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FIGURE 14-33 rna surrounds the peptidyl transferase center of the large riboso-mal subunit. The three-dimensional structure ot the bacterial 50S subunit is shown. The rRKAs are shown in gray and the ribosomal proteins are shown in purple. The 3' ends of the A and Psite tRNAs that are immediately adjacent to the pep tidyf transferase center are shewn in green and red, respectively. (Yusupov MM, Yusupova G.Z.. Baucom A., Lieberman K., Earnest T.M., Cate i.H„ and toiler HE 2001 Science 797: 883 ) Image prepared with MoJScnpt, BobScript, and Raster 3D.

How does the 23S rRNA catalyze peptide bond formation? The exact mechanism remains to be determined, hot some answers to this question are beginning to emerge. First, base-pairing between the 23S rRNA and the CCA ends of the WNAs in the A and the P sites help to position the alpha-ammo group of the aminoacyl-tRNA to attack the carbonyl group of the growing polypeptide attached to the peptidyl-tRNA. These interactions ore also likely to stabilize the aminoacyl-tRNA after accommodation.

Because close proximity of substrates is rarely sufficient to generate high levels of catalysis, it is hypothesized that other elements of the ribosomal RNA change the chemical environment of the peptidyl transferase active site. For example, it has been proposed that nucleotides in the peptidyl transferase center accept a hydrogen from the alpha amino group of the aminoacyl-tRNA, making the associated nitrogen a stronger nucleophile. This is a common mechanism used by many proteins to stimulate nucleophilic attack of carbonyl groups.

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