Role of the Ribosome in Peptidyl Transfer. (A) The peptidyl transferase center in the structure of the 50S subunit from Haloarcula marismortuii. The P loop and A loop of 23S RNA are shown in red and blue. The coordinates of the Yarus inhibitor (C-C-dA-phosphoramide-puromycin, yellow) have been combined with those of an A-site substrate to show the CCA ends of P- and A-site tRNAs in red and blue, respectively. There are no ribosomal proteins within 18 Å of this site. (B) Details of the interaction of key bases of 23S RNA with the Yarus inhibitor. In the structure, the N3 of A2451 was found to be 3 Å away from, and presumably hydrogen-bonded to, one of the non-bridging phosphoramide oxygens of the inhibitor.
Mechanism for peptide bond formation within the ribosome (peptidyl transferase activity). The aa-tRNA is present initially in its protonated form. The ribosomal base (adenosine 2451) then removes a proton from this ammonium group to generate the free amino group. The pKa values for the base and the ammonium group are expected to be nearly matched, so deprotonation should be quite feasible thermodynamically. The reaction products are the aa-tRNA with a free amino group and the protonated adenosine 2451 base. The amino group is a strong enough nucleophile to attack the ester linkage of the peptidyl-tRNA. This reaction generates a tetrahedral intermediate that collapses to release the tRNA previously linked to the polypeptide chain. The protonated adenosine 2451 can act as a general acid to facilitate this reaction. This generates the product with the new peptide bond formed, but in an N-protonated form. The pKa of this product is expected to be very low, so that it would readily give up a proton to generate the final product.
