Ribosome 50S subunit

FIGURE 3.7 A cryo-EM map of the Escherichia coli ribosome (complexed with fMet-tRNAf Met and mRNA) where fMet = formylmethionine obtained from 73,000 particles at a resolution of 11.5 A. (a-d) Four views of the map, with the ribosome 30S subunit painted in yellow, the ribosome 50S subunit in blue, helix 44 of 16S RNA in red, and fMet-tRNA at the P site in green. Inset on top juxtaposes the experimental tRNA mass (green, on left) with the appearance of the X-ray structure of tRNA at 11 A resolution (on right). Arrows mark points at which tRNA contacts the surrounding ribosome mass. Landmarks h = head and sp = spur of the 30S subunit. CP = central protuberance LI = LI stalk and St = L7/L12 stalk base of the 50S subunit. 

Ribosomes Bacterial cells contain about 15,000 ribosomes. Each is composed of a small (SOS) subunit and a large (50S) subunit. The mass of a single ribosome is 2.3 X 10 daltons. It consists of 65% RNA and 35% protein. Ribosomes are the sites of protein synthesis. The mRNA binds to ribosomes, and the mRNA nucleotide sequence specifies the protein that is synthesized. 

Finally, to produce the structural and functional devices of the cell, polypeptides are synthesized by ribosomal translation of the mRNA. The supramolecular complex of the E. coli ribosome consists of 52 protein and three RNA molecules. The power of programmed molecular recognition is impressively demonstrated by the fact that aU of the individual 55 ribosomal building blocks spontaneously assemble to form the functional supramolecular complex by means of noncovalent interactions. The ribosome contains two subunits, the 308 subunit, with a molecular weight of about 930 kDa, and the 1590-kDa 50S subunit, forming particles of about 25-nm diameter. The resolution of the well-defined three-dimensional structure of the ribosome and the exact topographical constitution of its components are still under active investigation. Nevertheless, the localization of the multiple enzymatic domains, e.g., the peptidyl transferase, are well known, and thus the fundamental functions of the entire supramolecular machine is understood [24]. 

Of the fonr possible optical isomers of chloramphenicol, only the o-threo form is active. This antibiotic selectively inhibits protein synthesis in bacterial ribosomes by binding to the 50S subunit in the region of the A site involving the 23 S rRNA. The normal binding of the aminoacyl-tRNA in the A site is affected by chloramphenicol in such a... 

Transcription and protein synthesis in the chloroplast can be inhibited by antibiotics because chloroplast ribosomes are similar in structure to those of bacteria. Chloroplast ribosomes are 70S in size, comprising a large 50S subunit (containing... 

Ribosomes (79-87) are small organelles 17-23 nm in diameter. They can exist in clusters known as polysomes or be attached to the er where they bind to pores in the er membrane. A major constituent of the er pore is translocon, the heterotrimetric Sec 61 protein complex. Sec 61 binds to the 80s ribosomes (86). Ribosomes consist of subunits, a 30s subunit (16srRNA and 21 proteins), and a 50s subunit (23s and 5s RNAs, > proteins and the catalytic site of peptidyl transferase). Ribosomes are the sites of protein synthesis. 

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). 

This exit tunnel through the 50S subunit was first revealed by 3-D image reconstruction 20 years ago (Yonath et al., 1987) by two giants of ribosome research, Ada Yonath and the late Heinz-Giinther Wittmann (in whose laboratory in Berlin I spent a very fruitful stay 1970-1973). 

The peptidyl transferase centre of the ribosome is located in the 50S subunit, in a protein-free environment (there is no protein within 15 A of the active site), supporting biochemical evidence that the ribosomal RNA, rather than the ribosomal proteins, plays a key role in the catalysis of peptide bond formation. This confirms that the ribosome is the largest known RNA catalyst (ribozyme) and, to date, the only one with synthetic activity. Adjacent to the peptidyl transferase centre is the entrance to the protein exit tunnel, through which the growing polypeptide chain moves out of the ribosome. 

