The Ribosome in Focus

ing research had led to a general understanding of riboThe recent solution of ribosome structure at atomic ressome morphology and function. Electron microscopy of olution by X-ray crystallography represents a quantum negatively stained 50S and 30S subunits from E. coli leap in our understanding of the mechanism of protein showed that the former possesses a chunky, almost synthesis. Notably, the major functional sites are mainly spherical, body adorned with a central protuberance composed of RNA and the activity that catalyzes peptide and two flanking arms, while the latter is characterized bond formation appears to be a ribozyme. A high-resoluby a body and head, joined by a narrow neck, and a tion crystallographic structure seemed little more than platform that extends from the body on one side. The a pipe dream to many when Ada Yonath pioneered the positions of the ribosomal proteins relative to these enwork in the late 1970s. Although high-resolution diffracvelopes were located by immune electron microscopy tion patterns were obtained within a few years, solving and neutron scattering, and the placement of functional the phasing of the patterns remained the major sticking sites, including those for peptidyl transfer, decoding, point. Improvements in computing, the use of extremoA-, P-, and E-site tRNAs, and the protein cofactors that phile ribosomes and cryo-temperatures to stabilize stimulate initiation, elongation, and termination were incrystals in the X-ray beam, and the advent of tunable ferred from a wide array of experimental approaches. high-energy synchrotron radiation all contributed to The informative, if somewhat blurred, picture of the riboprogress, while low-resolution structures obtained by some that emerged from these studies was subsecryo electron microscopy (cryo-EM) helped solve the quently improved by images derived from cryo-EM and phasing (Ban et al., 1998; Harms et al., 1999). Three has now been brought into sharp focus by the highother groups entered the fray in the mid 1990s, and the resolution crystal structures of the 50S and 30S subpace of progress in the last couple of years has been units. Solution of these structures is a salutary achievebreathtaking. To date, the 50S subunit from the haloment in structural biology, at once providing a basis philic archaeon Haloarcula marismortui has been solved for explaining in detail the vast amount of biophysical, at 2.4 Å (Ban et al., 2000) and the 30S subunit from biochemical, and genetic data on the E. coli ribosome the thermophilic (eu)bacterium Thermus thermophilus that have been accumulated over the past 40 years as at 3.0–3.3 Å (Schluenzen et al., 2000; Wimberly et al., well as the foundation for a more focused and sophisti2000). Although the structure of the T. thermophilus 70S cated examination of ribosome structure and function ribosome complexed with mRNA and tRNAs is not yet in the future. at atomic resolution, crystallographic analysis at 7.8 Å Ribosomal RNA shows how the subunits interact with each other and The secondary structure of the ribosomal RNAs, prewith their tRNA ligands (Cate et al., 1999). dicted from a comparison of rRNA sequences over a What the Ribosome Does wide phylogenetic range (Gutell, 1996), is largely correct Ribosomes are the molecular machines that manufac(Figure 2). There are, however, far more tertiary interacture proteins according to the blueprints of the mRNAs tions than could be predicted, and these create a web that encode them. Specific interactions of the ribosome of contacts that stabilize the rRNA structure. Many of with mRNAs, tRNAs, and a number of nonribosomal the nucleotides indicated as single stranded in the secprotein cofactors guarantee that polypeptide chains are ondary structure diagrams are involved in such interaccorrectly initiated, elongated, and terminated. Incoming tions or participate in somewhat irregular helix extenamino acid monomers enter the ribosomal A site in the sions. The six domains of the 23S rRNA and the 5S rRNA form of aminoacyl-tRNAs complexed with elongation of the large subunit pack closely together into a tightly factor Tu (EF-Tu) and GTP (Figure 1a). The growing polyintegrated structure (Figures 2a and 3a). Despite this peptide chain, situated in the P site as peptidyl-tRNA, consolidated packing scheme, it is of interest that virtuis then transferred to aminoacyl-tRNA (Figure 1b) and ally all portions of the 23S rRNA that contact or neighbor the new peptidyl-tRNA, extended by one residue, is the 39 end of tRNA at the A, P, and E sites occur within translocated to the P site with the aid of elongation highly conserved segments of domain 5, which may factor G (EF-G) and GTP (Figure 1c) as the deacylated therefore be a candidate for the primordial ribozyme tRNA is released from the ribosome through one or more that carried out peptide bond formation. By contrast, the exit (E) sites. The 50S subunit encompasses the peptidyl three domains of the 16S rRNA correspond to distinct transferase center, where peptide bond formation takes morphological features within the small subunit, all of place, while the 30S subunit contains the decoding site, which radiate from the neck region (Figures 2b and 3b). where complementary interactions between mRNA coAccordingly, the small subunit is less rigid than the large, don and tRNA anticodon ensure the fidelity of translawith a single RNA helix connecting the head to the body.