Limited Set of Amino Acid Residues in a Class Ia Aminoacyl-tRNA Synthetase Is Crucial for tRNA Binding

Biochemistry

Volumn 42, Issue 51, 2003, Pages 15092-15101

  Geslain, Renaud ^a   Bey, Gilbert ^b   Cavarelli, Jean ^b   Eriani, Gilbert ^a  

^a INST DE BIOL MOLEC ET CELLULAIRE   (France)

^b CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; CATALYSIS; CRYSTALLOGRAPHY; ENZYMES; MUTAGENESIS; RNA; YEAST;

MUTATIONS;

AMINO ACIDS;

AMINO ACID TRANSFER RNA LIGASE; MAGNESIUM; TRANSFER RNA;

AMINOACYLATION; ANTICODON; ARTICLE; CRYSTALLOGRAPHY; GENE OVEREXPRESSION; MUTAGENESIS; MUTATION; NEUROSPORA CRASSA; NONHUMAN; NORTHERN BLOTTING; PRIORITY JOURNAL; PROTEIN RNA BINDING; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE;

ACYLATION; ALANINE; AMINO ACIDS; ANTICODON; ARGININE-TRNA LIGASE; BINDING SITES; GENES, LETHAL; MUTAGENESIS, SITE-DIRECTED; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; RNA, TRANSFER, ARG; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

BACTERIA (MICROORGANISMS); FUNGI; NEUROSPORA CRASSA; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE;

EID: 0348224052     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi035581u     Document Type: Article

References (48)

