1887

Chapter 26 : Ribosomal Elongation Cycle

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in
Zoomout

Ribosomal Elongation Cycle, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818142/9781555811846_Chap26-1.gif /docserver/preview/fulltext/10.1128/9781555818142/9781555811846_Chap26-2.gif

Abstract:

This chapter provides a brief review of the reactions of the elongation cycle, and discusses recent data that clarify and explain some points of the divergent aspects of the current models of the elongation cycle. It shows that the location and the features of the deacylated tRNA in either the P or E site are extremely sensitive to the buffer conditions applied. These data explain the discrepancies of the current models of the elongation cycle and the controversy about the features and importance of the E site. It shows that the striking differences can be traced back to differences in the buffer systems used by the two groups. It presents contact patterns of deacylated tRNA with the ribosomal subunits and the P/E hybrid site, and contact patterns of tRNAs in the ribosomal pre and post states. cells grow happily in DO instead of HO, thus replacing all the protons with deuterons. The crystal structure of the ternary complex has demonstrated that EF-Tu is more than 50 Å from the anticodon. The central enzymatic activity of the ribosome is the formation of the peptide bond that is formed at an active center on the large ribosomal subunit, the PTF center. Different affinity-labeling approaches were applied to identify components at or near the peptidyltransferase (PTF) center. As a topographical method, affinity labeling cannot directly identify the component actually involved in the enzymatic activity.

Citation: Nierhaus K, Dabrowski M, Einfeldt E, Kamp D, Marquez V, Patzke S, Schäfer M, Stelzl U, Spahn C, Burkhardt N, Diedrich G, Blaha G, Willumeit R, Stuhrmann H. 2000. Ribosomal Elongation Cycle, p 319-336. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch26

Key Concept Ranking

Saccharomyces cerevisiae
0.51724136
Translocation
0.46046424
Escherichia coli
0.45785648
0.51724136
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of Figure 1
Figure 1

Models of the elongation cycle. (A) Hybrid-site model. (B) Allosteric three-site model. For explanations, see the text.

Citation: Nierhaus K, Dabrowski M, Einfeldt E, Kamp D, Marquez V, Patzke S, Schäfer M, Stelzl U, Spahn C, Burkhardt N, Diedrich G, Blaha G, Willumeit R, Stuhrmann H. 2000. Ribosomal Elongation Cycle, p 319-336. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch26
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
Figure 2

Relative accessibilities of the phosphate groups of a phosphorothioated tRNA on either subunit and a 70S ribosome. The relative accessibility of a phosphate position means the accessibility relative to that of the corresponding position of a deacylated tRNA in solution. (Left) Accessibility graphs of tRNAs bound to ribosomal subunits or 70S ribosomes, always in the presence of poly(U). The axes indicate the relative accessibilities (1, full accessibility; 0, full protection); the axis gives the nucleotide position. (A) Comparison of the accessibility pattern of a tRNA bound to the P site of a 70S ribosome (red) with that of a tRNA bound to 30S subunits (green). (B) Same as graph A except that the pattern obtained with 50S subunits is shown (blue). (Right) The same patterns projected onto the three-dimensional model of tRNA with a color code for the accessibility of a phosphate group. (Taken from .)

Citation: Nierhaus K, Dabrowski M, Einfeldt E, Kamp D, Marquez V, Patzke S, Schäfer M, Stelzl U, Spahn C, Burkhardt N, Diedrich G, Blaha G, Willumeit R, Stuhrmann H. 2000. Ribosomal Elongation Cycle, p 319-336. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch26
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3
Figure 3

Contact border of a deacylated tRNA at the 70S P site separating the tRNA regions contacting the small and the large ribosomal subunit. (Taken from .)

