Visualization of release factor 3 on the ribosome during termination of protein synthesis

Nature

Volumn 427, Issue 6977, 2004, Pages 862-865

  Klaholz, Bruno P ^a,b   Myasnikov, Alexander G ^c   Van Heel, Marin ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b UNIVERSITÉ DE STRASBOURG   (France)

^c MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

BIOSYNTHESIS; ELECTRON MICROSCOPY; ESCHERICHIA COLI; HYDROLYSIS; RNA;

CRYO-ELECTRON MICROSCOPY; RELEASE FACTORS (RF);

PROTEINS;

GUANOSINE DIPHOSPHATE; GUANOSINE TRIPHOSPHATASE; GUANOSINE TRIPHOSPHATE; PEPTIDE CHAIN RELEASE FACTOR 3; PEPTIDE-CHAIN-RELEASE FACTOR 3; POLYPEPTIDE; RELEASE FACTOR 3; RELEASING FACTOR; TRANSFER RNA; TRANSLATION TERMINATION FACTOR; UNCLASSIFIED DRUG;

BIOLOGY;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATIONAL TRANSITION; CRYOELECTRON MICROSCOPY; ENZYME ACTIVITY; ESCHERICHIA COLI; GENETICS; HYDROLYSIS; METABOLISM; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN SYNTHESIS REGULATION; PROTEIN TRANSPORT; REACTION ANALYSIS; RIBOSOME; RNA TRANSLATION; ULTRASTRUCTURE;

CRYOELECTRON MICROSCOPY; ESCHERICHIA COLI; GUANOSINE TRIPHOSPHATE; MODELS, MOLECULAR; PEPTIDE CHAIN TERMINATION, TRANSLATIONAL; PEPTIDE TERMINATION FACTORS; PROTEIN BINDING; PROTEIN CONFORMATION; RIBOSOMES; RNA, TRANSFER;

ESCHERICHIA COLI; NEGIBACTERIA;

EID: 1542378898     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature02332     Document Type: Article

References (28)

1. Freistroffer, D. V., Pavlov, M. Y., MacDougall, J., Buckingham, R. H. & Ehrenberg, M. Release factor RF3 in E. coli accelerates the dissociation of release factors RF1 and RF2 from the ribosome in a GTP-dependent manner. EMBO J. 16, 4126-4133 (1997).
2. Grentzmann, G. et al. Release factor RF-3 GTPase activity acts in disassembly of the ribosome termination complex. RNA 4, 973-983 (1998).
3. Kisselev, L., Ehrenberg, M. & Frolova, L. Termination of translation: interplay of mRNA, rRNAs and release factors? EMBO J. 22, 175-182 (2003).
4. Zavialov, A. V., Buckingham, R. H. & Ehrenberg, M. A posttermination ribosomal complex is the guanine nucleotide exchange factor for peptide release factor RF3. Cell 107, 115-124 (2001).
5. Klaholz, B. P. et al. Structure of the Escherichia coli ribosomal termination complex with release factor 2. Nature 421, 90-94 (2003).
6. Rawat, U. B. et al. A cryo-electron microscopic study of ribosome-bound termination factor RF2. Nature 421, 87-90 (2003).
7. Yusupov, M. M. et al. Crystal structure of the ribosome at 5.5 Å resolution. Science 292, 883-896 (2001).
8. Laurberg, M. et al. Structure of a mutant EF-G reveals domain III and possibly the fusidic acid binding site. J. Mol. Biol. 303, 593-603 (2000).
9. Stark, H. et al. Visualization of elongation factor Tu on the Escherichia coli ribosome. Nature 389, 403-406 (1997).
10. Valle, M. et al. Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process. EMBO J. 21, 3557-3567 (2002).
11. Stark, H. et al. Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex. Nature Struct. Biol. 9, 849-854 (2002).
12. Agrawal, R. K., Penczek, P., Grassucci, R. A. & Frank, J. Visualization of elongation factor G on the Escherichia coli 70S ribosome: the mechanism of translocation. Proc. Natl Acad. Sci. USA 95, 6134-6138 (1998).
13. Stark, H., Rodnina, M. V., Wieden, H. J., van Heel, M. & Wintermeyer, W. Large-scale movement of elongation factor G and extensive conformational change of the ribosome during translocation. Cell 100, 301-309 (2000).
14. Aevarsson, A. et al. Three-dimensional structure of the ribosomal translocase: elongation factor G from Thermus thermophilus. EMBO J. 13, 3669-3677 (1994).
15. Czworkowski, J., Wang, J., Steitz, T. A. & Moore, P. B. The crystal structure of elongation factor G complexed with GDP, at 2.7 Å resolution. EMBO J. 13, 3661-3668 (1994).
16. Wilson, D. N. et al. in The Ribosome, Structure, Function, Antibiotics and Cellular Interactions (ed. Garrett, R. A.) 495-508 (American Society for Microbiology Press, Washington, DC, 2000).
17. Aevarsson, A. Structure-based sequence alignment of elongation factors Tu and G with related GTPases involved in translation. J. Mol. Evol. 41, 1096-1104 (1995).
18. Agrawal, R. K., Heagle, A. B., Penczek, P., Grassucci, R. A. & Frank, J. EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome. Nature Struct Biol. 6, 643-647 (1999).
19. Lancaster, L., Kiel, M. C., Kaji, A. & Noller, H. F. Orientation of ribosome recycling factor in the ribosome from directed hydroxyl radical probing. Cell 111, 129-140 (2002).
20. Mora, L., Zavialov, A., Ehrenberg, M. & Buckingham, R. H. Stop codon recognition and interactions with peptide release factor RF3 of truncated and chimeric RF1 and RF2 from Escherichia coli. Mol. Microbiol. 50, 1467-1476 (2003).
21. Zavialov, A. V., Mora, L., Buckingham, R. H. & Ehrenberg, M. Release of peptide promoted by the GGQ motif of class I release factors regulates the GTPase activity of RF3. Mol. Cell 10, 789-798 (2002).
22. van Heel, M. et al. Single-particle cryo electron microscopy: towards atomic resolution. Quart. Rev. Biophys. 33, 307-369 (2000).
23. van Heel, M., Harauz, G., Orlova, E. V., Schmidt, R. & Schatz, M. A new generation of the IMAGIC image processing system. J. Struct. Biol. 116, 17-24 (1996).
24. Rosenthal, P. B. & Henderson, R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 31, 721-745 (2003).
25. 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).
26. Brünger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905-921 (1998).
27. Plewniak, F. et al. PipeAlign: a new toolkit for protein family analysis. Nucleic Acids Res. 31, 3829-3832 (2003).
28. Matadeen, R. et al. The Escherichia coli large ribosomal subunit at 7.5 A resolution. Structure Fold Des. 15, 1575-1583 (1999).