Solvation change and ion release during aminoacylation by aminoacyl-tRNA synthetases

Nucleic Acids Research

Volumn 31, Issue 20, 2003, Pages 6035-6042

  Banerjee, Rajat ^a   Mandal, Amit Kumar ^a   Saha, Rajesh ^a   Guha, Soumi ^a   Samaddar, Soma ^a   Bhattacharyya, Anusree ^a   Roy, Siddhartha ^a  

^a BOSE INSTITUTE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE; GLUTAMATE TRANSFER RNA LIGASE; GLUTAMINE TRANSFER RNA LIGASE; POTASSIUM CHLORIDE; TRANSFER RNA; WATER;

AMINOACYLATION; ARTICLE; CONCENTRATION RESPONSE; CONFORMATIONAL TRANSITION; CONSTANTS AND COEFFICIENTS; CONTROLLED STUDY; ENZYME MECHANISM; ESCHERICHIA COLI; ION TRANSPORT; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; NONHUMAN; OSMOTIC PRESSURE; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN TARGETING; RNA BINDING; SOLVATION; STOICHIOMETRY; WATER TRANSPORT;

AMINO ACYL-TRNA SYNTHETASES; DOSE-RESPONSE RELATIONSHIP, DRUG; GLUTAMATE-TRNA LIGASE; KINETICS; POTASSIUM CHLORIDE; PROTEIN BINDING; RNA, TRANSFER, AMINO ACYL; RNA, TRANSFER, GLU; SOLVENTS; WATER;

ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0344874252     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg779     Document Type: Article

References (32)