Citation: Nierhaus K, Dabrowski M, Einfeldt E, Kamp D, Marquez V, Patzke S, Schäfer M, Stelzl U, Spahn C, Burkhardt N, Diedrich G, Blaha G, Willumeit R, Stuhrmann H. 2000. Ribosomal Elongation Cycle, p 319-336. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch26
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 4
Figure 4

Deacylated tRNAs in the P and P/E sites as observed in polyamine and conventional buffer systems, respectively ( ). (Top) Mutual arrangement of tRNAs in the two sites. The anticodon regions are highlighted in red and overlap; therefore, both positions cannot be occupied simultaneously in the same ribosome. (Bottom) tRNAs in the two positions seen within the ribosome. Landmarks of the small 30S subunit: h, head; sp, spore. Landmarks of the large 50S subunit: L1, L1 protuberance; CP, central protuberance; St, L12 stalk. (Adapted from .)

Citation: Nierhaus K, Dabrowski M, Einfeldt E, Kamp D, Marquez V, Patzke S, Schäfer M, Stelzl U, Spahn C, Burkhardt N, Diedrich G, Blaha G, Willumeit R, Stuhrmann H. 2000. Ribosomal Elongation Cycle, p 319-336. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch26
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 5
Figure 5

Difference patterns of thioated tRNAs. E, P, and A mark the respective tRNA binding sites. Red, positions where the relative intensities of the two states compared differed by at least a factor of 2; blue, no difference according to this criterion. (A) Differences in the protection patterns of AcPhe-tRNA before and after translocation. (B) Differences of tRNA in the P site and AcPhe-tRNA in the P site. (C) Differences in the protection patterns of tRNA before and after translocation. (D) Differences in the protection patterns of deacylated tRNA in the P site and in the A site [A(deac)]. (Adapted from .)

Citation: Nierhaus K, Dabrowski M, Einfeldt E, Kamp D, Marquez V, Patzke S, Schäfer M, Stelzl U, Spahn C, Burkhardt N, Diedrich G, Blaha G, Willumeit R, Stuhrmann H. 2000. Ribosomal Elongation Cycle, p 319-336. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch26
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 6
Figure 6

The -ε model of the elongation cycle. E, P, and A mark the respective tRNA binding sites. The essential feature is a movable ribosomal -ε domain that connects both subunits through the intersubunit space, binds both tRNAs of an elongating ribosome, and carries them from the A and P sites to the P and E sites, respectively, during translocation. The model keeps all the features of the allosteric three-site model (Fig. 1B) but explains the reciprocal linkage between the A and E sites by the fact that the -ε domain moves out of the A site during translocation, leaving the decoding center alone at the A site, rather than by an allosteric coupling. Yellow and green, the two binding regions of the -ε domain; blue, the decoding center at the A site.

Citation: Nierhaus K, Dabrowski M, Einfeldt E, Kamp D, Marquez V, Patzke S, Schäfer M, Stelzl U, Spahn C, Burkhardt N, Diedrich G, Blaha G, Willumeit R, Stuhrmann H. 2000. Ribosomal Elongation Cycle, p 319-336. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch26
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 7
Figure 7

tRNA arrangement in PRE (left-hand panels) and POST (right-hand panels) states. The green and red tRNAs are thought to be at the A and P sites, respectively, of PRE states and at the P and E sites, respectively, of POST states. (A and B) 70S ribosome; (C and D) 30S subunit; (E and F) 50S subunit. (From .)

Citation: Nierhaus K, Dabrowski M, Einfeldt E, Kamp D, Marquez V, Patzke S, Schäfer M, Stelzl U, Spahn C, Burkhardt N, Diedrich G, Blaha G, Willumeit R, Stuhrmann H. 2000. Ribosomal Elongation Cycle, p 319-336. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch26
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 8
Figure 8

The tRNAs present on the elongating ribosome in the PRE and POST states. (A) tRNA position observed in poly(U)-programmed ribosomes saturated with deacylated tRNAs in the presence of the conventional buffer system. (B) tRNAs in the POST state in the presence of the polyamine system (adapted from Agrawal et al., 1998). (C) Same as panel B, but the top of the 70S ribosome has been cut off. (D) Same as panel B, but a slice of the ribosome is shown with the tRNAs kept at the P and E sites. A, P, and E mark the respective tRNA binding sites, and E2 marks the corresponding tRNA position. Landmarks of the small subunit: ch, tentative mRNA channel through the neck of the 30S subunit; h, head; pt, platform; 1b, part of bridge 1 connecting the subunits. Landmarks of the large subunit: CP, central protuberance; St, L12 stalk.

