Figure 1. Peptide-bond formation on the ribosome. (a) Reaction scheme. The α-amino group of aminoacyl-tRNA in the A site (yellow) attacks the carbonyl carbon of the peptidyl-tRNA in the P site (orange) to produce a new peptidyl-tRNA that is one amino acid longer in the A site and a deacylated tRNA in the P site. The peptidyl-transferase center is on the 50S subunit (green). On the 30S subunit (gray), aminoacyl-tRNA are recognized according to the match between their anticodons and the codon of mRNA in the A site. (b) Structure of the ribosome with bound tRNAs. The model is based on the crystal structure of E. coli ribosomes 12 and 58. The tRNA positions in the P site and the A site have been adjusted according to [13]. Ribosomal protein L1 and the L12 stalk [59] are shown for orientation.

Figure 2. Active-site residues of 50S subunits from H. marismortui with either bound substrate (a) or a transition-state analog (b). (a) Base-pairs formed between cytosine residues of the tRNA analogs in the A site (yellow) and P site (orange) with 23S rRNA bases (green) are indicated (PDB code: 1VQN) [10]. The α-amino group of the A-site substrate (blue) is positioned for the attack on the carbonyl carbon of the ester that links the peptide moiety of the P-site substrate (green). (b) Transition-state analog (TSA) bound to the peptidyl-transferase center (PDB code: 1VQP) [9]. The hydrogen bond between the nucleophilic nitrogen (blue) and the 2′-OH of A76 at the P site is indicated. Structures in (a) and (b) are shown in different orientations.

Figure 3. A-site substrates and substrate analogs. Reactive nucleophilic groups are circled. A76 is the 3′-terminal residue of tRNA to which the amino acid/growing polypeptide is attached; the rest of the tRNA molecule is not shown for simplicity. Puromycin is O-methyl tyrosine that is linked to N6-dimethyl adenosine via an amide bond; C-puromycin is puromycin with an additional cytidine residue that is analogous to C75 of tRNA.

Figure 4. Entropic catalysis by the ribosome. Activation parameters are shown for the second-order uncatalyzed (k_non) and ribosome-catalyzed peptide-bond formation at substrate limitation (k_cat/K_M) or saturation (k_cat) 25 and 26. Abbreviations: S1, P-site substrate; S2, A-site substrate; P, reaction products. Reproduced, with permission, from Ref. [25].

Figure 5. Concerted proton-shuttle mechanism. The P-site and A-site tRNA substrates are blue and red, respectively, ribosome residues are green, and ordered water molecules that stabilize the developing charges are gray. The attack of the α-NH₂ group on the ester carbon results in a six-membered transition state, in which the 2′-OH group of the A-site A76 ribose moiety donates its proton to the adjacent 3′ oxygen while simultaneously receiving one of the amino protons 9 and 42. Alternatively, the water molecule (*) might be used for a proton shuttle. Modified, with permission, from Ref. [60].