Structural insight into the role of the ribosomal tunnel in cellular regulation

Nature Structural Biology

Volumn 10, Issue 5, 2003, Pages 366-370

  Berisio, Rita ^a,b   Schluenzen, Frank ^a   Harms, Joerg ^a   Bashan, Anat ^c   Auerbach, Tamar ^c,d   Baram, David ^c   Yonath, Ada ^a,c  

^a MAX PLANCK UNIT FOR STRUCTURAL MOLECULAR BIOLOGY   (Germany)

^b CNR   (Italy)

^c WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^d FREIE UNIVERSITÄT BERLIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC AGENT; AZITHROMYCIN; ERYTHROMYCIN; MACROLIDE; RIBOSOME PROTEIN; RIBOSOME RNA; RNA; TROLEANDOMYCIN;

ARTICLE; BIOSYNTHESIS; CELL; CRYSTAL STRUCTURE; DEINOCOCCUS RADIODURANS; DRUG BINDING; DRUG PROTEIN BINDING; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE; REGULATORY MECHANISM; RIBOSOME; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; RIBOSOMAL PROTEINS; RIBOSOMES; SIGNAL TRANSDUCTION;

DEINOCOCCUS RADIODURANS;

EID: 0037407668     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsb915     Document Type: Article

References (34)

1. Milligan, R.A. & Unwin, P.N. Location of exit channel for nascent protein in 80S ribosome. Nature 319, 693-695 (1986).
2. Yonath, A., Leonard, K.R. & Wittmann, H.G. A tunnel in the large ribosomal subunit revealed by three-dimensional image reconstruction. Science 236, 813-816 (1987).
3. Gabashvili, I.S. et al. The polypeptide tunnel system in the ribosome and its gating in erythromycin resistant mutants of L4 and L22. Mol. Cell 8, 181-188 (2001).
4. Tenson, T. & Ehrenberg, M. Regulatory nascent peptides in the ribosomal tunnel. Cell 108, S91-594 (2002).
5. Morris, D.R. & Geballe, A.P. Upstream open reading frames as regulators of mRNA translation. Mol. Cell. Biol. 20, 8635-8642 (2000).
6. Sarker, S., Rudd, K.E. & Oliver, D. Revised translation start site for secM defines an atypical signal peptide that regulates E. coli secA expression. J. Bacteriol. 182, 5592-5595 (2000).
7. Nakatogawa, H. & Ito, K. The ribosomal exit tunnel functions as a discriminating gate. Cell 108, 629-636 (2002).
8. Gong, F. & Yanofsky, C. Instruction of translating ribosome by nascent peptide. Science 297, 1864-1867 (2002).
9. Stroud, R.M. & Walter, P. Signal sequence recognition and protein targeting. Curr. Opin. Struct. Biol. 9, 754-759 (1999).
10. Nissen, P., Hansen, J., Ban, N., Moore, P.B. & Steitz, T.A. The structural basis of ribosome activity in peptide bond synthesis. Science 289, 920-930 (2000).
11. Harms, J. et al. High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell 107, 679-688 (2001).
12. Unge, J. et al. The crystal structure of ribosomal protein L22 from Thermus thermophilus: insights into the mechanism of erythromycin resistance. Structure 6, 1577-1586 (1998).
13. Schluenzen, F. et al. Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria. Nature 413, 814-821 (2001).
14. Hansen, J.L. et al. The structures of four macrolide antibiotics bound to the large ribosomal subunit. Mol. Cell 10, 117-128 (2002).
15. Schluenzen, F. et al. Structural basis for the antibiotic activity of ketolides and azalides. Structure 11, 329-338 (2003).
16. Periti, P., Tonelli, F., Mazzei, T. & Ficari, F. Antimicrobial chemoimmunoprophylaxis in colorectal surgery with cefotetan and thymostimulin: prospective, controlled multicenter study. Italian Study Group on Antimicrobial Prophylaxis in Abdominal Surgery. J. Chemother 5, 37-42 (1993).
17. Chepkwony, H.K., Roets, E. & Hoogmartens, J. Liquid chromatography of troleandomycin. J. Chromatogr. A 914, 53-58 (2001).
18. Tenson, T. & Mankin, A.S. Short peptides conferring resistance to macrolide antibiotics. Peptides 22, 1661-1668 (2001).
19. Verdier, L., Gharbi-Benarous, J., Bertho, G., Mauvais, P. & Girault, J.P. Antibiotic resistance peptides: interaction of peptides conferring macrolide and ketolide resistance with Staphylococcus aureus ribosomes: conformation of bound peptides as determined by transferred NOE experiments. Biochemistry 41, 4218-4229 (2002).
20. Douthwaite, S., Hansen, L.H. & Mauvais, P. Macrolide-ketolide inhibition of MLS-resistant ribosomes is improved by alternative drug interaction with domain II of 23S rRNA. Mol. Microbiol. 36, 183-193 (2000).
21. Weisblum, B. Erythromycin resistance by ribosome modification. Antimicrob. Agents Chemother 39, 577-585 (1995).
22. Hansen, L.H., Mauvais, P. & Douthwaite, S. The macrolide-ketolide antibiotic binding site is formed by structures in domains II and V of 23S ribosomal RNA. Mol. Microbiol. 31, 623-631 (1999).
23. Xiong, L., Shah, S., Mauvais, P. & Mankin, A.S. A ketolide resistance mutation in domain II of 23S rRNA reveals the proximity of hairpin 35 to the peptidyl transferase centre. Mol. Microbiol. 31, 633-639 (1999).
24. Goldman, R.C., Fesik, S.W. & Doran, C.C. Role of protonated and neutral forms of macrolides in binding to ribosomes from Gram-positive and Gram-negative bacteria. Antimicrob. Agents Chemother. 34, 426-431 (1990).
25. Davydova, N., Streltsov, V., Wilce, M., Liljas, A. & Garber, M. L22 ribosomal protein and effect of its mutation on ribosome resistance to erythromycin. J. Mol. Biol. 322, 635-644 (2002).
26. Liao, S., Lin, J., Do, H. & Johnson, A.E. Both lumenal and cytosolic gating of the aqueous ER translocon pore are regulated from inside the ribosome during membrane protein integration. Cell 90, 31-41 (1997).
27. Stern, S., Moazed, D. & Noller, H.F. Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension. Methods Enzymol. 164, 481-489 (1988).
28. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326 (1997).
29. Bailey, S. The CCP4 suite - programs for protein crystallography. Acta Crystallogr. D 50, 760-763 (1994).
30. Brunger, A.T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905-921 (1998).
31. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110-119 (1991).
32. Flocco, M.M. & Mowbray, S.L. Cα-based torsion angles: a simple tool to analyze protein conformational changes. Protein Sci. 4, 2118-2122 (1995).
33. Carson, M. Ribbons. Methods Enzymol. 277, 493-505 (1997).
34. Wallace, A.C., Laskowski, R.A. & Thornton, J.M. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 8, 127-134 (1995).