Citation: Nierhaus K, Dabrowski M, Einfeldt E, Kamp D, Marquez V, Patzke S, Schäfer M, Stelzl U, Spahn C, Burkhardt N, Diedrich G, Blaha G, Willumeit R, Stuhrmann H. 2000. Ribosomal Elongation Cycle, p 319-336. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch26
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555818142.chap26
1. Agrawal, R.,, P. Penczek,, A. Malhotra,, R. Grassucci,, I. Gabashvili,, A. Heagle,, S. Srivastava,, M. Burkhardt,, R. Jünemann,, K. Nierhaus,, and J. Frank. 1998. Binding positions of tRNAs in translating Escherichia coli ribosomes p. 717718. In Proceedings of the 14th International Congress of Electron Microscopy.
2. Agrawal, R. K.,, P. Penczek,, R. A. Grassucci,, N. Burkhardt,, K. H. Nierhaus,, and J. Frank. 1999. Effect of buffer conditions on the position of tRNA on the 70S ribosome as visualized by cryoelectron microscopy. J. Biol. Chem. 274:87238729.
3. Agraval, R. K.,, N. Burkhardt,, K. H. Nierhaus,, and J. Frank. Unpublished data.
4. Bilgin, N.,, L. A. Kirsebom,, M. Ehrenberg,, and C. G. Kurland. 1988. Mutations in ribosomal proteins L7/L12 perturb EF-G and EF-Tu functions. Biochimie 70:611618.
5. Bouadloun, F.,, D. Donner,, and C. G. Kurland. 1983. Codonspecific missense errors in vivo. EMBO J. 2:13511356.
6. Burkhardt, N.,, R. Jünemann,, C. M. T. Spahn,, and K. H. Nierhaus, 1998. Ribosomal tRNA binding sites: three-site models of translation. Crit. Rev. Biochem. Mol. Biol. 33:95149.
7. Cooperman, B. 1980. Photolabile antibiotics as probes of ribosomal structure and function. Ann. N.Y. Acad. Sci. 346:302323.
8. Cooperman, B. S.,, T. Wooten,, D. P. Romero,, and R. Traut. 1995. Histidine 229 in the protein L2 is apparently essential for 50S peptidyl transferase activity. Biochem. Cell Biol. 73:10871094.
9. Dabbs, E. R. 1991. Mutants lacking individual ribosomal proteins as a tool to investigate ribosomal properties. Biochimie 73:639645.
10. Dabrowski, M.,, C. M. T. Spahn,, and K. H. Nierhaus. 1995. Interaction of tRNAs with the ribosome at the A and P sites. EMBO J. 14:48724882.
11. Dabrowski, M.,, C. M. T. Spahn,, M. A. Schäfer,, S. Patzke,, and K. H. Nierhaus. 1998. Contact patterns of tRNAs do not change during ribosomal translocation. J. Biol. Chem. 273:3279332800.
12. Diedrich, G.,, C. Spahn,, M. A. Schäfer,, B. Cooperman,, and K. H. Nierhaus. Ribosomal protein L2 is involved in the association of the ribosomal subunits, tRNA binding to A and P sites and peptidyl transferase. Submitted for publication.
13. Echols, H.,, and M. F. Goodman. 1991. Fidelity mechanisms in DNA replication. Annu. Rev. Biochem. 60:477511.
14. Franceschi, F.,, and K. H. Nierhaus. 1990. Ribosomal proteins L15 and L16 are mere late assembly proteins of the large ribosomal subunit. J. Biol. Chem. 265:1667616682.
15. Geigenmüller, U.,, and K. H. Nierhaus. 1990. Significance of the third tRNA binding site, the E site, on E. coli ribosomes for the accuracy of translation: an occupied E site prevents the binding of non-cognate aminoacyl-transfer RNA to the A site. EMBO J. 9:45274533.
16. Gnirke, A.,, and K. H. Nierhaus. 1986. tRNA binding sites on the subunits of Escherichia coli ribosomes. J. Biol. Chem. 261: 1450614514.
