana,L.R. (2003) Crystal structures that suggest late development of genetic code components for differentiating aromatic side chains. Proc. Natl Acad. Sci. USA, 100, 15376-15380. (Pubitemid 38020997)
11. Yang,X.L., Skene,R.J., McRee,D.E. and Schimmel,P. (2002) Crystal structure of a human aminoacyl-tRNA synthetase cytokine. Proc. Natl Acad. Sci. USA, 99, 15369-15374. (Pubitemid 35403941)
12. Yu,Y., Liu,Y., Shen,N., Xu,X., Xu,F., Jia,J., Jin,Y., Arnold,E. and Ding,J. (2004) Crystal structure of human tryptophanyl-tRNA synthetase catalytic fragment. J. Biol. Chem., 279, 8378-8388.
13. Otani,A., Slike,B.M., Dorrell,M.I., Hood,J., Kinder,K., Ewalt,K.L., Cheresh,D., Schimmel,P. and Friedlander,M. (2002) A fragment of human TrpRS as a potent antagonist of ocular angiogenesis. Proc. Natl Acad. Sci. USA, 99, 178-183. (Pubitemid 34060337)
14. Wakasugi,K. and Schimmel,P. (1999) Two distinct cytokines released from a human aminoacyl-tRNA synthetases. Science, 284, 147-151. (Pubitemid 29282068)
15. Wakasugi,K., Slike,B.M., Hood,J., Otani,A., Ewalt,K.L., Friedlander,M., Cheresh,D.A. and Schimmel,P. (2002) A human aminoacyl-tRNA synthetase as a regulator of angiogenesis. Proc. Natl Acad. Sci. USA, 99, 173-177. (Pubitemid 34060336)
16. Ilyin,V., Temple,B., Hu,M., Li,G., Yin,Y., Vachette,P. and Carter,C.W.,Jr (2000) 2.9 Å crystal structure of ligand-free tryptophanyl-tRNA synthetase: domain movements fragment the adenine nucleotide binding site. Protein Sci., 9, 218-231. (Pubitemid 30126995)
17. Kise,Y., Lee,S.W., Park,S.G., Fukai,S., Sengoku,T., Ishii,R., Yokoyama,S., Kim,S. and Nureki,O. (2004) A short peptide insertion crucial for angiostatic activity of human tryptophanyl-tRNA synthetase. Nature Struct. Mol. Biol., 11, 149-156. (Pubitemid 38146518)
18. Kobayashi,T., Nureki,O., Ishitani,R., Yaremchuk,A., Tukalo,M., Cusack,S., Sakamoto,K. and Yokoyama,S. (2003) Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion. Nature Struct. Mol. Biol., 10, 425-432. (Pubitemid 36637639)
19. Yaremchuk,A., Kriklivyi,I., Tukalo,M. and Cusack,S. (2002) Class I tyrosyl-tRNA synthetase has a class II mode of tRNA recognition. EMBO J., 21, 3829-3840. (Pubitemid 34787055)
20. Xu,F., Chen,X., Xin,L., Chen,L., Jin,Y. and Wang,D. (2001) Species-pecific differences in the operational RNA code for aminoacylation of tRNATrp. Nucleic Acids Res., 29, 4125-4133. (Pubitemid 33019556)
21. Xue,H., Shen,W., Giege,R. and Wong,J.T. (1993) Identity elements of tRNATrp. J. Biol. Chem., 268, 9316-9322.
22. Otwinowski,Z. and Minor,W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Meth. Enzymol., 276A, 307-326. (Pubitemid 27085611)
23. Ruff,M., Krishnaswamy,S., Boeglin,M., Poterszman,A., Mitschler,A., Podjarny,A., Rees,B., Thierry,J.C. and Moras,D. (1991) Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyltRNA synthetase complexed with tRNAAsp. Science, 252, 1682-1689. (Pubitemid 21917086)
24. Brünger,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. et al. (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Cryst., D54, 905-921.
25. Jones,T.A., Zou,J.Y., Cowan,S.W. and Kjeldgaard,M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst., A47, 110-119.
26. Trp in Bacillus subtilis. J. Biol. Chem., 279, 41960-41965.
27. Trp from three biological domains. J. Biol. Chem., 277, 14343-14349.
28. Gln and ATP at 2.8 Å resolution. Science, 246, 1135-1142.
29. Rath,V.L., Silvian,L.F., Beijer,B., Sproat,B.S. and Steitz,T.A. (1998) How glutaminyl-tRNA synthetase selects glutamine. Structure, 6, 439-449. (Pubitemid 28205516)
30. Yesland,K.D. and Johnson,J.D. (1993) Anticodon bases C34 and C35 are major, positive identity elements in Saccharomyces cerevisiae tRNATrp. Nucleic Acids Res., 21, 5079-5084. (Pubitemid 23342516)
31. Retailleau,P., Huang,X., Yin,Y., Hu,M., Weinreb,V., Vachette,P., Vonrhein,C., Bricogne,G., Roversi,P., Ilyin,V. et al. (2003) Interconversion of ATP binding and conformational free energies by ryptophanyl-tRNA synthetase: structures of ATP bound to open and closed, pre-transition-state conformations. J. Mol. Biol., 325, 39-63. (Pubitemid 36152997)
32. Sprinzl,M., Horn,C., Brown,M., Loudovitch,A. and Steinberg,S. (1998) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res., 26, 148-153. (Pubitemid 28295271)
33. Trp by tryptophanyl-tRNA synthetase from Bacillus subtilis. Biochemistry, 41, 8087-8092.