Adenosine conformations of nucleotides bound to methionyl tRNA synthetase by transferred nuclear Overhauser effect spectroscopy

Biophysical Journal

Volumn 72, Issue 5, 1997, Pages 2275-2284

  Murali, Nagarajan ^a,c   Lin, Yan ^a   Mechulam, Yves ^b   Plateau, Pierre ^b   Nageswara Rao, B D ^a  

^a INDIANA UNIVERSITY   (United States)

^b LABORATOIRE DE BIOCHIMIE   (France)

^c FLORIDA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE; ADENOSINE PHOSPHATE; ADENOSINE TRIPHOSPHATE MAGNESIUM; ARGININE KINASE; CARRIER PROTEIN; CREATINE KINASE; METHIONINE DERIVATIVE; METHIONINE TRANSFER RNA LIGASE; NUCLEOTIDE; PYRUVATE KINASE;

ARTICLE; COMPLEX FORMATION; CONFORMATION; MOLECULAR MODEL; NUCLEAR OVERHAUSER EFFECT; TORSION;

ENTEROBACTERIA PHAGE T4;

EID: 0030897748     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(97)78872-6     Document Type: Article

References (52)

1. 5A, showing the pathway of phosphoryl transfer. Protein Sci. 4:1262-1271.
2. Altona, C., and M. Sundaralingam. 1972. Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. J. Am. Chem. Soc. 94:8205-8212.
3. Belrhali, H., A. Yaremchuk, M. Tukalo, K. Larsen, C. Berthet-Colominas, R. Leberman, B. Beijer, B. Sproat, J. Als-Nielsen, G. Grubel, J.-F. Legrand, M. Lehmann, and S. Cusack. 1994. Crystal structures at 2.5 angstrom resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate. Science. 263:1432-1436.
4. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4:187-217.
5. Brunie, S., C. Zelwer, and J.-L. Risler. 1990. Crystallographic study at 2.5 Å resolution of the interaction of methionyl-tRNA synthetase from Escherichia coli with ATP. J. Mol. Biol. 216:411-424.
6. Campbell, A. P., and B. D. Sykes. 1991. Theoretical evaluation of the two-dimensional transferred nuclear Overhauser effect. J. Magn. Reson. Imaging. 93:77-92.
7. Cassio, D., and J.-P. Waller. 1971. Modification of methionyl-tRNA synthetase by proteolytic cleavage and properties of the trypsin-modified enzyme. Eur. J. Biochem. 20:283-300.
8. Cavarelli, J., G. Eriani, B. Rees, M. Ruff, M. Boeglin, A. Mitschler, F. Martin, J. Gangloff, J.-C. Thierry, and D. Moras. 1994. The active site of yeast a-spartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction. EMBO J. 13:327-337.
9. De Leeuw, H. P. M., C. A. G. Haasnoot, and C. Altona. 1980. Empirical correlations between conformational parameters in β-D-furanoside fragments derived from a statistical survey of crystal structures of nucleic acid constituents. Isr. J. Chem. 20:108-126.
10. Eriani, G., M. Delarue, O. Poch, J. Gangloff, and D. Moras. 1990. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature. 347:203-206.
11. 31P NMR of the reversible methionine activation reaction catalyzed by methionyl-tRNA synthetase of Escherichia coli. J. Biol. Chem. 255: 8164-8169.
12. Fayat, G., M. Fromant, and S. Blanquet. 1977. Couplings between the sites for methionine and adenosine 5′-triphosphate in the amino acid activation reaction catalyzed by trypsin-modified methionyl-transfer RNA synthetase from Escherichia coli. Biochemistry. 16:2570-2579.
13. Fayat, G., and J.-P. Waller. 1974. The mechanism of action of methionyl-tRNA synthetase from Escherichia coli. Eur. J. Biochem. 44:335-342.
14. Fourmy, D., T. Meinnel, Y. Mechulam, and S. Blanquet. 1993. Mapping of the zinc binding domain of Escherichia coli methionyl-tRNA synthetase. J. Mol. Biol. 231:1068-1077.
15. Hecht, S. M. 1979. 2′-OH vs. 3′-OH specificity in tRNA aminoacylation. In Transfer RNA: Structure, Properties and Recognition. R. R. Shimmel, D. Soll, and J. N. Abelson, editors. Cold Spring Harbor Laboratory, New York. 345-360.
16. Higgins, C. F., I. D. Hiles, G. P. C. Salmonal, D. R. Gill, J. A. Downie, I. J. Evans, I. B. Holland, L. Gray, S. D. Buckel, A. W. Bell, and M. A. Hermodson. 1986. A family of related ATP-binding subunits coupled to many distinct biological processes in bacteria. Nature. 323:448-450.