17. Gnirke, A.,, U. Geigenmüller,, H.-J. Rheinberger,, and K. H. Nierhaus. 1989. The allosteric three-site model for the ribosomal elongation cycle. J. Biol. Chem. 264:72917301.
18. Grajevskaja, R. A.,, Y. V. Ivanov,, and E. S. Saminsky. 1982. 70S ribosomes of Escherichia coli have an additional site for deacylated tRNA. Eur. J. Biochem. 128:4752.
19. Green, R.,, E. Switzer,, and H. F. Noller. 1998. Ribosome-catalyzed peptide-bond formation with an A-site substrate covalently lnked to 23S ribosomal RNA. Science 280:286289.
20. Gregory, S.,, and A. Dahlberg. 1999. Mutations in the conserved P loop perturb the conformation of two structural elements in the peptidyl transferase center of 23S ribosomal RNA. J. Mol. Biol. 285:14751483.
21. Horsfield, J. A.,, D. N. Wilson,, S. A. Mannering,, F. M. Adamski,, and W. P. Tate, 1995. Prokaryotic ribosomes recode the HIV-1 gag-pol-1 frameshift sequence by an E/P site posttranslocation simultaneous slippage mechanism. Nucleic Acids Res. 23:14871494.
22. Jakubowski, H. 1994. Energy cost of translational proofreading in vivo. The aminoacylation of transfer RNA in Escherichia coli. Ann. N.Y. Acad. Sci. 745:420.
23. Kamekura, M.,, K. Hamana,, and S. Matsuzaki. 1987. Polyamine contents and amino acid decarboxylation activities of extremely halophilic achaebacteria and some eubacteria. FEMS Microbiol. Lett. 43:301305.
24. Khaitovich, P.,, A. Mankin,, R. Green,, L. Lancaster,, and H. Noller. 1999. Characterization of functionally active subribosomal particles from Thermus aquaticus. Proc. Natl. Acad. Sci. USA 96: 8590.
25. Kirillov, S. V.,, E. M. Makarov,, and Y. P. Semenkov. 1983. Quantitative study of interaction of deacylated tRNA with E. coli ribosomes. Role of 50S subunits in formation of the E. site. FEBS Lett. 157:9194.
26. Knop, W.,, M. Hirai,, H.-J. Schink,, H. B. Stuhrmann,, R. Wagner,, J. Zhao,, O. Schärpf,, R. R. Crichton,, M. Krumpolc,, K. H. Nierhaus,, A. Rijllart,, and T. O. Niinikoski. 1992. A new polarized target for neutron scattering studies on biomolecules: first results from apoferritin and the deuterated 50S subunit of ribosomes. J. Appl. Crystallogr. 25:155165.
27. Lewicki, B.,, and K. H. Nierhaus. Unpublished data.
28. Libby, R. T.,, J. L. Nelson,, J. M. Calvo,, and J. A. Gallant. 1989. Transcriptional proofreading in Escherichia coli. EMBO J. 8: 31533158.
29. Lieberman, K. R.,, and A. E. Dahlberg. 1994. The importance of conserved nucleotides of 23 S ribosomal RNA and transfer RNA in ribosome catalysed peptide bond formation. J. Biol. Chem. 269:1616316169.
30. Lill, R.,, J. M. Robertson,, and W. Wintermeyer. 1984. tRNA binding sites of ribosomes from Escherichia coli. Biochemistry 23: 67106717.
31. Lusk, J. E.,, R. J. P. Williams,, and E. P. Kennedy. 1968. Magnesium and the growth of Escherichia coli. J. Biol. Chem. 243:26182624.
32. Maden, B.,, R. Traut,, R., and R. Monro. 1968. Ribosome-catalysed peptidyl transfer: the polyphenylalanine system. J. Mol. Biol. 35: 333345.
33. Moazed, D.,, and H. F. Noller. 1989. Intermediate states in the movement of transfer RNA in the ribosome. Nature 342:142148.
