tRNA conformity

Cold Spring Harbor Symposia on Quantitative Biology

Volumn 66, Issue , 2001, Pages 185-193

  Wolfson, A D ^a   LaRiviere, F J ^a   Pleiss, J A ^a   Dale, T ^a   Asahara, H ^a   Uhlenbeck, O C ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

TRANSFER RNA; AMINO ACID TRANSFER RNA LIGASE; ELONGATION FACTOR TU; METHYLTRANSFERASE; NUCLEOTIDE; RIBONUCLEASE P;

BINDING AFFINITY; CONFERENCE PAPER; CRYSTAL STRUCTURE; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; RIBOSOME; RNA BINDING; RNA CONFORMATION; RNA SEQUENCE; STRUCTURE ACTIVITY RELATION; THERMODYNAMICS; THERMUS THERMOPHILUS; YEAST; ARTICLE; NUCLEOTIDE SEQUENCE; PROTEIN BINDING; PROTEIN FUNCTION;

ESCHERICHIA COLI; THERMUS; THERMUS THERMOPHILUS;

EID: 0035787895     PISSN: 00917451     EISSN: None     Source Type: Book Series    
DOI: 10.1101/sqb.2001.66.185     Document Type: Conference Paper

References (49)

1. Abrahamson J.K., Laue T.M., Miller D.L., and Johnson A.E. 1985. Direct determination of the association constant between elongation factor Tu X GTP and aminoacyl-tRNA using fluorescence. Biochemistry 24: 692.
2. Bareket-Samish A., Cohen I., and Haran T.E. 1998. Direct versus indirect readout in the interaction of the trp repressor with noncanonical binding sites. J. Mol Biol. 277: 107l.
3. Becker H.D. and Kern D. 1998. Thermus thermophilus: A link in evolution of the tRNA-dependent amino acid amidation pathways. Proc. Natl. Acad. Sci. 95: 12832.
4. Curran J.F. and Yarus M. 1986. Base substitutions in the tRNA TRNA anticodon arm do not degrade the accuracy of reading frame maintenance. Proc. Natl. Acad. Sci. 83: 6538.
5. -. 1989. Rates of aminoacyl-tRNA selection at 29 sense codons in vivo. J. Mol. Biol. 209: 65.
6. Dao V., Guenther R., Malkiewicz A., Nawrot B., Sochacka E., Kraszewski A., Jankowska J., Everett K., and Agris P.F. 1994. Ribosome binding of DNA analogs of tRNA requires base modifications and supports the "extended anticodon." Proc. Natl. Acad. Sci. 91: 2125.
7. Feinberg J.S. and Joseph S. 2001. Identification of molecular interactions between P-site tRNA and the ribosome essential for translocation. Proc. Natl. Acad. Sci. 98: 11120.
8. Fersht A.R. and Dingwall C. 1979. Evidence for the double-sieve editing mechanism in protein synthesis. Steric exclusion of isoleucine by valyl-tRNA synthetases. Biochemistry 18: 2627.
9. Giege R., Sissler M., and Florentz C. 1998. Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res. 26: 5017.
10. Holbrook S.R. and Kim S.H. 1997. RNA crystallography. Biopolymers 44: 3.
11. Hou Y.M. and Schimmel P. 1992. Novel transfer RNAs that are active in Escherichia coli. Biochemistry. 31: 4157.
12. Ibba M. and Söll D. 2000. Aminoacyl-tRNA synthesis, Annu. Rev. Biochem. 69: 617.
13. Jakubowski H. 1988. Negative correlation between the abundance of Escherichia coli aminoacyl-tRNA families and their affinities for elongation factor Tu- GTP. J. Theor. Biol. 133: 363.
14. Janiak F., Dell V.A., Abrahamson J.K., Watson B.S., Miller D.L., and Johnson A.E. 1990. Fluorescence characterization of the interaction of various transfer RNA species with elongation factor Tu.GTP: Evidence for a new functional role for elongation factor Tu in protein biosynthesis. Biochemistry 29: 4268.
15. Kjeldgaard M., Nissen P., Thirup S., and Nyborg J. 1993. The crystal structure of elongation factor EF-Tu from Thermus aquaticus in the GTP conformation. Structure 1: 35.
16. Knowlton R.G. and Yarus M. 1980. Discrimination between aminoacyl groups on su+7 tRNA by elongation factor Tu. J. Mol. Biol. 139: 721.
17. Koval'chuke O.V., Potapov A.P., El'skaya A.V., Potapov V.K., Krinetskaya N.F., Dolinnaya N.G., and Shabarova Z.A. 1991. Interaction of ribo- and deoxyriboanalogs of yeast tRNA(Phe) anticodon arm with programmed small ribosomal subunits of Escherichia coli and rabbit liver. Nucleic Acids Res. 19: 4199.
18. LaRiveire F.J., Wolfson A.D., and Uhlenbeck O.C. 2001. Thermodynamic compensation as a mechanism to achieve the uniform binding of aminoacyl-tRNA to elongation factor Tu. Science 294: 165.
19. Leonard D.A. and Kerppola T.K. 1998. DNA bending determines Fos-Jun heterodimer orientation. Nat. Struct. Biol. 5: 877.
20. Louie A. and Jumak F. 1985. Kinetic studies of Escherichia coli elongation factor Tu-guanosine 5′- triphosphate-aminoacyl-tRNA complexes. Biochemistry 24: 6433.
21. Louie A., Ribeiro N.S., Reid B.R., and Jurnak F. 1984. Relative affinities of all Eseherichia coli aminoacyl-tRNAs for elongation factor Tu-GTP. J. Biol. Chem. 259: 5010.
22. Martin A.M., Sam M.D., Reich N.O., and Perona J.J. 1999. Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease. Nat. Struet. Biol. 6: 269.