1. Soll, D. (1990) The accuracy of aminoacylation-ensuring the fidelity of the genetic code. Experientia, 46, 1089-1096.
2. Giege., R., Sissler, M. and Florentz, C. (1998) Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res., 26, 5017-5035.
3. Ibba, M. and Soll, D. (1999) Quality control mechanisms during translation. Science, 286, 1893-1897.
4. Garner, M.M. and Rau, D.C. (1995) Water release associated with specific binding of gal repressor. EMBO J., 14, 1257-1263.
5. Ha, J.H., Capp, M.W., Hohenwalter, M.D., Baskerville, M. and Record, M.T. (1992) Thermodynamic stoichiometries of participation of water, cations and anions in specific and non-specific binding of lac repressor to DNA. Possible thermodynamic origins of the 'glutamate effect' on protein-DNA interactions. J. Mol. Biol., 228, 252-264.
6. de Haseth, P.L., Lohman, T.M. and Record, M.T. (1977) Nonspecific interaction of lac repressor with DNA: an association reaction driven by counterion release. Biochemistry, 16, 4783-4790.
7. Lynch, T.W. and Sligar, S.G. (2000) Macromolecular hydration changes associated with BamHI binding and catalysis. J. Biol. Chem., 275, 30561-30565.
8. Robinson, C.R. and Sligar, S.G. (1998) Changes in solvation during DNA binding and cleavage are critical to altered specificity of the EcoRI endonuclease. Proc. Natl Acad. Sci. USA, 95, 2186-2191.
9. Hayase, Y., Jahn, M., Rogers, M.J., Sylvers, L.A., Koizumi, M., Inoue, H., Ohtsuka, E. and Soll, D. (1992) Recognition of bases in Escherichia coli tRNA(Gln) by glutaminyl-tRNA synthetase: a complete identity set. EMBO J., 11, 4159-4165.
10. Hou, Y.M. and Schimmel, P. (1989) Modeling with in vitro kinetic parameters for the elaboration of transfer RNA identity in vivo. Biochemistry, 28, 4942-4947.
11. Brisson, A., Brun, Y.V., Bell, A.W., Roy, P.H. and Lapointe, J. (1989) Overproduction and domain structure of the glutamyl-tRNA synthetase of Escherichia coli. Biochem. Cell Biol., 67, 404-410.
12. Hoben, P., Royal, N., Cheung, A., Yamao, F., Biemann, K. and Soll, D. (1982) Escherichia coli glutaminyl-tRNA synthetase. II. Characterization of the glnS gene product. J. Biol. Chem., 257, 11644-11650.
13. Bhattacharyya, T., Bhattacharyya, A. and Roy, S. (1991) A fluorescence spectroscopic study of glutaminyl-tRNA synthetase from Escherichia coli and its implications for the enzyme mechanism. Eur. J. Biochem., 200, 739-745.
14. Perona, J.J., Swanson, R., Steitz, T.A. and Soll, D. (1988) Overproduction and purification of Escherichia coli tRNA(2gln) and its use in crystallization of the glutaminyl-tRNA synthetase-tRNA(Gln) complex. J. Mol. Biol., 202, 121-126.
15. Sylvers, L.A., Rogers, K.C., Shimizu, M., Ohtsuka, E. and Soll, D. (1993) A 2-thiouridine derivative in tRNAGlu is a positive determinant for aminoacylation by Escherichia coli glutamyl-tRNA synthetase. Biochemistry, 32, 3836-3841.
16. Madore, E., Florentz, C., Giege, R. and Lapointe, J. (1999) Magnesium-dependent alternative foldings of active and inactive Escherichia coli tRNA(Glu) revealed by chemical probing. Nucleic Acids Res., 27, 3583-3588.
17. Record, M.T., Jr, deHaseth, P.L. and Lohman, T.M. (1977) Interpretation of monovalent and divalent cation effects on the lac repressor-operator interaction. Biochemistry, 16, 4791-4796.
18. Kern, D. and Lapointe, J. (1981) The catalytic mechanism of glutamyl-tRNA synthetase of Escherichia coli. A steady-state kinetic investigation. Eur. J. Biochem., 115, 29-38.
19. Lloyd, A.J., Thomann, H.U., Ibba, M. and Soll, D. (1995) A broadly applicable continuous spectrophotometric assay for measuring aminoacyl-tRNA synthetase activity. Nucleic Acids Res., 23, 2886-2892.
20. Jahn, M., Rogers, M.J. and Soll, D. (1991) Anticodon and acceptor stem nucleotides in tRNA(Gln) are major recognition elements for E. coli glutaminyl-tRNA synthetase. Nature, 352, 258-260.
21. Rogers, K.C. and Soll, D. (1993) Discrimination among tRNAs intermediate in glutamate and glutamine acceptor identity. Biochemistry, 32, 14210-14219.
22. Roy, S. and Redfield, A.G. (1983) Assignment of imino proton spectra of yeast phenylalanine transfer ribonucleic acid. Biochemistry, 22, 1386-1390.
23. Sherlin, L.D. and Perona, J.J. (2003) tRNA-dependent active site assembly in a class I aminoacyl-tRNA synthetase. Structure, 11, 591-603.
24. Nureki, O., Vassylyev, D.G., Katayanagi, K., Shimizu, T., Sekine, S., Kigawa, T., Miyazawa, T., Yokoyama, S. and Morikawa, K. (1995) Architectures of class-defining and specific domains of glutamyl-tRNA synthetase. Science, 267, 1958-1965.
25. Sekine, S., Nureki, O., Shimada, A., Vassylyev, D.G. and Yokoyama, S. (2001) Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase. Nature Struct. Biol., 8, 203-206.
26. Norberg, J. (2003) Association of protein-DNA recognition complexes: electrostatic and non-electrostatic effects. Arch. Biochem. Biophys., 410, 48-68.
27. Florentz, C., Kern, D. and Giege, R. (1990) Stimulatory effect of ammonium sulfate at high concentrations on the aminoacylation of tRNA and tRNA-like molecules. FEBS Lett., 261, 335-338.
28. Talbot, S.J. and Altman, S. (1994) Kinetic and thermodynamic analysis of RNA-protein interactions in the RNase P holoenzyme from Escherichia coli. Biochemistry, 33, 1406-1411.
29. Bedouelle, H. and Nageotte, R. (1995) Macromolecular recognition through electrostatic repulsion. EMBO J., 14, 2945-2950.
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 non-cognate tRNA anticodons. J. Mol. Biol., 233, 615-628.
31. Mandal, A.K., Samaddar, S., Banerjee, R., Lahiri, S., Bhattacharyya, A. and Roy, S. (2003) Glutamate counteracts the denaturing effect of urea through its effect on the denatured state. J. Biol. Chem., 278, 36077-36084.
32. Giege, R., Sissler, M. and Florentz, C. (1998) Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res., 26, 5017-5035.