A structural understanding of the dynamic ribosome machine (original) (raw)
References
Palade, G. E. A small particulate component of the cytoplasm. J. Biophys. Biochem. Cytol.1, 59–68 (1955). ArticleCAS Google Scholar
Watson, J. D. Involvement of RNA in the synthesis of proteins. Science140, 17–26 (1963). ArticleCAS Google Scholar
Lake, J. A. Ribosomal structure determined by electron microscopy of E. coli small subunits, large subunits and monomeric ribosomes. J. Mol. Biol.105, 131–159 (1976). ArticleCAS Google Scholar
Schuwirth, B. S. et al. Structures of the bacterial ribosome at 3.5 Å resolution. Science310, 827–834 (2005). Presents the first complete atomic structure of the 70S ribosome fromE. coliderived from a high-resolution map, but without bound substrates. ArticleCAS Google Scholar
Selmer, M. et al. Structure of the 70S ribosome complexed with mRNA and tRNA. Science313, 1935–1942 (2006). The most complete and accurate structure of the 70S ribosome published to date also has bound mRNA, as well as tRNAs at the A site (partial), P site and E site. ArticleCAS Google Scholar
Korostelev, A., Trakhanov, S., Laurberg, M. & Noller, H. F. Crystal structure of a 70S ribosome–tRNA complex reveals functional interactions and rearrangements. Cell126, 1066–1077 (2006). Article Google Scholar
Ogle, J. M. et al. Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science292, 897–902 (2001). The structure of the 30S subunit with mRNA and an anticodon stem-loop RNA mimic of tRNA shows how decoding occurs in the A site. ArticleCAS Google Scholar
Nissen, P., Ban, N., Hansen, J., Moore, P. B. & Steitz, T. A. The structural basis of ribosome activity in peptide bond synthesis. Science289, 920–930 (2000). ArticleCAS Google Scholar
Schmeing, T. M., Huang, K. S., Strobel, S. A. & Steitz, T. A. An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA. Nature438, 520–524 (2005). Shows that the binding of an appropriate A-site substrate to the 50S subunit complex with a P-site substrate induces an active site conformational change that is essential for catalysis. ArticleCAS Google Scholar
Schmeing, T. M., Huang, K. S., Kitchen, D. E., Strobel, S. A. & Steitz, T. A. Structural insights into the roles of water and the 2′ hydroxyl of the P site tRNA in the peptidyl transferase reaction. Mol. Cell20, 437–448 (2005). ArticleCAS Google Scholar
Schmeing, T. M. et al. A pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunits. Nature Struct. Biol.9, 225–230 (2002). CASPubMed Google Scholar
Green, R. & Noller, H. F. Ribosomes and translation. Annu. Rev. Biochem.66, 679–716 (1997). ArticleCAS Google Scholar
Nissen, P., Ippolito, J. A., Ban, N., Moore, P. B. & Steitz, T. A. RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc. Natl Acad. Sci. USA98, 4899–4903 (2001). ArticleCAS Google Scholar
Ogle, J. M., Murphy, F. V. I., Tarry, M. J. & Ramakrishnan, V. Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell111, 721–732 (2002). ArticleCAS Google Scholar
Rodnina, M. V. & Wintermeyer, W. Fidelity of aminoacyl-tRNA selection on the ribosome's kinetic and structural mechanisms. Annu. Rev. Biochem.70, 415–435 (2001). ArticleCAS Google Scholar
Valle, M. et al. Cryo-EM reveals an active role for aminoacyl tRNA in the accommodation process. EMBO J.21, 3557–3567 (2002). ArticleCAS Google Scholar
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). CASPubMed Google Scholar
Valle, M. et al. Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy. Nature Struct. Biol.10, 899–906 (2003). ArticleCAS Google Scholar
Berk, V., Zhang, W., Pai, R. D. & Cate, J. H. D. Structural basis for mRNA and tRNA positioning on the ribosome. Proc. Natl Acad. Sci. USA103, 15830–15834 (2006). ArticleCAS Google Scholar
Maguire, B. A., Benaminov, A. D., Ramu, H., Mankin, A. S. & Zimmermann, R. A. A protein component at the heart of an RNA machine: the importance of protein L27 for the function of the bacterial ribosome. Mol. Cell.20, 427–435 (2005). ArticleCAS Google Scholar