23. McClain W.H. 1994. The tRNA identity problem: Past, present and future. In tRNA: Structure, biosynthesis and function. (ed. D. Söll and U.L. RajBhandary), p. 335. ASM Press, Washington, D.C.
24. McClain W.H., Schneider J., Bhattacharya S., and Gabriel K. 1998. The importance of tRNA backbone-mediated interactions with synthetase for aminoacylation. Proc. Natl. Acad. Sci. 95: 460.
25. Nazarenko I.A., Harrington K.M., and Uhlenbeck O.C. 1994. Many of the conserved nucleotides of tRNA(Phe) are not essential for ternary complex formation and peptide elongation. EMBO J. 13: 2464.
26. Nicholls A., Sharp K.A., and Honig B. 1991. Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11: 281.
27. Nissan T.A., Oliphant B., and Perona J.J. 1999. An engineered class I transfer RNA with a class II tertiary fold. RNA 5: 434.
28. Nissen P., Thirup S., Kjeldgaard M., and Nyborg J. 1999. The crystal structure of Cys-tRNACys-EF-Tu-GDPNP reveals general and specific features in the ternary complex and in tRNA. Struct. Fold. Des. 7: 143.
29. Nissen P., Kjeldgaard M., Thirup S., Polekhina G., Reshetnikova L., Clark B.F., and Nyborg J. 1995. Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. Science 270: 1464.
30. Normanly J., Ogden R.C., Horvath S.J., and Abelson J.N. 1986. Changing the identity of a transfer RNA. Nature 321: 2163.
31. Ott G., Schiesswohl M., Kiesewetter S., Forster C., Arnold L., Erdmann V.A., and Sprinzl M. 1990. Ternary complexes of Escherichia coli aminoacyl-tRNAs with the elongation factor Tu and GTP: Thermodynamic and structural studies. Biochim. Biophys. Acta 1050: 222.
32. Pape T., Wintermeyer W., and Rodnina M.V. 1998. Complete kinetic mechanism of elongation factor Tu-dependent binding of aminoacyl-tRNA to the A site of the E. coli ribosome. EMBO J. 17: 7490.
33. -. 1999. Induced fit in initial selection and proofreading of aminoacyl-tRNA on the ribosome. EMBO J. 18: 3800.
34. Pleiss J.A. and Uhlenbeck O.C. 2001. Identification of thermodynamically relevant interactions between EF-Tu and backbone elements of tRNA. J. Mol. Biol. 308: 895.
35. Raftery L.A. and Yarus M. 1987. Systematic alterations in the anticodon arm make tRNA(Glu)-Suoc a more efficient suppressor. EMBO J. 6: 1499.
36. Rould M.A., Perona J.J., Söll D., and Steitz T.A. 1989. Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 Å resolution. Science 246: 1135.
37. Rudinger J., Hillenbrandt R., Sprinzl M., and Giege R. 1996. Antideterminants present in minihelix(Sec) hinder its recognition by prokaryotic elongation factor Tu. EMBO J. 15: 650.
38. Ruff M., Krishnaswamy S., Boeglin M., Poterszman A., Mitschler A., Podjarny A., Recs B., Thierry J.C., and Moras D. 1991. Class II aminoacyl transfer RNA synthetases: Crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). Science 252: 1682.
39. Saks M.E., Sampson J.R., and Abelson J.N. 1994. The transfer RNA identity problem: A search for rules. Science 263: 191.
40. Shen L.X., Cai Z., and Tinoco I., Jr. 1995. RNA structure at high resolution. FASEB J. 9: 1023.
41. Sherman J.M., Rogers M.J., and Söll D. 1992. Competition of aminoacyl-tRNA synthetases for tRNA ensures the accuracy of aminoacylation [corrected and republished article originally printed in Nucleic Acids Res. [1992] 20: 1547. Nucleic Acids Res. 20: 2847.
42. Sorensen M.A. and Pedersen S. 1991. Absolute in vivo translation rates of individual codons in Escherichia coli. The two glutamic acid codons GAA and GAG are translated with a threefold difference in rate. J. Mol. Biol. 222: 265.
43. Stanzel M., Schon A., and Sprinzl M. 1994. Discrimination against misacylated tRNA by chloroplast elongation factor Tu. Eur. J. Biochem. 219: 435.
44. Swanson R., Hoben P., Sumner-Smith M., Uemura H., Watson L., and Söll D. 1988. Accuracy of in vivo aminoacylation requires proper balance of tRNA and aminoacyl-tRNA synthetase. Science 242: 1548.
45. Thomas L.K., Dix D.B., and Thompson R.C. 1988. Codon choice and gene expression: Synonymous codons differ in their ability to direct aminoacylated-transfer RNA binding to ribosomes in vitro. Proc. Natl. Acad. Sci. 85: 4242.
46. von Ahsen U., Green R., Schroeder R., and Noller H.F. 1997. Identification of 2′-hydroxyl groups required for interaction of a tRNA anticodon stem-loop region with the ribosome. RNA 3: 49.
47. Wagner T. and Sprinzl M. 1980. The complex formation between Escherichia coli aminoacyl-tRNA, elongation factor Tu and GTP. The effect of the side-chain of the amino acid linked to tRNA. Eur. J. Biochem. 108: 213.
48. Yarus M. 1972. Intrinsic precision of aminoacyl-tRNA synthesis enhanced through parallel systems of ligands. Nat. New Biology 239: 106.
49. Yusupov M.M., Yusupova G.Z., Baucom A., Lieberman K., Earnest T.N., Cate J.H., and Noller H.F. 2001. Crystal structure of the ribosome at 5.5 A resolution. Science 292: 883.