tRNA anticodon recognition and specification within subclass IIb aminoacyl-tRNA synthetases

Journal of Molecular Biology

Volumn 278, Issue 4, 1998, Pages 801-813

  Commans, Stéphane ^a   Lazard, Myriam ^a   Delort, Florence ^a   Blanquet, Sylvain ^a   Plateau, Pierre ^a  

^a Lab Biochim URA 1970 CNRS Ecl P   (France)

Author keywords

Aminoacyl tRNA synthetase; Functional effects of mutations; OB fold; RNA protein interactions; tRNA identity

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE; LYSINE TRANSFER RNA; TRANSFER RNA;

AMINO TERMINAL SEQUENCE; ANTICODON; ARCHAEBACTERIUM; ARTICLE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; ENZYME SPECIFICITY; ESCHERICHIA COLI; MOLECULAR MODEL; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING;

ARCHAEA; ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0032525069     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1711     Document Type: Article

References (44)

1. 15N NMR relaxation study. J. Mol. Biol. 260:1996;570-587
2. 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
3. Bentley R.C., Keene J.D. Recognition of U1 and U2 small nuclear RNAs can be altered by a 5-amino-acid segment in the U2 small nuclear ribonucleoprotein particule (snRNP) B″ protein and through interactions with U2 snRNP-A′ protein. Mol. Cell Biol. 11:1991;1829-1839
4. Bjürk G.R. Biosynthesis and function of modified nucleosides. Söll D., RajBhandary U.L. tRNA: Structure, Biosynthesis, and Function. 1995;165-205 ASM Press, Washington, DC
5. Bochkarev A., Pfuetzner R.A., Edwards A.M., Frappier L. Structure of the single-stranded-DNA-binding domain of replication protein A bound to DNA. Nature. 385:1997;176-181
6. Brevet A., Chen J., Lévêque F., Blanquet S., Plateau P. Comparison of the enzymatic properties of the two Escherichia coli lysyl-tRNA synthetase species. J. Biol. Chem. 270:1995;14439-14444
7. Brick P., Bhat T.N., Blow D.M. Structure of tyrosyl-tRNA synthetase refined at 2.3 Å resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate. J. Mol. Biol. 208:1988;83-98
8. Bycroft M., Hubbard T.J.P., Proctor M., Freund S.M.V., Murzin A.G. The solution structure of the S1 RNA binding domain a member of an ancient nucleic acid-binding fold. Cell. 88:1997;235-242
9. Asp recognition by its cognate class II aminoacyl-tRNA synthetase. Nature. 362:1993;181-184
10. Lys. J. Mol. Biol. 253:1995;100-113
11. Commans S., Blanquet S., Plateau P. A single substitution in the motif 1 of Escherichia coli lysyl-tRNA synthetase induces cooperativity toward amino acid binding. Biochemistry. 34:1995;8180-8189
12. Curnow A.W., Ibba M., Söll D. tRNA-dependent asparagine formation. Nature. 382:1996;589-590
13. Cusack S. Eleven down and nine to go. Nature Struct. Biol. 2:1995;824-831
14. Cusack S., Berthet-Colominas C., Härtlein M., Nassar N., Leberman R. A second class of synthetase structure revealed by X-ray analysis of Escherichia coli seryl-tRNA synthetase at 2.5 Å Nature. 347:1990;249-255
15. Lys transcript anticodon recognition and conformational changes upon binding of a lysyl-adenylate analogue. EMBO J. 15:1996;6321-6334
16. Dardel F. MC-Fit using Monte-Carlo methods to get accurate confidence limits on enzyme parameters. Comput. Applic. Biosci. 10:1994;273-275
17. Delarue M., Moras D. The aminoacyl-tRNA synthetase family modules at work. BioEssays. 15:1993;675-687
18. 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
19. Hirel P.H., Lévêque F., Mellot P., Dardel F., Panvert M., Mechulam Y., Fayat G. 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. 70:1988;773-782