Moore, P. B. & Steitz, T. A. The structural basis of large ribosomal subunit function. Annu. Rev. Biochem.72, 813–850 (2003). ArticleCAS Google Scholar
Hansen, J. L., Schmeing, T. M., Moore, P. B. & Steitz, T. A. Structural insights into peptide bond formation. Proc. Natl Acad. Sci. USA99, 11670–11675 (2002). ArticleCAS Google Scholar
Koshland, D. E. Mechanism of transfer enzymes. In The Enzymes (Boyer, P. D., Lardy, H. & Myrback, K., eds) 305–346 (Academic Press, New York, 1959). Google Scholar
Bennett, W. S. & Steitz, T. A. Glucose-induced conformational change in yeast hexokinase. Proc. Natl Acad. Sci. USA75, 4848–4852 (1976). Article Google Scholar
Beringer, M. & Rodnina, M. V. The ribosomal peptidyl transferase. Mol. Cell26, 311–321 (2007). ArticleCAS Google Scholar
Caskey, C. T., Beaudet, A. L., Scolnick, E. M. & Rosman, M. Hydrolysis of fMet-tRNA by peptidyl transferase. Proc. Natl Acad. Sci. USA68, 3163–3167 (1971). ArticleCAS Google Scholar
Pape, T., Wintermeyer, W. & Rodnina, M. V. Conformational switch in the decoding region of 16S rRNA during aminoacyl-tRNA selection on the ribosome. Nature Struct. Biol.7, 104–107 (2000). ArticleCAS Google Scholar
Paige, M. I. & Jencks, W. P. Entropic contributions to rate acceleration in enzymatic and intramolecular reactions and the chelate effect. Proc. Natl Acad. Sci. USA68, 1678–1683 (1971). Article Google Scholar
Youngman, E. M., Brunelle, J. L., Kochaniak, A. B. & Green, R. The active site of the ribosome is composed of two layers of conserved nucleotides with distinct roles in peptide bond formation and peptide release. Cell117, 589–599 (2004). ArticleCAS Google Scholar
Dorner, S., Panuschka, F., Schmid, W. & Barta, A. Mononucleotide derivatives as ribosomal P-site substrates reveal an important contribution of the 2′-OH activity. Nucl. Acids Res.31, 6536–6542 (2003). ArticleCAS Google Scholar
Weinger, J. S., Parnell, K. M., Dorner, S., Green, R. & Strobel, S. A. Substrate-assisted catalysis of peptide bond formation by the ribosome. Nature Struct. Biol.11, 1101–1106 (2004). Biochemical demonstration of the large contribution of the 2′ hydroxyl group of A76 of the P-site substrate to peptide bond formation. ArticleCAS Google Scholar
Moazed, D. & Noller, H. F. Intermediate states in the movement of transfer RNA in the ribosome. Nature342, 142–148 (1989). ArticleCAS Google Scholar
Gao, N. et al. Mechanism for the disassembly of the post termination complex inferred from cryo-EM studies. Mol. Cell18, 663–674 (2005). ArticleCAS Google Scholar
Valle, M., Zavialov, A., Sengupta, J., Rawat, U., Ehrenberg, M. & Frank, J. Locking and unlocking of ribosomal motions. Cell114, 123–134 (2003). ArticleCAS Google Scholar
Ævarsson, A. et al. Three-dimensional structure of the ribosomal translocase: elongation factor G from Thermus thermophilus. EMBO J.13, 3669–3677 (1994). Article Google Scholar
Czworkowski, J., Wang, J., Steitz, T. A. & Moore, P. B. The crystal structure of elongation factor G complexed with DGP, at 2.7 Å resolution. EMBO J.13, 3661–3668 (1994). ArticleCAS Google Scholar
Rodnina, M., Savelsbergh, A., Katunin, V. I. & Wintermeyer, W. Hydrolysis of GTP by elongation factor G drives tRNA movement on the ribosome. Nature385, 37–41 (1979). Article Google Scholar
Frank, J. & Agrawal, R. K. A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature406, 318–322 (2000). The important rotation of the small subunit relative to the large subunit on EFG–GTP binding is shown in this cryo-EM study. ArticleCAS Google Scholar
Connell, S. R. et al. Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors. Mol. Cell25, 751–764 (2007). The highest-resolution cryo-EM structure of the 70S ribosome with bound EFG gives insights into the mechanism of its function in translocation. ArticleCAS Google Scholar
