The 2.0 Å crystal structure of Thermus thermophilus methionyl-tRNA synthetase reveals two RNA-binding modules

Structure

Volumn 8, Issue 2, 2000, Pages 197-208

  Sugiura, Ikuko ^a   Nureki, Osamu ^b   Ugaji Yoshikawa, Yoshiko ^a   Kuwabara, Sachiko ^a   Shimada, Atsushi ^b   Tateno, Masaru ^c   Lorber, Bernard ^d   Giegé, Richard ^d   Moras, Dino ^e   Yokoyama, Shigeyuki ^b,c   Konno, Michiko ^a  

^a OCHANOMIZU UNIVERSITY   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c INST OF PHYS AND CHEMICAL RESEARCH   (Japan)

^d INSTITUT DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

^e INSTITUT DE GÉNÉTIQUE ET DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

Author keywords

Methionyl tRNA synthetase; RNA binding molecule; Rossmann fold; Thermus thermophilus; tRNA

Indexed keywords

METHIONINE TRANSFER RNA LIGASE; TRANSFER RNA; RNA BINDING PROTEIN;

ALPHA HELIX; ANTICODON; ARTICLE; CRYSTAL STRUCTURE; ENZYME STRUCTURE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; RNA BINDING; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; THERMUS THERMOPHILUS; CHEMICAL STRUCTURE; CHEMISTRY; ENZYME ACTIVE SITE; METABOLISM; PROTEIN CONFORMATION; X RAY CRYSTALLOGRAPHY;

ESCHERICHIA; RUMEX; THERMUS THERMOPHILUS;

ANTICODON; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; METHIONINE-TRNA LIGASE; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; RNA-BINDING PROTEINS; THERMUS THERMOPHILUS;

EID: 0034651315     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(00)00095-2     Document Type: Article

References (55)