1. 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.
2. Cusack, S., Berthet-Colominas, C., Härtlein, M., Nassar, N., and Leberman, R. (1990) A second class of synthetase structure revealed by X-ray analysis of Escherichia coli seryl-tRNA synthetase, Nature 347, 249-255.
3. Cavarelli, J., Delagoutte, B., Eriani, G., Gangloff, J., and Moras, D. (1998) L-Arginine recognition by yeast arginyl-tRNA synthetase, EMBO J. 17, 5438-5448.
4. Delagoutte, B., Moras, D., and Cavarelli, J. (2000) tRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates binding, EMBO J. 19, 5599-5610.
5. Geslain, R., Martin, F., Delagoutte, B., Cavarelli, J., Gangloff, J., and Eriani, G. (2000) In vivo selection of lethal mutations reveals two functional domains in arginyl-tRNA synthetase, RNA 6, 434-448.
6. Kunkel, T. A. (1985) Rapid and efficient site-specific mutagenesis without phenotypic selection, Proc. Natl. Acad. Sci. U.S.A. 82, 488-492.
7. Eriani, G., Cavarelli, J., Martin, F., Dirheimer, G., Moras, D., and Gangloff, J. (1993) Role of dimerization in yeast aspartyl-tRNA synthetase and importance of the class II invariant proline, Proc. Natl. Acad. Sci. U.S.A. 90, 10816-10820.
8. Varshney, U., Lee, C. P., and RajBhandary, U. L. (1991) Direct analysis of aminoacylation levels of tRNAs in vivo. Application to studying recognition of E. coli initiator tRNA mutants by glutaminyl-tRNA synthetase, J. Biol. Chem. 266, 24712-24718.
9. Asp with arginine, J. Intl. Res. Commun. 1, 8.
10. McClain, W. H., and Foss, K. (1988) Changing the acceptor identity of a transfer RNA by altering nucleotides in a "variable pocket", Science 241, 1804-1807.
11. Lys identity elements, Nucl. Acids Res. 20, 2335-2339.
12. Schulman, L. H., and Pelka, H. (1989) The anticodon contains a major element of the identity of arginine transfer RNAs, Science 246, 1595-1597.
13. Arg eliminates species-specific aminoacylation. Biochim. Biophys. Acta 1473, 356-362.
14. Geslain, R., Martin, R., Camasses, A., and Eriani, G. (2003) A yeast knockout strain to discriminate between active and inactive tRNA molecules, Nucl. Acids Res. 31, 4729-4737.
15. Shimada, A., Nureki, O., Goto, M., Takahashi, S., and Yokoyama, S. (2001) Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase, Proc. Natl. Acad. Sci. U.S.A. 98, 13537-13542.
16. Sprinzl, M., Horn, C., Brown, M., Ioudovitch, A., and Steinberg, S. (1998) Compilation of tRNA sequences and sequences of tRNA genes, Nucl. Acids Res. 26, 148-153.
17. Sissler, M., Giegé, R., and Florentz, C. (1996) Arginine aminoacylation identity is context-dependent and ensured by alternate recognition sets in the anticodon loop of accepting tRNA transcripts, EMBO J. 15, 5069-5076.
18. Newberry, K. J., Hou, Y. M., and Perona, J. J. (2002) Structural origins of amino acid selection without editing by cysteinyl-tRNA synthetase, EMBO J. 21, 2778-2787.
19. Mechulam, Y., Schmitt, E., Maveyraud, L., Zelwer, C., Nureki, O., Yokoyama, S., Konno, M., and Blanquet, S. (1999) Crystal structure of Escherichia coli methionyl-tRNA synthetase highlights species-specific features, J. Mol. Biol. 294, 1287-1297.
20. Cusack, S., Yaremchuk, A., and Tukalo, M. (2000) The 2 Å crystal structure of leucyl-tRNA synthetase and its complex with a leucyladenylate analogue, EMBO J. 19, 2351-2361.
21. Nureki, O., Vassylyev, D., Tateno, M., Shimada, A., Nakama, T., Fukai, S., Konno, M., Hendrickson, T., Schimmel, P., and Yokoyama, S. (1998) Enzyme structure with two catalytic sites for double-sieve selection of substrate, Science 280, 578-582.
22. Val and valyl-tRNA synthetase, Cell 103, 793-803.
23. Ile and mupirocin, Science 285, 1074-1077.
24. Val recognition by valyl-tRNA synthetase, RNA 9, 100-111.
25. Ghosh, G., Kim, H. Y., Demaret, J. P., Brunie, S., and Schulman, L. H. (1991) Arginine-395 is required for efficient in vivo and in vitro aminoacylation of transfer RNAs by Escherichia coli methionyl-transfer RNA synthetase, Biochemistry 30, 11767-11774.
26. Kim, H. Y., Pelka, H., Brunie, S., and Schulman, L. H. (1993) Two separate peptides in Escherichia coli methionyl-tRNA synthetase form the anticodon binding site for methionine, Biochemistry 32, 10506-10511.
27. Despons, L., Senger, B., Fasiolo, F., and Walter, P. (1992) Binding of the yeast tRNA(Met) anticodon by the cognate methionyl-tRNA synthetase involves at least two independent peptide regions, J. Mol. Biol. 225, 897-907.
28. Kim, S., Ribas de Pouplana, L., and Schimmel, P. (1994) An RNA binding site in a tRNA synthetase with a reduced set of amino acids, Biochemistry 33, 11040-11045.
29. Ghosh, G., Pelka, H., and Schulman, L. D. H. (1990) Identification of the anticodon recognition site of Escherichia coli methionyl-tRNA synthetases, Biochemistry 29, 2220-2225.
30. Schmitt, E., Meinnel, T., Panvert, M., Mechulam, Y., and Blanquet, S. (1993) Two acidic residues of Escherichia coli methionyl-tRNA synthetase act as negative discriminants towards the binding of noncognate tRNA anticodons, J. Mol. Biol. 233, 615-628.
31. Meinnel, T., Mechulam, Y., LeCorre, D., Panvert, M., Blanquet, S., and Fayat, G. (1991) Selection of suppressor methionyl-tRNA synthetases: mapping the tRNA anticodon binding site, Proc. Natl. Acad. Sci. U.S.A. 88, 291-295.
32. Auld, D. S., and Schimmel, P. (1995) Switching recognition of two tRNA synthetases with an amino acid swap in a designed peptide, Science 267, 1994-1996.
33. Perret, V., Garcia, A., Grosjean, H., Ebel, J.-P., Florentz, C., and Giegé, R. (1990) Relaxation of transfer RNA specificity by removal of modified nucleotides, Nature 344, 787-789.
34. Pütz, J., Florentz, C., Benseler, F., and Giegé, R. (1994) A single methyl group prevents the mischarging of a tRNA, Nat. Struct. Biol. 1, 580-582.
35. Rould, M. A., Perona, J. J., and Steitz, T. A. (1991) Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase, Nature 352, 213-218.
36. Sherlin, L., and Perona, J. (2003) tRNA-dependent active site assembly in a class I aminoacyl-tRNA synthetase, Structure 11, 591-603.
37. Sekine, S., Nureki, O., Dubois, D., Bernier, S., Chenevert, R., Lapointe, J., Vassylyev, D., and Yokoyama, S. (2003) ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding, EMBO J. 22, 676-688.
38. Lazard, M., Agou, F., Kerjan, P., and Mirande, M. (2000) The tRNA-dependent activation of arginine by arginyl-tRNA synthetase requires interdomain communication, J. Mol. Biol. 302, 991-1004.
39. Kern, D., and Lapointe, J. (1979) The 20 aminoacyl-tRNA synthetases from Escherichia coli. General separation procedure and comparison of the influence of pH and divalent cations on their catalytic activities, Biochimie 61, 1257-1272.
40. Airas, R. K. (1996) Differences in the magnesium dependences of the class I and class II aminoacyl-tRNA synthetases from Escherichia coli, Eur. J. Biochem. 240, 223-231.
41. Gangloff, J., Schutz, A., and Dirheimer, G. (1976) Arginyl-tRNA synthetase from baker's yeast. Purification and some properties, Eur. J. Biochem. 65, 177-182.
42. 2+ concentration, FEBS Lett. 411, 123-127.
43. Romani, A., and Scarpa, A. (1992) Regulation of cell magnesium, Arch. Biochem. Biophys. 298, 1-12.
44. 2+ by Saccharomyces cerevisiae, Biochim. Biophys. Acta 1323, 310-318.
45. 2+-dependent control of its synthesis and degradation, J. Biol. Chem. 276, 16216-16222.
46. Kiga, D., Sakamoto, K., Sato, S., Hirao, I., and Yokoyama, S. (2001) Shifted positioning of the anticodon nucleotide residues of amber suppressor tRNA species by Escherichia coli arginyl-tRNA synthetase, Eur. J. Biochem. 268, 6207-6213.
47. DeLano, W. L. (2002) The PyMOL Molecular Graphics System, http://www.pymol.org.
48. Perona, J. J., Rould, M. A., and Steitz, T. A. (1993) Structural basis for transfer RNA aminoacylation by Escherichia coli glutaminyl-tRNA synthetase, Biochemistry 32, 8758-8771.