34. Moazed, D.,, and H. F. Noller. 1990. Binding of tRNA to the ribosomal A and P sites protects two distinct sets of nucleotides in the 16S rRNA. J. Mol. Biol. 211:135145.
35. Monro, R. 1967. Catalysis of peptide bond formation by 50S ribosomal subunits from Escherichia coli. J. Mol. Biol. 26:147151.
36. Müller, E. C.,, and B. Wittman-Liebold. 1997. Phylogenetic relationship of organisms obtained by ribosomal protein comparison. Cell. Mol. Life Sci. 53:3450.
37. Nierhaus, K. H. 1990. The allosteric three-site model for the ribosomal elongation cycle: features and future. Biochemistry 29: 49975008.
38. Nierhaus, K. H.,, H. Schulze,, and B. S. Cooperman. 1980. Molecular mechanisms of the ribosomal peptidyltransferase centre. Biochem. Int. 1:185192.
39. Nierhaus, K. H.,, D. Beyer,, M. Dabrowski,, M. A. Schäfer,, C. M. T. Spahn,, J. Wadzack,, K.-U. Bittner,, N. Burkhardt,, G. Diedrich,, R. Jünemann,, D. Kamp,, H. Voss,, and H. B. Stuhrmann. 1995. The elongating ribosome: structural and functional aspects. Biochem. Cell Biol. 73:10111021.
40. Nierhaus, K. H.,, R. Jünemann,, and C. M. T. Spahn. 1997. Are the current three-site models valid descriptions of the ribosomal elongation cycle? Proc. Natl. Acad. Sci. USA 94:1049910500.
41. Nierhaus, K. H.,, J. Wadzack,, N. Burkhardt,, R. Jünemann,, W. Meerwinck,, R. Willumeit,, and H. B. Stuhrmann. 1998. Structure of the elongating ribosome: arrangement of the two tRNAs before and after translocation. Proc. Natl. Acad. Sci. USA 95: 945950.
42. Nissen P., , M. Kjeldgaard, , S. Thirup, , G. Polekhina, , L. Reshetnikova, , B. F. C. Clark, , and J. Nyborg. 1995. Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. Science 270:14641472.
43. Nitta, I.,, Y. Kamada,, H. Noda,, T. Ueada,, and K. Watanabe. 1998. Reconstitution of peptide bond formation with Escherichia coli 23S ribosomal RNA domains. Science 281:666669.
44. Nitta, I.,, Y. Kamada,, H. Noda,, T. Ueada,, and K. Watanabe. 1999. Peptide bond formation: retraction. Science 283:20192020.
45. Noller, H. F.,, D. Moazed,, S. Stern,, T. Powers,, P. N. Allen,, J. M. Robertson,, B. Weiser,, and K. Triman,. 1990. Structure of rRNA and its functional interactions in translation, p. 7392. In W. Hill, , A. Dahlberg, , R. A. Garrett, , P. B. Moore, , D. Schlessinger, , and J. R. Warner (ed.), The Ribosome: Structure, Function, and Evolution. American Society for Microbiology, Washington, D.C.
46. Paulsen, H.,, and W. Wintermeyer. 1986. tRNA topography during translocation: steady-state and kinetic fluorescence energytransfer studies. Biochemistry 25:27492756.
47. Porse, B. T.,, and R. A. Garrett. 1995 Mapping important nucleotides in the peptidyl transferase centre of 23 S rRNA using a random mutagenesis approach. J. Mol. Biol. 249:110.
48. Potapov, A. P.,, F. J. Triana-Alonso,, and K. H. Nierhaus. 1995. Ribosomal decoding processes at codons in the A or P sites depend differently on 2′-OH groups. J. Biol. Chem. 270:1768017684.
49. Purohit, P.,, and S. Stern. 1994. Interactions of a small RNA with antibiotic and RNA ligands of the 30S subunit. Nature 370:659662.
50. Remme, J.,, T. Margus,, R. Villems,, and K. H. Nierhaus. 1989. The third ribosomal tRNA-binding site, the E site, is occupied in native polysomes. Eur. J. Biochem. 183:281284.
