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 Atomic structure of the 50S Subunit from Haloarcula marismortui. Proteins are shown in blue and the two RNA strands in orange and yellow. [1] The small patch of green in the center of the subunit is the active site.  Atomic structure of the 50S large subunit of the ribosome, facing the 30S small ribosomal subunit. Proteins are colored in blue and RNA in ochre. The active site, adenine 2486, is highlighted in red. Image created from using PyMol
Structure 50S, roughly equivalent to the 60S ribosomal subunit in eukaryotic cells, is the large subunit of the 70S ribosome of prokaryotes. The 50S subunit is primarily composed of proteins but also contains single-stranded RNA known as ribosomal RNA (rRNA). rRNA forms secondary and tertiary structures to maintain the structure and carry out the catalytic functions of the ribosome. Electron microscopy and x-ray crystallography have yielded electron density maps allowing the structure of 50S in Haloarcula marismortui to be determined up to 2.4-angstrom resolution. The large ribosomal subunit (50S) is approximately twice as massive as the small ribosomal subunit (30S). The model of 50S determined in 2000 by the Steitz lab includes 2711 of the 2923 nucleotides of 23S rRNA, all 122 nucleotides of its 5S rRNA, and structure of 27 of its 31 proteins. Ribosomal proteins Ribosomal proteins are mostly on the surface of the 50S subunit, though some extend into the active site. Seventeen proteins are globular and the remaining 13 either have protruding extensions or are entirely extended. The proteins do not shield all rRNA surfaces but act like mortar filling the gaps and cracks between RNA bricks . The main function of protein is to stabilize the tertiary structure and orientation of the rRNA. The burial of a large amount of surface area may be required to provide the free energy required to immobilize the structure of molecules, thus making it possible to form interior protein-poor catalytic regions. Some ribosomal proteins may also aid in interactions with elongation factors. Ribosomal RNA The secondary structure of 23S is divided into six large domains, within which domain V is most important in its peptidyl transferase activity. Each domain contains normal secondary structure (e.g., base triple, tetraloop, cross-strand purine stack) and is also highly symmetric in tertiary structure and is protrude by proteins between their helices. At tertiary structure level, the large subunit rRNA is a single and gigantic domain while the small subunit contains three structural domains. This difference reflects the less flexibility of big subunit required by its function. Function 50S includes the activity that catalyzes peptide bond formation (peptidyl transfer reaction), prevents premature polypeptide hydrolysis, provides a binding site for the G-protein factors (assists initiation, elongation, and termination), and helps protein folding after synthesis. Promotes peptidyl transfer reaction and prevents peptidyl hydrolysis An induced-fit mechanism has been revealed for how 50S catalyze peptidyl transfer reaction and prevent peptidyl hydrolysis. The amino group of aminoacyl-tRNA (binds to A site) attacks the carbon of carbonyl group of peptidyl-tRNA (binds to P site) and finally yields a peptide extended by one amino acid esterified to the A site bound-tRNA and a deacylated tRNA in the P site. When A site is unoccupied, nucleotide U2620 (E. coli U2585) and A2486 (2451), C2106 (2063) sandwich the carbonyl group in the middle, forcing it into an orientation facing the A site. This orientation prevents any nucleophilic attack from A site because the optimal attacking angle is 105 degrees from the plane of the ester group. When tRNA with compete CCA sequence at its acceptor stem is bound to A site, C74 of tRNA stacking with U2590 (2555) induces a conformational change in the ribosome, resulting in movement of U2541 (2506), U2620 (2585) through G2618 (2583). The displacements of bases allow ester group adopts a new conformation assessable to nucleophilic attack from A site. The N3 (nitrogen) of A2486 (2451) is nearest to the peptide bond being synthesized and may function as a general base to facilitate the nucleophilic attack by the amino group of aminoacyl-tRNA (in A site). The pKa of A2486 (2451) is about 5 units higher in order to hydrogen bond with the amino group thus increasing its nucleophilicity. The elevation of pKa is achieved through a charge relay mechanism. A2486 (2451) interacts with G2482 (G2447), which hydrogen-bonds with the buried phosphate of A2486 (2450). This buried phosphate can stabilize normally rare imino tautomeric forms of both bases, resulting in an increase in negative charge density on N3. Help protein formation After initiation, elongation, and termination, there is a fourth step of the disassembly of the post-termination complex of ribosome, mRNA, and tRNA, which is prerequisite for the next round of protein synthesis. Large ribosomal subunit has a role in protein folding both in vitro and in vivo. Large ribosomal subunit provides a hydrophobic surface for the hydrophobic collapse step of protein folding. The newly synthesis protein needs fully access to the large subunit to fold and this process may take a period of time (5 minutes for beta-galactosidase). See also References - 2. Nissen P, Hansen J, Ban N, Moore P, Steitz T (2000). The structural basis of ribosome activity in peptide bond synthesis . Science 289 (5481): 920-29.
- 3. Schmeing T, Huang K, Strobel S, Steitz T (2005). An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA . Nature 438: 520-24.
- 4. Basu A, Ghosh J, Bhattacharya A, Pal S, Chowdhury S, DasGupta C (2003). Splitting of ribosome into its subunits by unfolded polypeptide chains . Current Science 84: 1123-25.
External links ca:50S zh:50S
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