17. Hirel, P.-H., F. Lévêque, P. Mellot, F. Dardel, M. Panvert, Y. Mechulam, and G. Fayat. 1988. Genetic engineering of methionyl-tRNA synthetase: in vitro regeneration of an active synthetase by proteolytic cleavage of a methionyl-tRNA synthetase-β-galactosidase chimeric protein. Biochimie. 70:773-782.
18. Hountondji, C., P. Dessen, and S. Blanquet. 1993. The SKS AND KMSKS signature of Class I amino acyl tRNA synthetases correspond to the GKT/S sequence characteristic of the ATP-binding site of many proteins. Biochimie. 75:1137-1142.
19. Jackson, P. L., H. N. B. Moseley, and N. R. Krishna. 1995. Relative effects of protein-mediated and ligand-mediated spin-diffusion pathways on transferred NOESY, and implications on the accuracy of the bound ligand conformation. J. Magn. Reson. Imaging. B107:289-292.
20. Jarori, G. K., N. Murali, and B. D. Nageswara Rao. 1994. Two-dimensional transferred nuclear Overhauser effect spectroscopy study of the conformation of MgATP bound at the active and ancillary sites of rabbit muscle pyruvate kinase. Biochemistry. 33:6784-6791.
21. Jarori, G. K., N. Murali, and B. D. Nageswara Rao. 1995. Conformation of MgATP bound to 5-phospho-α-D-ribose 1-diphosphate synthetase by two-dimensional transferred nuclear Overhauser effect spectroscopy. Eur J. Biochemistry. 230:517-524.
22. Kalk, A., and H. J. C. Berendson. 1976. Proton magnetic relaxation and spin diffusion in proteins. J. Magn. Reson. Imaging. 24:343-366.
23. Keepers, J. W., and T. L. James. 1984. A theoretical study of distance determinations from NMR. Two-dimensional nuclear Overhauser spectra. J. Magn. Reson. Imaging. 57:404-426.
24. Koning, T. M. G., R. Boelens, and R. Kaptein. 1990. Calculation of the nuclear Overhauser effect and the determination of proton-proton distances in the presence of internal motions. J. Magn. Reson. Imaging. 90:111-123.
25. Kumar, A., R. R. Ernst, and K. Wüthrich. 1980. A two-dimensional nuclear Overhauser enhancement (2D NOE) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules. Biochem. Biophys. Res. Commun. 95:1-6.
26. Landy, S. B., and B. D. Nageswara Rao. 1989. Dynamical NOE in multi-spin systems undergoing chemical exchange. J. Magn. Reson. Imaging. 81:371-377.
27. 1H-transferred NOE measurements on complexes of methionyl tRNA synthetase and pyruvate kinase. Eur. J. Biochem. 205:59-69.
28. Lee, W., and N. R. Krishna. 1992. Influence of conformational exchange slow on the chemical shift scale on 2D NOESY spectra of biomolecules existing in multiple conformations. J. Magn. Reson. Imaging. 98:36-48.
29. London, R. E., M. E. Perlman, and D. G. Davis. 1992. Relaxation-matrix analysis of the transferred nuclear Overhauser effect for finite exchange rates. J. Magn. Reson. Imaging. 97:79-98.
30. Macura, S., Y. Huang, D. Sueter, and R. R. Ernst. 1981. Two-dimensional chemical exchange and cross-relaxation spectroscopy of coupled nuclear spins. J. Magn. Reson. Imaging. 43:259-281.
31. McPhillips, T. M., B. T. Hsu, M. A. Sherman, M. T. Mas, and D. C. Rees. 1996. Structure of the R65Q mutant of yeast 3-phosphoglycerate kinase complexed with Mg-AMP-PNP and 3-phospho-D-glycerate. Biochemistry. 35:4118-4127.
32. Meinnel, T., Y. Mechulam, and S. Blanquet. 1995. Aminoacyl-tRNA synthetases: occurrence, structure and function. In tRNA: Structure, Biosynthesis and Function. D. Soll, D. Raj Bhandary, and V. Raj Bhandary, editors. American Society for Microbiology, Washington, DC.
33. Meinnel, T., Y. Mechulam, D. LeCorre, M. Panvert, S. Blanquet, and G. Fayat. 1991. Selection of suppressor methionyl-tRNA synthetases: mapping the tRNA anticodon binding site. Proc. Natl. Acad. Sci. USA. 88:291-295.