51. Rheinberger, H. J. 1991. The function of the translating ribosome: allosteric three-site model of elongation. Biochimie 73:10671088.
52. Rheinberger, H.-J.,, and K. H. Nierhaus. 1980. Simultaneous binding of the 3 tRNA molecules by the ribosome of E. coli. Biochem. Int. 1:297303.
53. Rheinberger, H.-J.,, and K. H. Nierhaus. 1986. Allosteric interactions between the ribosomal transfer RNA-binding sites A and E. J. Biol. Chem. 261:91339139.
54. Rheinberger, H.-J.,, H. Sternbach,, and K. H. Nierhaus. 1981. Three tRNA binding sites on E. coli ribosomes. Proc. Natl. Acad. Sci. USA 78:53105314.
55. Rheinberger, H.-J.,, U. Geigenmüller,, A. Gnirke,, T. P. Hausner,, J. Remme,, H. Saruyam,, and K. H. Nierhaus,. 1990. Allosteric three-site model for the ribosomal elongation cycle, p. 318330. In W. E. Hill, , A. E. Dahlberg, , R. A. Garrett, , P. B. Moore, , D. Schlessinger, , and J. R. Warner (ed.) , The Ribosome: Structure, Function, and Evolution. American Society for Microbiology, Washington, D.C.
56. Rychlik, I.,, and J. Cerna. 1980. Peptidyl transferase—involvement of histidine in substrate binding and peptide bond formation. Biochem. Int. 1:193200.
57. Samaha, R. R.,, R. Green,, and H. F. Noller. 1995. A base pair between tRNA and 23S rRNA in the peptidyl transferase center of the ribosome. Nature 377:309314.
58. Schäfer, M. A.,, S. Patzke,, and K. H. Nierhaus. Unpublished data.
59. Schatz, D.,, R. Leberman,, and F. Eckstein. 1991. Interaction of Escherichia coli tRNASer with its cognate aminoacyl-tRNA synthetase as determined by footprinting with phosphorothioatecontaining tRNA transcripts. Proc. Natl. Acad. Sci. USA 88: 61326136.
60. Schilling-Bartetzko, S.,, A. Bartetzko,, and K. H. Nierhaus. 1992a. Kinetic and thermodynamic parameters for transfer RNA binding to the ribosome and for the translocation reaction. J. Biol. Chem. 267:47034712.
61. Schilling-Bartetzko, S.,, F. Franceschi,, H. Sternbach,, and K. H. Nierhaus. 1992b. Apparent association constants of transfer RNAs for the ribosomal A-site, P-site, and E-site. J. Biol. Chem. 267:46934702.
62. Schulze, H.,, and K. H. Nierhaus. 1982. Minimal set of ribosomal components for the reconstitution of the peptidyltransferase activity. EMBO J. 1:609613.
63. Sonenberg, N.,, M. Wilchek,, and A. Zamir. 1973. Mapping of Escherichia coli ribosomal components involved in peptidyl tranferase activity. Proc. Natl. Acad. Sci. USA 70:14231426.
64. Spahn, C. M. T.,, and K. H. Nierhaus. 1998. Models of the elongation cycle: an evaluation. Biol. Chem. 379:753772.
65. Spahn, C. M. T.,, J. Remme,, M. A. Schäfer,, and K. H. Nierhaus. 1996a. Mutational analysis of two highly conserved UGG sequences of 23 S rRNA from Escherichia coli. J. Biol. Chem. 271: 3284932856.
66. Spahn, C. M. T.,, M. A. Schäfer,, A. A. Krayevsky,, and K. H. Nierhaus. 1996b. Conserved nucleotides of 23 S rRNA located at the ribosomal peptidyltransferase center. J. Biol. Chem. 271: 3285732862.
67. Stark, H.,, E. V. Orlova,, J. Rinke-Appel,, N. Junke,, F. Mueller,, M. Rodnina,, W. Wintermeyer,, R. Brimacombe,, and M. vanHeel. 1997a. Arrangement of tRNAs in pre- and posttranslocational ribosomes revealed by electron cryomicroscopy. Cell 88:1928.
