Modulation of substrate specificity within the amino acid editing site of leucyl-tRNA synthetase

Biochemistry

Volumn 46, Issue 11, 2007, Pages 3331-3337

  Zhai, Yuxin ^a,c   Nawaz, Mir Hussain ^a,b   Lee, Keun Woo ^a,d   Kirkbride, Erin ^a   Briggs, James M ^a   Martinis, Susan A ^a,b  

^a University of Houston   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^c UNIVERSITY OF TEXAS MEDICAL SCHOOL   (United States)

^d Gyeongsang National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BINDING ENERGY; BIOSYNTHESIS; ESCHERICHIA COLI; RNA;

COGNATE AMINO ACIDS; PROTEIN SYNTHESIS; SYNTHETASES;

ENZYMES;

AMINO ACID; AMINO ACID TRANSFER RNA LIGASE; ARGININE; ISOLEUCINE TRANSFER RNA LIGASE; LEUCINE TRANSFER RNA LIGASE; THREONINE; TRANSFER RNA; VALINE;

ARTICLE; BINDING SITE; CONTROLLED STUDY; COVALENT BOND; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; ENZYME SUBSTRATE COMPLEX; ESCHERICHIA COLI; HYDROLYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN SYNTHESIS;

AMINO ACID SEQUENCE; BINDING SITES; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DNA MUTATIONAL ANALYSIS; ESCHERICHIA COLI; LEUCINE-TRNA LIGASE; PROTEIN STRUCTURE, TERTIARY; SUBSTRATE SPECIFICITY;

ESCHERICHIA COLI;

EID: 33947412310     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi061778l     Document Type: Article

References (29)

1. Martinis, S. A., Plateau, P., Cavarelli, J., and Florentz, C. (1999) Aminoacyl-tRNA synthetases: a family of expanding functions, EMBO J. 18, 4591-4596.
2. Martinis, S. A., Plateau, P., Cavarelli, J., and Florentz, C. (1999) Aminoacyl-tRNA synthetases: a new image for a classical family, Biochimie 81, 683-700.
3. Hendrickson, T. L., and Schimmel, P. (2003) Transfer RNA-dependent amino acid discrimination by aminoacyl-tRNA synthetases, in Translation Mechanisms (LaPointe, J., and Brakier-Gingras, L., Eds.) pp 34-64, Klumer Academic/Plenum Publishers, New York.
4. Fersht, A. R. (1977) Editing mechanisms in protein synthesis. Rejection of valine by the isoleucyl-tRNA synthetase, Biochemistry 16, 1025-1030.
5. Fersht, A. R. (1998) Sieves in sequence, Science 280, 541.
6. Fersht, A. R., and Dingwall, C. (1979) Evidence for the double-sieve editing mechanism in protein synthesis. Steric exclusion of isoleucine by valyl-tRNA synthetases, Biochemistry 18, 2627-2631.
7. Cusack, S., Yaremchuk, A., and Tukalo, M. (2000) The 2 Å crystal structure of leucyl-tRNA synthetase and its complex with a leucyl-adenylate analogue, EMBO J. 19, 2351-2361.
8. Nureki, O., Vassylyev, D. G., Tateno, M., Shimada, A., Nakama, T., Fukai, S., Konno, M., Hendrickson, T. L., Schimmel, P., and Yokoyama, S. (1998) Enzyme structure with two catalytic sites for double-sieve selection of substrate, Science 280, 578-582.
9. Val recognition by valyl-tRNA synthetase, RNA 9, 100-111.
10. Starzyk, R. M., Webster, T. A., and Schimmel, P. (1987) Evidence for dispensable sequences inserted into a nucleotide fold, Science 237, 1614-1618.
11. Lin, L., Hale, S. P., and Schimmel, P. (1996) Aminoacylation error correction, Nature 384, 33-34.
12. Leu, Biochemistry 40, 5376-5381.
13. Bishop, A. C., Nomanbhoy, T. K., and Schimmel, P. (2002) Blocking site-to-site translocation of a misactivated amino acid by mutation of a class I tRNA synthetase, Proc. Natl. Acad. Sci. U.S.A. 99, 585-590.
14. Lincecum, T. L., Jr., Tukalo, M., Yaremchuk, A., Mursinna, R. S., Williams, A. M., Sproat, B. S., Van Den Eynde, W., Link, A., Van Calenbergh, S., Grøtli, M., Martinis, S. A., and Cusack, S. (2003) Structural and mechanistic basis of pre- and posttransfer editing by leucyl-tRNA synthetase, Mol. Cell 11, 951-963.
15. Fukai, S., Nureki, O., Sekine, S., Shimada, A., Tao, J., Vassylyev, D. G., and Yokoyama, S. (2000) Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase, Cell 103, 793-803.
16. Mursinna, R. S., Lee, K. W., Briggs, J. M., and Martinis, S. A. (2004) Molecular dissection of a critical specificity determinant within the amino acid editing domain of leucyl-tRNA synthetase, Biochemistry 43, 155-165.
17. Mursinna, R. S., and Martinis, S. A. (2002) Rational design to block amino acid editing of a tRNA synthetase, J. Am. Chem. Soc. 124, 7286-7287.
18. Tang, Y., and Tirrell, D. A. (2002) Attenuation of the editing activity of the Escherichia coli leucyl-tRNA synthetase allows incorporation of novel amino acids into proteins in vivo, Biochemistry 41, 10635-10645.
19. Tocchini-Valentini, G., Saks, M. E., and Abelson, J. (2000) tRNA leucine identity and recognition sets, J. Mol. Biol. 298, 779-793.
20. Cazenave, C., and Uhlenbeck, O. C. (1994) RNA template-directed RNA synthesis by T7 RNA polymerase, Proc. Natl. Acad. Sci. U.S.A. 91, 6972-6976.
21. Zhai, Y., and Martinis, S. A. (2005) Two conserved threonines collaborate in the Escherichia coli leucyl-tRNA synthetase amino acid editing mechanism, Biochemistry 44, 15437-15443.
22. Martinis, S. A., and Fox, G. E. (1997) Non-standard amino acid recognition by Escherichia coli leucyl-tRNA synthetase, Nucleic Acids Symp. Ser. 36, 125-128.
23. Leu in the post-transfer-editing conformation, Nat. Struct. Mol. Biol. 12, 923-930.
24. Leu reveal two modes of discriminator-base recognition, Nat. Struct. Mol. Biol. 12, 915-922.
25. Schimmel, P., and Ribas de Pouplana, L. (2001) Formation of two classes of tRNA synthetases in relation to editing functions and genetic code, Cold Spring Harb Symp. Quant. Biol. 66, 161-166.
26. Fukunaga, R., Fukai, S., Ishitani, R., Nureki, O., and Yokoyama, S. (2004) Crystal structures of the CP1 domain from Thermus thermophilus isoleucyl-tRNA synthetase and its complex with L-valine, J. Biol. Chem. 279, 8396-8402.
27. Fukunaga, R., and Yokoyama, S. (2006) Structural basis for substrate recognition by the editing domain of isoleucyl-tRNA synthetase, J. Mol. Biol. 359, 901-912.
28. Hendrickson, T. L., Nomanbhoy, T. K., de Crecy-Lagard, V., Fukai, S., Nureki, O., Yokoyama, S., and Schimmel, P. (2002) Mutational separation of two pathways for editing by a class I tRNA synthetase, Mol. Cell 9, 353-362.
29. Schmidt, E. (1996) Amino acid recognition by a class I tRNA synthetase, Ph.D. Thesis, Massachusetts Institute of Technology, Cambridge, Massachusetts.