Advertisement

The Arrangement of tRNA in the Ribosome

  • Alexander S. Spirin
  • Valery I. Lim
  • Richard Brimacombe

Abstract

The main reaction performed by the translating ribosome is transpeptidation. Two substrates participating in the reaction are peptidyltRNA and aminoacyl-tRNA:

\( {\text{Pept(n) - tRNA' + Aa - tRNA''}} \to {\text{ tRN}}{{\text{A'}}_{{\text{OH}}}}{\text{ + Pept(n + 1) - tRNA''}}{\text{.}} \)

The substrate-binding sites of the ribosome for the two substrates, peptidyl-tRNA and aminoacyl-tRNA, are called the P and A sites, respectively. This is the principal definition of the two sites.

Keywords

Anticodon Loop Peptidyl Transferase Peptidyl Transferase Center tRNA Anticodon mRNA Analogue 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Dontsova, O., Kopylov, A. and Brimacombe, R., 1991, The location of messenger-RNA in the ribosomal 30S initiation complex. Site-directed cross-linking of messenger-RNA analogs carrying several photo-reactive labels simultaneously on either side of the AUG start codon, EMBO J. 10:2613PubMedGoogle Scholar
  2. Dontsova, O., Dokudovskaya, S., Kopylov, A., Bogdanov, A., Rinke-Appel, J., Jünke, N., and Brimacombe, R., 1992, Three widely separated positions in the 16S RNA lie in or close to the ribosomal decoding region; a site-directed cross-linking study with mRNA analogues, EMBO J. 11:3105PubMedGoogle Scholar
  3. Frank, J., Radermacher, M., Wagenknecht, T., and Verschoor, A., 1988, Studying ribosome structure by electron microscopy and computer-image processing, Methods Enzymol. 164:3PubMedCrossRefGoogle Scholar
  4. Frank, J., Verschoor, A., Radermacher, M., and Wagenknecht, T., 1990, Morphologies of eubacterial and eucaryotic ribosomes as determined by three-dimensional electron microscopy, in: “The Ribosome. Structure, Function, and Evolution”, W.E. Hill, A.E. Dahlberg, R.A. Garrett, P.B. Moore, D. Schlessinger, and J. Warner, eds., ASM Press, Washington, D.C., p.107Google Scholar
  5. Frank, J., Penczek, P., Grassucci, R., and Srivastava, S., 1991, Three-dimensional reconstruction of the 70S Escherichia coli ribosome in ice: the distribution of ribosomal RNA, J. Cell Biol 115:597.PubMedCrossRefGoogle Scholar
  6. Girshovich, A.S., Bochkareva, E.S., and Vasiliev, V.D., 1986, Localization of elongation factor Tu on the ribosome, FEBS Lett 197:192PubMedCrossRefGoogle Scholar
  7. Gold, L., 1988, Posttranscriptional regulatory mechanisms in Escherichia coli, Annu. Rev. Biochem. 57:199PubMedCrossRefGoogle Scholar
  8. Johnson, A.E., Adkins, H.J., Matthews, E.A., and Cantor, C.R., 1982, Distance moved by transfer RNA during translocation from the A site to the P site on the ribosome, J. Mol. Biol. 156:113PubMedCrossRefGoogle Scholar
  9. Kim, S.H., Suddath, F.L., Quigley, G.J., McPherson, A., Sussman, J.L., Wang, A.H.J., Seeman, N.C., and Rich, A., 1974, Three-dimensional tertiary structure of yeast phenylalanine transfer RNA, Science 185:435PubMedCrossRefGoogle Scholar
  10. Lake, J.A., 1977, Aminoacyl-tRNA-binding at the recognition site is the first step of the elongation cycle of protein synthesis, Proc. Natl. Acad. Sci. USA 74:1903PubMedCrossRefGoogle Scholar
  11. Lake, J., 1980, Ribosome structure and functional sites, in: “Ribosomes. Structure, Function, and Genetics”, G. Chambliss, G.R. Craven, J. Davies, K. Davis, L. Kahan, and M. Nomura, eds., University Park Press, Baltimore, p.207Google Scholar
  12. Lim, V., Venclovas, C., Spirin, A., Brimacombe, R., Mitchell, P., and Müller, F., 1992, How are tRNAs and mRNA arranged in the ribosome? An attempt to correlate the stereochemistry of the tRNA-mRNA interaction with constraints imposed by the ribosomal topography, Nucleic Acids Res. 20:2627PubMedCrossRefGoogle Scholar
  13. McDonald, J.J., and Rein, R., 1987, A stereochemical model of the transpeptidation complex, J. Biomolec. Struct. Dynamics 4:729CrossRefGoogle Scholar
  14. Moras, D., Comarmond, M.B., Fischer, J., Weiss, R., Thierry, J.C., Ebel, J.P., and Giegé, R., 1980, Crystal-structure of yeast transfer RNA-Asp, Nature 288:669PubMedCrossRefGoogle Scholar
  15. Nagano, K., Takagi, H., and Hard, M., 1991, The side-by-side model of transfer-RNA molecules allowing the alpha-helical conformation of the nascent polypeptide during the ribosomal transpeptidation, Biochimie 73:947PubMedCrossRefGoogle Scholar