1. Eriani G., Delarue M., Poch O., Gangloff J., Moras D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature. 347:1990;203-206.
2. Cusack S. Eleven down and nine to go. Nat. Struct. Biol. 2:1995;824-831.
3. Cavarelli J., Delagoutte B., Eriani G., Gangloff J., Moras D. L-arginine recognition by yeast arginyl-tRNA synthetase. EMBO J. 17:1998;5438-5448.
4. Brick P., Bhat T.N., Blow D.M. Structure of tyrosyl-tRNA synthetase refined at 2.3 Å resolution. J. Mol. Biol. 208:1989;83-98.
5. Doublié S., Bricogne G., Gilmore C., Carter C.W. Jr. Tryptophanyl-tRNA synthetase crystal structure reveals an unexpected homology to tyrosyl-tRNA synthetase. Structure. 3:1995;17-31.
6. Gln and ATP at 2.8 Å resolution. Science. 246:1989;1135-1142.
7. Brunie S., Zelwer C., Risler J.L. Crystallographic study at 2.5 Å resolution of the interaction of methionyl-tRNA synthetase from Escherichia coli with ATP. J. Mol. Biol. 216:1990;411-424.
8. Nureki O., Morikawa K.et al. Architectures of class-defining and specific domains of glutamyl-tRNA synthetase. Science. 267:1995;1958-1965.
9. Nureki O., Yokoyama S.et al. Enzyme structure with two catalytic sites for double-sieve selection of substrate. Science. 280:1998;578-582.
10. Ile and mupirocin. Science. 285:1999;1074-1077.
11. Kohda D., Yokoyama S., Miyazawa T. Functions of isolated domains of methionyl-tRNA synthetase from an extreme thermophile, Thermus thermophilus HB8. J. Biol. Chem. 262:1987;558-563.
12. Cassio D., Waller J.-P. Modification of methionyl-tRNA synthetase by proteolytic cleavage and properties of the trypsin-modified enzyme. Eur. J. Biochem. 20:1971;283-300.
13. Met to methionyl-tRNA synthetase from Escherichia coli. J. Mol. Biol. 103:1976;765-784.
14. Asp recognition by its cognate class II aminoacyl-tRNA synthetase. Nature. 362:1993;181-184.
15. Ser. Science. 263:1994;1404-1410.
16. Lys transcript: anticodon recognition and conformational changes upon binding of a lysyl-adenylate analogue. EMBO J. 15:1996;6321-6334.
17. Pro anticodon recognition by Thermus thermophilus prolyl-tRNA synthetase. Structure. 6:1998;101-108.
18. Phe. Structure. 15:1997;59-68.
19. Ghosh G., Pelka H., Schulman L.H. Identification of the tRNA anticodon recognition site of Escherichia coli methionyl-tRNA synthetase. Biochemistry. 29:1990;2220-2225.
20. Meinnel T., Mechulam Y., Corre D.L., Panvert M., Blanquet S., Fayat G. Selection of suppressor methionyl-tRNA synthetases: mapping the tRNA anticodon binding site. Proc. Natl Acad. Sci. USA. 88:1991;291-295.
21. Ghosh G., Kim H.Y., Demaret J.-P., Brunie S., Schulman L.H. Arginine-395 is required for efficient in vivo and in vitro aminoacylation of tRNAs by Escherichia coli methionyl-tRNA synthetase. Biochemistry. 30:1991;11767-11774.
22. Kim H.Y., Pelka H., Brunie S., Schulman L.H. Two separate peptides in Escherichia coli methionyl-tRNA synthetase form the anticodon binding site for methionine tRNA. Biochemistry. 32:1993;10506-10511.
23. Fourmy D., Meinnel T., Mechulam Y., Blanquet S. Mapping of the zinc binding domain of Escherichia coli methionyl-tRNA synthetase. J. Mol. Biol. 231:1993;1068-1077.
24. Fourmy D., Mechulam Y., Blanquet S. Crucial role of an idiosyncratic insertion in the Rossmann fold of class I aminoacyl-tRNA synthetases: The case of methionyl-tRNA synthetase. Biochemistry. 34:1995;15681-15688.
25. Fourmy D., Dardel F., Blanquet S. Methionyl-tRNA synthetase zinc binding domain. Three-dimensional structure and homology with rubredoxin and gag retroviral proteins. J. Mol. Biol. 231:1993;1078-1089.
26. Nureki O., Kohno T., Sakamoto K., Miyazawa T., Yokoyama S. Chemical modification and mutagenesis studies on zinc binding of aminoacyl-tRNA synthetases. J. Biol. Chem. 268:1993;15368-15373.
27. Nureki O., Yokoyama S.et al. Methionyl-tRNA synthetase gene from an extreme thermophile, Thermus thermophilus HB8. J. Biol. Chem. 266:1991;3268-3277.
28. Mechulam Y., Blanquet S.et al. Crystal structure of Scherichia coli methionyl-tRNA synthetase highlights species-specific features. J. Mol. Biol. 294:1999;1287-1297.
29. Landro J.A., Schimmel P. Zinc-dependent cell growth conferred by mutant tRNA synthetase. J. Biol. Chem. 269:1994;20217-20220.
30. Landro J.A., Schmidt E., Schimmel P., Tierney D.L., Penner-Hahn J.E. Thiol ligation of two zinc atoms to a class I tRNA synthetase: evidence for unshared thiols and role in amino acid binding and utilization. Biochemistry. 33:1994;14213-14220.
31. Landro J.A., Schimmel P. Metal-binding site in a class I tRNA synthetase localized to a cysteine cluster inserted into nucleotide-binding fold. Proc. Natl Acad. Sci. USA. 90:1993;2261-2265.
32. Lin L., Hale S.P., Schimmel P. Aminoacylation error correction. Nature. 384:1996;33-34.
33. Liu J., Lapointe J.et al. The zinc-binding site of Escherichia coli glutamyl-tRNA synthetase is located in the acceptor-binding domain. J. Biol. Chem. 270:1995;15162-15169.
34. Gln-ATP complex. Nucl. Acids Mol. Biol. 6:1992;225-245.
35. Rogers M.J., Adachi T., Inokuchi H., Söll D. Functional communication in the recognition of tRNA by Escherichia coli glutaminyl-tRNA synthetase. Proc. Natl Acad. Sci. USA. 91:1994;291-295.
36. Holm L., Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:1993;123-138.
37. Shiba K., Schimmel P. Functional assembly of a randomly cleaved protein. Proc. Natl Acad. Sci. USA. 89:1992;1880-1884.
38. Auld D.S., Schimmel P. Switching recognition of two tRNA synthetases with an amino acid swap in a designed peptide. Science. 267:1995;1994-1996.
39. Rould M.A., Perona J.J., Steitz T.A. Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase. Nature. 352:1991;213-218.
40. Berthet-Colominas C., Seignovert L., Hartlein M., Grotli M., Cusack S., Leberman R. The crystal structure of asparaginyl-tRNA synthetase from Thermus thermophilus and its complexes with ATP and asparaginyl-adenylate: the mechanism of discrimination between asparagine and aspartic acid. EMBO J. 17:1998;2947-2960.
41. Arnez J.G., Harris D.C., Mitschler A., Rees B., Francklyn C.S., Moras D. Crystal structure of histidyl-tRNA synthetase from Escherichia coli complexed with histidyl-adenylate. EMBO J. 14:1995;4143-4155.
42. Logan D.T., Mazauric M.-H., Kern D., Moras D. Crystal structure of glycyl-tRNA synthetase from Thermus thermophilus. EMBO J. 14:1995;4156-4167.
43. Oubridge C., Ito N., Evans P.R., Teo D.-H., Nagai K. Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature. 372:1994;432-438.
44. Allain F.H.-T., Gubser C.C., Howe P.W.A., Nagai K., Neuhaus D., Varani G. Specificity of ribonucleoprotein interaction determined by RNA folding during complex formation. Nature. 380:1996;646-650.
45. Kigawa T., Muto Y., Yokoyama S. Cell-free synthesis and amino acid-selective stable isotope labeling of proteins for NMR analysis. J. Bio. NMR. 6:1995;129-134.
46. 15N heteronulcear NMR studies of Escherichia coli thioredoxin in samples isotopically labeled by residue type. Biochemistry. 24:1985;7263-7268.
47. Otwinowski Z., Minor W. Processing X-ray diffraction data collected in oscillation mode. Methods Enz. 276:1996;307-326.
48. The CCP4 Suite: programs for protein crystallography. Acta Crystallogr. D. 50:1994;760-763.
49. De la Fortelle E., Bricogne G. Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enz. 276:1996;472-494.
50. Jones T.A., Zou J.Y., Cowan S.W., Kjeldgarrd M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A. 47:1991;110-119.
51. Brünger A.T. X-PLOR Version 3.1: A System for X-ray Crystallography and NMR. 1993;Yale University Press, New Haven, CT.
52. Brünger A.T. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature. 355:1992;472-475.
53. Insight II User Guide, version 2.3.0. 1993;Biosym Technologies, San Diego.
54. Kraulis P.J. Molscript: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:1991;946-950.
55. Mettitt E.A., Murphy E.P. Raster3D Version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr. D. 50:1994;869-873.