68. Stark, H.,, M. V. Rodnina,, J. Rinke-Appel,, R. Brimacombe,, W. Wintermeyer,, and M. van Heel. 1997b. Visualization of elongation factor Tu on the Escherichia coli ribosome. Nature 389: 403406.
69. Stuhrmann, H. B.,, N. Burkhardt,, G. Diedrich,, R. Jünemann,, W. Meerwinck,, M. Schmitt,, J. Wadzack,, R. Willumeit,, J. Zhao,, and K. H. Nierhaus. 1995. Proton- and deuteron spin targets in biological structure research. Nucleic Instr. Methods Phys. Res. 356:124132.
70. Tabor, C. W.,, and H. Tabor. 1985. Polyamines in microorganisms. Microbiol. Rev. 49:8199.
71. Tanaka, K.,, and H. Teraoka. 1966. Binding of erythromycin to Escherichia coli ribosomes. Biochim. Biophys. Acta 114:204206.
72. Tapio, S.,, and C. G. Kurland. 1986. Mutant EF-Tu increases missense error in vitro. Mol. Gen. Genet. 205:186188.
73. Thompson, R. C.,, and A. M. Karim. 1982. The accuracy of protein biosynthesis is limited by its speed: high fidelity selection by ribosomes of aminoacyl-tRNA ternary complexes containing GTP[γ S]. Proc. Natl. Acad. Sci. USA 79:49224926.
74. Triana-Alonso, F. J.,, K. Chakraburtty,, and K. H. Nierhaus. 1995. The elongation factor 3 unique in higher fungi and essential for protein biosynthesis is an E site factor. J. Biol. Chem. 270:2047320478.
75. Ühlein, M.,, W. Weglöhner,, H. Urlaub,, and B. Wittmann-Liebold. 1998. Ribosomal protein L2 is essential for protein biosynthesis: replacement of E. coli L2 with the archaebacterial and human homologues in vivo. Biochem. J. 331:423430.
76. Wadzack, J.,, N. Burkhardt,, R. Jünemann,, G. Diedrich,, K. H. Nierhaus,, J. Frank,, P. Penczek,, W. Meerwinck,, M. Schmitt,, R. Willumeit,, and H. B. Stuhrmann. 1997. Direct localization of the tRNAs within the elongating ribosome by means of neutron scattering (proton-spin contrast-variation). J. Mol. Biol. 266:343356.
77. Wintermeyer, W.,, R. Lill,, and J. M. Robertson,. 1990. Role of the tRNA exit site in ribosomal translocation, p. 348357. In W. Hill, , A. Dahlberg, , R. A. Garrett, , P. B. Moore, , D. Schlessinger, , and J. R. Warner (ed.), The Ribosome: Structure, Function, and Evolution. American Society for Microbiology, Washington, D.C.
78. Wower, J.,, I. K. Wower,, S. V. Kirillov,, K. V. Rosen,, S. S. Hixson,, and R. A. Zimmermann. 1995. Peptidyl transferase and beyond. Biochem. Cell Biol. 73:10411047.

Tables

Generic image for table
Table 1

Two views of the E site

Citation: Nierhaus K, Dabrowski M, Einfeldt E, Kamp D, Marquez V, Patzke S, Schäfer M, Stelzl U, Spahn C, Burkhardt N, Diedrich G, Blaha G, Willumeit R, Stuhrmann H. 2000. Ribosomal Elongation Cycle, p 319-336. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch26
Generic image for table
Table 2

Concentrations of ions and polyamines important for ribosomal functions

Citation: Nierhaus K, Dabrowski M, Einfeldt E, Kamp D, Marquez V, Patzke S, Schäfer M, Stelzl U, Spahn C, Burkhardt N, Diedrich G, Blaha G, Willumeit R, Stuhrmann H. 2000. Ribosomal Elongation Cycle, p 319-336. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch26

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error