More recently, however, this mechanism was questioned by several researchers [156-158]. In the case of E. coli 50S subunits, the pH-dependent modification of A2451 by DMS (A2486 in Haloarcula marismortui) occurred only in its inactive conformation [157]. Under the conditions wherein the ribosomes were fully active, in contrast, the modification of A2451 by DMS could not be recognized. These results indicate that A2451 becomes shielded from chemical modification by a conformational change upon activation. Thus, it was concluded that the conditional modification of A2451 by DMS... 

Bacterial ribosomes consists of a small 30S and a large 50S subunit (Fig. 6).32... 

Macrolides, lincosamides and streptogramins are protein biosynthesis inhibitors that bind to 50S subunit of the ribosome and inhibit peptidyl tRNA translocation from the A-site to the P-site." Macrolides have a glycosylated 14-, 15- or 16-membered lactone ring structure and are produced by several species of Streptomyces. Lincosamide antibiotics were isolated initially from Streptomyces lincolnensis but later isolated from different species of Streptomcyces. Streptogramins were also isolated from Streptomycesgraminofaciens and subsequently from several different Streptomyces species. There are two structurally different streptogramins, A and B they are bacteriostatic individually and can be bactericidal when combined. 

Prokaryotic ribosomes contain three rRNAs 16S rRNA in the small (30S) subunit and 23S and 5S rRNA molecules in the large (50S) subunit. 

We have shown that out of fifteen forms of three-dimensional crystals from ribosomal particles, grown so far in our laboratory, some appear suitable for crystallographic data collection when using synchrotron radiation at temperatures between 19 °C and —180 °C 50S subunits from H. marismortui., and from B. stearothermophilus, including the -BLl 1 mutant, and the new crystal forms from B. stearothermophilus SOS and Thermus thermophilus 30S subunits which have only recently been grown in non-volatile precipitants We also plan to continue research on biochemically modified particles, such as SOS with one tRNA and its nascent polypeptide chain (which have already been crystallized). 

Figure 14 Separation of the Ribosomal Proteins of the 50S Subunit of Thermus thermophilus by RP-HPLC8...

Linezolid inhibits protein synthesis by preventing formation of the ribosome complex that initiates protein synthesis. Its unique binding site, located on 23S ribosomal RNA of the 50S subunit, results in no cross-resistance with other drug classes. Resistance is caused by mutation of the linezolid binding site on 23S ribosomal RNA. 

Linezolid Prevents bacterial protein synthesis by binding to the 23S ribosomal RNA of 50S subunit Bacteriostatic activity against susceptible bacteria Infections caused by methicillin-resistant staphylococci and vancomycin-resistant enterococci Oral, IV hepatic clearance (half-life 6 h) dosed twice-daily Toxicity Duration-dependent bone marrow suppression, neuropathy, and optic neuritis serotonin-syndrome may occur when coadministered with other serotonergic drugs (eg, selective serotonin reuptake inhibitors)... 

All ribosomes have two subunits, and each subunit contains several protein chains and one or more chains of RNA (ribosomal RNA, or rRNA). In the ribosome from E. coli, the smaller of the two subunits is known as the 30S subunit and the larger is referred to as the 50S subunit. (The unit S stands for Svedberg, a measure of how rapidly a particle sediments in a centrifuge.) The two subunits combine to form the active 70S ribosomal assembly. The special RNA molecules that are a part of the ribosome are quite distinct from messenger or transfer RNA molecules, and they play important roles in forming the overall ribosomal quaternary structure and in aligning mRNA and tRNA molecules during protein biosynthesis. 

FIGURE 1 The 50S subunit of a bacterial ribosome (PDB ID 1 NKW). The protein backbones are shown as blue wormlike structures the rRNA components are transparent. The unstructured extensions of many of the ribosomal proteins snake into the rRNA structures, helping to stabilize them. 

Prevents premature binding of tRNAs to A site Facilitates binding of fMet-tRNA 61 to 30S ribosomal subunit Binds to 30S subunit prevents premature association of 50S subunit enhances specificity of P site for fMet-tRNA 61... 

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