  16. Noller, H.F., Moazed, D., Stern, S., Powers, T., Allen, P.N., Robertson, J.M., Weiser, B., and Triman, K., 1990, Structure of rRNA and its functional interactions in translation, in: “The Ribosome. Structure, Function, and Evolution”, W.E. Hill, A.E. Dahlberg, R.A. Garrett, P.B. Moore, D. Schlessinger, and J.R. Warner, eds., ASM Press, Washington, D.C., p.73Google Scholar
  17. Ofengand, J., Ciesiolka, J., Denman, R., and Nurse, K., 1986, Structural and functional interactions of the tRNA-ribosome complex, in:“Structure, Function, and Genetics of Ribosomes”, B. Hardesty, and G. Kramer, eds., Springer-Verlag, New York, p.473CrossRefGoogle Scholar
  18. Paulsen, H., Robertson, H.J., and Wintermeyer, W., 1983, Topological arrangement of two transfer RNAs on the ribose. Fluorescence energy transfer measurements between A and P site-bound TrnaPhe, J. Mol. Biol. 167:411.PubMedCrossRefGoogle Scholar
  19. Prabahakaran, M., and Harvey, S.C., 1989, Models for two tRNAs bound to successive codons on mRNA on the ribosome, J. Biomolec. Struct. Dynamics 7:167.Google Scholar
  20. Rich, A., 1974, How transfer RNA may move inside the ribosome, in: “Ribosomes”, M. Nomura, A. Tissières, and P. Lengyel, eds., Cold Spring Harbor Press, New York, p.871Google Scholar
  21. Rinke-Appel, J., Jünke, N., Stade, K., and Brimacombe, R., 1991, The path of messenger-RNA through the Escherichia coli ribosome. Site-directed cross-linking of messenger-RNA analogs carrying a photo-reactive label at various points 3’ to the decoding site, EMBO J. 10:2195PubMedGoogle Scholar
  22. Robertus, J.D., Ladner, J.E., Finch, J.T., Rhodes, D., Brown, R.S., Clark, B.F.C., and Klug, A., 1974, Structure of yeast phenylalanine tRNA at 3 Å resolution, Nature 250:546PubMedCrossRefGoogle Scholar
  23. Smith, D., and Yarns, M., 1989, tRNA-tRNA interactions within cellular ribosomes, Proc. Natl. Acad. Sci. USA 86:4397PubMedCrossRefGoogle Scholar
  24. Spirin, A.S., 1983, Location of tRNA on the ribosome, FEBS Leu. 156:217CrossRefGoogle Scholar
  25. Spirin, A.S., 1985, Ribosomal translocation: facts and models, Prog. Nucleic Acid Res. Mol. Biol. 32:75PubMedCrossRefGoogle Scholar
  26. Spirin, A.S., and Lim, V., 1986, Stereochemical analysis of ribosomal transpeptidation, translocation, and nascent peptide folding, in: “Structure, Function, and Genetics of Ribosomes”, B. Hardesty, and G. Kramer, eds., Springer-Verlag, New York, p.556CrossRefGoogle Scholar
  27. Stade, K., Rinke-Appel, J., and Brimacombe, R., 1989, Site-directed cross-linking of mRNA analogues to the Escherichia coli ribosome; identification of 30S ribosomal components that can be cross-linked to the mRNA at various points 5’ with respect to the decoding site, Nucleic Acids Res. 17:9889PubMedCrossRefGoogle Scholar
  28. Sundaralingam, M., Brennan, T., Yathindra, N., and Ichikawa, T., 1975, Stereochemistry of messenger RNA (codon)-transfer RNA (anticodon) interaction on the ribosome during peptide bond formation, in: “Structure and Conformation of Nucleic Acids and Protein-Nucleic Acid Interactions”, M. Sundaralingam, and S.T. Rao, eds., University Park Press, Baltimore, p.101Google Scholar
  29. Van Heel, M., and Stöffler-Meilicke, M., 1985, Characteristic views of E.coli and B.stearothermophilus 30S ribosomal subunits in the electron microscope, EMBO J. 4:2389PubMedGoogle Scholar
  30. Wagenknecht, T., Carazo, J.M., Radermacher, M., and Frank, J., 1989, Three-dimensional reconstruction of the ribosome from Escherichia coli, Biophys. J. 55:455PubMedCrossRefGoogle Scholar
  31. Wower, J., and Zimmermann, R.A., 1991, A consonant model of the transfer RNA-ribosome complex during the elongation cycle of translation, Biochimie 73:961PubMedCrossRefGoogle Scholar
  32. Wower, J., Hixson, S.S., and Zimmermann, R.A., 1989, Labeling the peptidyl-transferase center of the Escherichia coli ribosome with photoreactive tRNAPhe derivatives containing azidoadenosine at the 3’ end of the acceptor arm: A model of the tRNA-ribosome complex, Proc. Natl. Acad. Sci. USA 86:5232PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 1993

Authors and Affiliations

  • Alexander S. Spirin
    • 1
  • Valery I. Lim
    • 1
  • Richard Brimacombe
    • 2
  1. 1.Institute of Protein ResearchRussian Academy of SciencesMoscow RegionRussia
  2. 2.Abteilung WittmannMax-Planck-Institut für Molekulare GenetikBerlin 33Germany

Personalised recommendations