34. Mellot, P., Y. Mechulam, D. LeCorre, S. Blanquet, and G. Fayat. 1989. Identification of an amino acid region supporting specific methionyl-tRNA synthetase: tRNA recognition. J. Mol. Biol. 208:429-443.
35. Moseley, H. N. B., E. V. Curto, and N. R. Krishna. 1995. Complete relaxation and conformation exchange matrix (CORCEMA) analysis of NOESY spectra of interaction systems: two-dimensional transferred NOESY. J. Magn. Reson. Imaging. B108:243-261.
36. Murali, N., G. K. Jarori, S. B. Landy, and B. D. Nageswara Rao. 1993. Two-dimensional transferred nuclear Overhauser effect spectroscopy (TRNOESY) studies of nucleotide conformations in creatine kinase complexes: effects due to nonspecific binding. Biochemistry. 32: 12941-12948.
37. Murali, N., G. K. Jarori, and B. D. Nageswara Rao. 1994. Two-dimensional transferred nuclear Overhauser effect spectroscopy (TRNOESY) studies of nucleotide conformations in arginine kinase complexes. Biochemistry. 33:14227-14236.
38. 13C]ATP in enzyme complexes and viscous solutions: glycosidic rotation persists at high viscosities and is arrested in enzyme complexes. J. Am. Chem. Soc. 114:1566-1573.
39. Ni, F., and Y. Zhu. 1994. Accounting for ligand-protein interaction in the relaxation-matrix analysis of transferred nuclear Overhauser effects. J. Magn. Reson. Imaging. B102:180-184.
40. Nirmala, N. R., G. M. Lippens, and K. Hallenga. 1992. Theory and experimental results of transfer NOE experiments. II. The influence of residual mobility and relaxation centers inside the protein on the size of transfer NOEs. J. Magn. Reson. Imaging. 100:25-42.
41. Perona, J. J., M. A. Rould, and T. A. Steitz. 1993. Structural basis for transfer RNA aminoacylation by Escherichia coli glutaminyl-tRNA synthetase. Biochemistry. 32:8758-8771.
42. Rosevear, P. R., H. N. Bramson, C. O'Brian, E. T. Kaiser, and A. S. Mildvan. 1983. Nuclear Overhauser effect studies of the conformation of tetraaminecobalt (III)-adenosine 5′-triphosphate free and bound to bovine heart protein kinase. Biochemistry. 22:3439-3447.
43. Rosevear, P. R., P. Desmeules, G. L. Kenyon, and A. S. Mildvan. 1981. Nuclear magnetic resonance studies of the role of histidine residues at the active site of rabbit muscle creatine kinase. Biochemistry. 20: 6155-6164.
44. Rosevear, P. R., V. M. Powers, D. Dowhan, A. S. Mildvan, and G. L. Kenyon. 1987. Nuclear Overhauser effect studies of the conformation of magnesium adenosine 5′-triphosphate bound to rabbit muscle creatine kinase. Biochemistry. 26:5338-5344.
45. Sanger, W. 1984. Principles of Nucleic Acid Structure. C. R. Cantor, editor. Springer-Verlag, New York. 9-28.
46. Schulz, G. E. 1992. Binding of nucleotides by proteins. Curr. Opin. Struct. Biol. 2:61-67.
47. Smith, C. A., and I. Rayment. 1996. Active site comparisons highlight structural similarities between myosin and other P-loop proteins. Biophys. J. 70:1590-1602.
48. States, D. J., R. A. Haberkorn, and D. J. Ruben. 1982. A two-dimensional nuclear Overhauser experiment with pure absorption phase in four quadrants. J. Magn. Reson. Imaging. 48:286-292.
49. Traut, T. W. 1994. The functions and consensus motifs of nine types of peptide segments that form different types of nucleotide-binding sites. Eur. J. Biochem. 222:9-19.
50. Williams, J. S., and P. R. Rosevear. 1991a. Nuclear Overhauser effect studies on the conformations of Mg(α,β-methylene)ATP bound to Escherichia coli methionyl-tRNA synthetase. J. Biol. Chem. 266:2089-2098.
51. Williams, J. S., and P. R. Rosevear. 1991b. Nuclear Overhauser effect studies of the conformations of μg (α,β-methylene) ATP bound to Escherichia coli isoleucyl-tRNA synthetase. Biochem. Biophys. Res. Commun. 176:682-689.
52. Zheng, J., and C. B. Post. 1993. Protein indirect relaxation effects in exchange-transferred NOESY by a rate-matrix analysis. J. Magn. Reson. Imaging. B101:262-270.