Ribosome decoding center

Figure 10 Alteration of the genetic code for incorporation of non-natural amino acids, (a) In nonsense suppression, the stop codon UAG is decoded by a non-natural tRNA with the anticodon CUA. In vivo decoding of the UAG codon by this tRNA is in competition with termination of protein synthesis by release factor 1 (RFl). Purified in vitro translation systems allow omission of RF1 from the reaction mixture, (b) A new codon-anticodon pair can be created using four-base codons such as GGGU. Crystal structures of these codon-anticodon complexes in the ribosomal decoding center revealed that the C in the third anticodon position interacts with both the third and fourth codon position (purple line) while the extra A in the anticodon loop does not contact the codon.(c) Non-natural base pairs also allow creation of new codon-anticodon pairs. Shown here is the interaction of the base Y with either base X or (hydrogen bonds are indicated by red dashes).

In order to allow for translocation of the tRNA-mRNA complex, the ribosome will have to undergo conformational changes as well. The contacts described above between the decoding center and the codon-anticodon helix as well as the base pairs between the SOS A and P loops and the tRNA acceptor stems will have... 

Upon encountering a stop codon on the mRNA, the ribosome will halt incorporation of further amino acids into the polypeptide as there is no tRNA complementary to a stop codon (UAG, UGA, UAA). In order to liberate the polypeptide, the ester bond between the peptide and the tRNA residing in the P site has to be hydrolyzed — a reaction that is also catalyzed in the peptidyltransferase center. It is critical for protein synthesis that peptide release is tightly coupled to the presence of a stop codon in the decoding center to avoid premature termination resulting in shortened, nonfunctional proteins. Both functions, recognizing the stop codon and triggering... 

Murphy, F. V., 4th Ramakrishnan, V. Structure of a purine-purine wobble base pair in the decoding center of the ribosome. Nat. Struct. Mol. Biol. 2004,11, 1251-1252. 

Eleven subunit-subunit interactions have been identified between the 40S and 60S subunits of the yeast ribosome and once the two ribosomal subunits have assembled, they form a communicating ensemble (Gabashvili et al. 1999, 2003 Spahn et al. 2001). For example, the PTC of the large subunit has to be coordinated with the decoding center of the small subunit. After all, the distance between the two most important functional sites of the ribosome is approximately 75 A (Nakamura and Ito 2003 Ma and Nussinov 2004). Interaction between these sites that are far apart can be achieved either via transmission of conformational changes within and between the subunits or via ribosome-associated factors connecting the different sites. Both principles operate during protein synthesis (Rospert 2004). 

Velichutina IV, Dresios J, Hong JY, Li C, Mankin A, Synetos D, Liebman SW (2000) Mutations in helix 27 of the yeast Saccharomyces cerevisiae 18S rRNA affect the function of the decoding center of the ribosome. RNA 6 1174-1184... 

The aminoglycoside antibiotics streptomycin (Box 20-B),c d u v the neomycins,w paromomycin (see drawing below),c x z gentamycin,aa and kanamycin have one structural unit in common. They often bind to 16S ribosomal RNA in the decoding center. 

Figure 29-12 (A) Classic version of the polypeptide elongation cycle. The green color traces the pathway of an incoming tRNA carrying a new aminoa-cyl group. The decoding center is at the lower end of the A and P sites, while the peptidyltransferase is at the upper edge. The drawing is schematic, and the orientations of the tRNAs in the three sites are not pictured correctly. Here Tu=EF-Tu and G=EF-G. (B) Path of transfer RNA through ribosome.

Ribosome function is complex numerous cofactors are required for initiation, elongation, and termination (for a detailed description please see ref 33). Independent functions can be ascribed to the two subunits. Peptide bond formation takes place on the 50S subunit within the peptidyl transferase center, whereas decoding of the mRNA takes place on the 308 subunit within the decoding A- and P-sites. tRNAs in the P-site and the A-site span both subunits and couple the two events. After each round of peptide bond formation, a translocation step takes place that involves the movement of the mRNA through the ribosome, transfer of the P-site tRNA to the E (or exit)-site, and transfer of the A-site tRNA to the P-site. Most antibiotics target one of the listed steps decoding at either the A-site or the P-site, peptide bond formation within the peptidyl transferase center, or translocation. 

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