20. Ibba M., Morgan S., Curnow A.W., Pridmore D.R., Vothknecht U.C., Gardner W., Lin W., Woese C.R., Söll D. A euryarchaeal lysyl-tRNA synthetase resemblance to class I synthetases. Science. 278:1997;1119-1122
21. Ibba M., Bono J.L., Rosa P.A., Söll D. Archaeal-type lysyl-tRNA synthetase in the Lyme disease spirochete Borrelia burgdorferi. Proc. Natl Acad. Sci. USA. 94:1997;14383-14388
22. Kasai H., Murao K., Nishimura S., Liehr J.G., Crain P.F., McCloskey J.A. Structure determination of a modified nucleoside isolated from Escherichia coli transfer ribonucleic acid, N-[N-[(9-β-D-Ribofuranosylpurin-6-yl)carbamoyl]threonyl]2-amido-2- hydroxymethylpropane-1,3-diol. Eur. J. Biochem. 69:1976;435-444
23. Lévêque F., Plateau P., Dessen P., Blanquet S. Homology of lysS and lysU, the two Escherichia coli genes encoding distinct lysyl-tRNA synthetase species. Nucl. Acids Res. 18:1990;305-312
24. Lévêque F., Gazeau M., Fromant M., Blanquet S., Plateau P. Control of Escherichia coli lysyl-tRNA synthetase expression by anaerobiosis. J. Bacteriol. 173:1991;7903-7910
25. Asn. J. Biol. Chem. 268:1993;18335-18339
26. Asp acylation. J. Mol. Biol. 234:1993;965-974
27. fMet by Escherichia coli RNase P is specified by a guanosine of the 5′-flanking sequence. J. Biol. Chem. 270:1995;15908-15914
28. met expressed from a synthetic gene in vivo. Nucl. Acids Res. 16:1988;8095-8096
29. Meinnel T., Mechulam Y., Blanquet S. Aminoacyl-tRNA synthetases occurrence, structure and function. Söll D., RajBhandary U.L. tRNA: Structure, Biosynthesis, and Function. 1995;251-292 ASM Press, Washington, DC
30. Murzin A.G. OB(oligonucleotide/oligosaccharide binding)-fold common structural and functional solution for non-homologous sequences. EMBO J. 12:1993;861-867
31. Nagai K., Oubridge C., Ito N., Avis J., Evans P. The RNP domain a sequence-specific RNA-binding domain involved in processing and transport of RNA. Trends Biochem. Sci. 20:1995;235-240
32. Onesti S., Miller A.D., Brick P. The crystal structure of the lysyl-tRNA synthetase (LysU) from Escherichia coli. Structure. 3:1995;163-176
33. Oubridge C., Ito N., Evans P.R., Teo C.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
34. Asp by cognate aspartyl-tRNA synthetase. Science. 252:1991;1696-1699
35. Gln and ATP at 2.8 Å resolution. Science. 246:1989;1135-1142
36. Asp. Science. 252:1991;1682-1689
37. Sambrook J., Fritsch E.F., Maniatis T. Molecular Cloning: A Laboratory Manual. 2nd edit. :1989;Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
38. Sanger F., Nicklen S., Coulson A.R. DNA sequencing chain terminating inhibitors. Proc. Natl Acad. Sci. USA. 74:1977;5463-5467
39. Sayers J.R., Schmidt W., Eckstein F. 5′-3′ Exonucleases in phosphorothioate-based oligonucleotide-directed mutagenesis. Nucl. Acids Res. 16:1988;791-802
40. Scherly D., Boelens W., Dathan N.A., van Verooij W.J., Mattaj I.W. Major determinants of the specificity of interaction between small nuclear ribonucleoproteins U1A and U2B″ and their cognate RNAs. Nature. 345:1990;502-506
41. Sullivan M.A., Cannon J.F., Webb F.H., Bock R.M. Anti-suppressor mutation in Escherichia coli defective in biosynthesis of 5-methylaminomethyl-2-thiouridine. J. Bacteriol. 161:1985;368-376
42. Lys identity elements. Nucl. Acids Res. 20:1992;2335-2339
43. Wilkinson A.J., Fersht A.R., Blow D.M., Winter G. Site-directed mutagenesis as a probe of enzyme structure and catalysis tyrosyl-tRNA synthetase cysteine-35 to glycine-35 mutation. Biochemistry. 22:1983;3581-3586
44. Yokoyama S., Nishimura S. Modified nucleosides and codon recognition. Söll D., RajBhandary U.L. tRNA: Structure, Biosynthesis, and Function. 1995;207-223 ASM Press, Washington, DC