Schmeing, T. M., Moore, P. B. & Steitz, T. A. Structure of deacylated tRNA mimics bound to the E site of the large ribosomal subunit. RNA9, 1345–1352 (2003). ArticleCAS Google Scholar
Schroeder, S., Blaha, G., Tirado-Rives, J., Steitz, T. A. & Moore, P. B. The structures of antibiotics bound to the E-site region of the 50S ribosomal subunit of Haloarcula marismortui; 13-deoxytedanolide and girodazole. J. Mol. Biol.367, 1471–1479 (2007). ArticleCAS Google Scholar
Milligan, R. A. & Unwin, P. N. In vitro crystallization of ribosomes from chick embryos. J. Cell Biol.95, 648–653 (1982). ArticleCAS Google Scholar
Ban, N., Nissen, P., Hansen, J., Moore, P. B. & Steitz, T. A. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science289, 905–920 (2000). ArticleCAS Google Scholar
Gabashvili, I. S. et al. The polypeptide tunnel system in the ribosome and its gating in erythromycin mutants of L4 and L22. Mol. Cell8, 181–188 (2001). ArticleCAS Google Scholar
Voss, N. R., Gerstein, M., Steitz, T. A. & Moore, P. B. The geometry of the ribosomal exit tunnel. J. Mol. Biol.360, 893–906 (2006). ArticleCAS Google Scholar
Gilbert, R. J. et al. Three dimensional structures of translating ribosomes by cryo-EM. Mol. Cell14, 57–66 (2004). ArticleCAS Google Scholar
Malkin, L. I. & Rich, A. Partial resistance of nascent polypeptide chains to proteolytic digestion due to ribosomal shielding. J. Mol. Biol.26, 329–346 (1967). ArticleCAS Google Scholar
Klein, D. J., Moore, P. B. & Steitz, T. A. The roles of ribosomal proteins in the structure, assembly and evolution of the large ribosomal subunit. J. Mol. Biol.340, 141–177 (2004). ArticleCAS Google Scholar
Ferhtz, L. et al. Trigger factor in complex with the ribosome forms a molecular cradle for nascent proteins. Nature431, 590–596 (2004). Article Google Scholar
Schlünzen, F. et al. The binding mode of the trigger factor in the ribosome: implications for protein folding and SRP interaction. Structure13, 1685–1694 (2005). Article Google Scholar
Petry, S. et al. Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon. Cell123, 1256–1266 (2005). Article Google Scholar
Ito, K., Uno, M. & Nakamura, Y. A tripeptide “anticodon” deciphers stop codons in messenger RNA. Nature403, 680–684 (2000). ArticleCAS Google Scholar
Borovinskaya, M. A. et al. Structural basis for aminoglycoside inhibition of bacterial ribosome recycling. Nature Struct. Mol. Biol.14, 727–732 (2007). ArticleCAS Google Scholar
Weixlbaumer, A. et al. Crystal structure of the ribosome recycling factor bound to the ribosome. Nature Struct. Mol. Biol.14, 733–737 (2007). ArticleCAS Google Scholar
van den Berg, B. et al. X-ray structure of a protein-conducting channel. Nature427, 36–44 (2004). ArticleCAS Google Scholar
Mitra, K. et al. Structure of the E. coli protein-conducting channel bound to a translating ribosome. Nature438, 318–324 (2005). ArticleCAS Google Scholar
Dever, T. E. Gene-specific regulation by general translation factors. Cell108, 545–556 (2002). ArticleCAS Google Scholar
Sonenberg, N. & Dever, T. E. Eukaryotic translation initiation factors and regulators. Curr. Opin. Struct. Biol.13, 56–63 (2003). ArticleCAS Google Scholar
Simonovic, M. & Steitz, T. A. Cross-crystal averaging reveals that the structure of the peptidyl-transferase center is the same in the 70S ribosome and 50S subunit. Proc. Natl Acad. Sci. USA.105, 500–505 (2008). ArticleCAS Google Scholar
Brunnelle, J. L. et al. The interaction between C75 of tRNA and the A loop of the ribosome stimulates peptidyl transferase activity. RNA12, 33–39 (2006). Article Google Scholar
Ramakrishnan, V. Ribosome structure and the mechanism of translation. Cell108, 557–572 (2002). ArticleCAS Google Scholar
Janosi, L., Shimizu, I., Kaji, A. Ribosome recycling factor (ribosome releasing factor) is essential for bacterial growth. Proc. Natl Acad. Sci. USA91, 4249–4253 (1994). ArticleCAS Google Scholar