Ribosome subunit structure

Carter AP, Clemons WM, Brodersen DE et al (2000) Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 407 340-348... 

Brodersen DE, Clemons WM, Carter AP et al (2000) The structural basis for the action of the antibiotics tetracycline, pactamycin and hygromycin B on the 30S ribosomal subunit. Cell 103 1143-1154... 

Biochemical and genetic experiments in yeast have revealed that the b poly(A) tail and its binding protein, Pablp, are required for efficient initiation of protein synthesis. Further studies showed that the poly(A) tail stimulates recruitment of the 40S ribosomal subunit to the mRNA through a complex set of interactions. Pablp, bound to the poly(A) tail, interacts with eIF-4G, which in turn binds to eIF-4E that is bound to the cap structure. It is possible that a circular structure is formed and that this helps direct the 40S ribosomal subunit to the b end of the mRNA. This helps explain how the cap and poly(A) tail structures have a synergistic effect on protein synthesis. It appears that a similar mechanism is at work in mammalian cells. 

Other antibiotics inhibit protein synthesis on all ribosomes (puromycin) or only on those of eukaryotic cells (cycloheximide). Puromycin (Figure 38—11) is a structural analog of tyrosinyl-tRNA. Puromycin is incorporated via the A site on the ribosome into the carboxyl terminal position of a peptide but causes the premature release of the polypeptide. Puromycin, as a tyrosinyl-tRNA analog, effectively inhibits protein synthesis in both prokaryotes and eukaryotes. Cycloheximide inhibits peptidyltransferase in the 60S ribosomal subunit in eukaryotes, presumably by binding to an rRNA component. 

The ribosome is a ribozyme this is how Cech (2000) commented on the report by Nissen et al. (2000) in Science on the successful proof of ribozyme action in the formation of the peptide bond at the ribosome. It has been known for more than 30 years that in the living cell, the peptidyl transferase activity of the ribosome is responsible for the formation of the peptide bond. This process, which takes place at the large ribosome subunit, is the most important reaction of protein biosynthesis. The determination of the molecular mechanism required more than 20 years of intensive work in several research laboratories. The key components in the ribosomes of all life forms on Earth are almost the same. It thus seems justified to assume that protein synthesis in a (still unknown) common ancestor of all living systems was catalysed by a similarly structured unit. For example, in the case of the bacterium E. coli, the two subunits which form the ribosome consist of 3 rRNA strands and 57 polypeptides. Until the beginning of the 1980s it was considered certain that the formation of the peptide bond at the ribozyme could only be carried out by ri-bosomal proteins. However, doubts were expressed soon after the discovery of the ribozymes, and the possibility of the participation of ribozymes in peptide formation was discussed. 

After attachment of amino acids to tRNA, the amino acids are assembled beginning with the amino terminus and proceeding in the direction of the carboxy terminus. The ribosome is the machinery that translates the mRNA into protein. The ribosome is a very complex protein that contains ribosomal RNA as a functional and structural component. The ribosome assembles around the mRNA, and the cap and other signals allow alignment of the mRNA into the correct position. The initial assembly of the mRNA into the ribosome requires association of the small ribosomal subunit with an initiator tRNA (Met or fMet). Small is a misstatement, because the small ribosomal subunit is a large, complex assembly of numerous smaller proteins—it s just smaller than the... 

Once the amino acid has been bound to its tRNA, it can pass to the next phase of protein synthesis, involving its interaction with mRNA, which takes place on the ribosome, a molecular machine of enormous complexity. The ribosome of E. coli is a ribonucleoprotein assembly of molecular weight 2700 kDa, and sedimentation constant of 70S9. It is made up of roughly two-thirds RNA and one-third protein, and can be separated into a small (30S) and a large (50S) subunit. The 30S subunit contains 21 proteins and one 16S RNA molecule, while the large subunit has 34 different proteins and two RNA molecules, one 23S and one 5S. Despite its size and complexity, the structure of both ribosomal subunits has been determined to atomic resolution (Figure 4.32), and very recently the atomic structure of the 70S ribosome has been determined at 2.8 A resolution (Selmer et al., 2006). 

The question can be raised as to whether the structure of the proteins within the ribosomal particle is the same as in the isolated state. The only direct evidence we have that the structures of proteins are not changed upon incorporation into the subunit is provided by the neutron-scattering studies of Nierhaus et al. (1983b). They showed that individual proteins in solution had radii of gyration indistinguishable from those obtained from their counterparts on the ribosomal subunits in the same buffers and under identical preparation conditions. 

Fig. 3. Secondary structure comparison between the RNA molecules from the small ribosomal subunits of human mitochondrion, E. coli, and yeast (Brimacombe, 1983). Relations between a, b, and c are as in Fig. 2.

Determination of the spatial juxtaposition of the proteins and RNA within the ribosomal subunits is a major goal in ribosome research. Key functional characteristics can be clearly understood only if the ribosome topography is known. As our understanding of the structure of the individual components increases, there is an increasing need to piece together the structure to provide the functional understanding desired. 

Of great interest is the fact that ribosomal subunits and ribosomes themselves have now been crystallized, and low-resolution structural maps have already been obtained. However, to grow suitable crystals and to resolve the ribosomal structure at a sufficiently high resolution remains a great challenge and task to biochemists and crystallographers. 

Figure 7 Multiple roles of the deubiquitinating enzymes. Deubiquitinating enzymes (DUBs) of the UCH type (dark scissors) process ubiquitin precursors. UCH-L1 generates monoubiquitins from tandemly linked ubiquitin gene product. UCH-L3 acts on ubiquitin synthesized as a protein fused to small ribosomal subunits. DUBs of the UBP type (shaded scissors) process ubiquitins linked in isopeptide linkage in polyubiquitin chains. DUBs also reverse the ubiquitination on erroneously targeted substrates (editing). Another important function of DUBs is disassembly of polyubiquitin chains as the ubiquitinated substrate is degraded. Ubiquitin attached to substrates after activation are indicated as lollipop-like structures with filled circles. Free ubiquitin or ubiquitin unit in precursor is shown with open circles.

The small ribosomal subunit binds to the mRNA. In prokaryotes, the 16S rRNA of the small subunit binds to the Shine-Dalgamo sequence in the 5 untranslated region of the niRNA. In eukaryotes, the small subunit binds to the 5 cap structure and slides down the message to the first AUG. 

Linezohd (Zyvox) is an oxazolidinone, a tive-membered heterocychc ring that forms the core of the hnezohd structure. The approval of hnezohd by the FDA in 2000 marked the first new structural class of antibacterial introduced into medical practice in the United States in 40 years. It is notable for its activity against methicillin-resistant Staph aureus, MRSA, and vancomycin-resistant Enterococcus faecium, VRE. It is bacteriostatic rather than bactericidal but finds significant use in patients with an intact immune system. Like several other classes of antibacterials, linezolid is an inhibitor of protein synthesis. It interacts specifically with the RNA component of a bacterial ribosome subunit to prevent initiation of protein synthesis. 

Cellular RNAs vary widely in their size, structure, and lifespan. The great majority of them are ribosomal RNA (rRNA), which in several forms is a structural and functional component of ribosomes (see p.250). Ribosomal RNA is produced from DNA by transcription in the nucleolus, and it is processed there and assembled with proteins to form ribosome subunits (see pp.208, 242). The bacterial 16S-rRNA shown in Fig. A, with 1542 nucleotides (nt), is a component of the small ribosomae subunit, while the much smaller 5S-rRNA (118 nt) is located in the large subunit. 

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