Peptidyltransferase center

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... 

The new crystal structure of the ribosome—RFl complex sheds more light into the interactions between the GGQ motif and the peptidyltransferase center. This complex represents the product state of peptide release since a deacylated tRNA is bound to the P site. Importantly, the main chain amide of the conserved glutamine hydrogen bonds to the 3 OH of A76 in the P site, which is the leaving group of the hydrolysis... 

Positions of a few proteins located by immunoelectron microscopy and three positions in the 16S RNA are marked. The puromycin binding site labeled Pm was mistakenly thought to be near the peptidyltransferase center. (B) The 50S subunit. Only a... 

Ban et al 7 Courtesy of T. A. Steitz. The peptidyltransferase center is marked by the green image of the transition state inhibitor shown in Fig. 29-13. (F) Model of three tRNAs bound to a ribosome from Thermus thermophilus in the A (a mi noacyl), P (pepti-dyl), and E (exit) sites. These are based on 0.75-nm X-ray data and a number of difference electron density maps. The 3-CCA end of the A-site tRNA is not modeled hut is... 

The ribosomal translocation process is quite complex. As the tRNAs move from A to P to E sites on the 16S RNA platform, the mRNA must also move in discrete single-codon steps. Tire acceptor stems of the tRNAs in the A and P sites must react at the appropriate times in the peptidyltransferase center. Study of protection from chemical probes suggests that tRNAs sometimes lie with the anticodon loop in the A site of the small ribosomal subunit, while the acceptor stem is in the P site of the large subunit (an A/P site as illustrated in Fig. 29-12B). Each aminoacyl-tRNA enters as a complex with EF-Tu and may initially bind with its anticodon in the A site and the acceptor stem with attached EF-Tu in a transient T site, the composite state being A/T. After loss of EF-Tu the acceptor stem can move into the A site to give an A/A state. The peptidyltransferase reaction itself necessarily involves movement at the acceptor stems by 0.1 nm or more. However, additional movement of 1 nm is needed to move the two tRNAs into states A/P and P/E, respectively. Movement of the mRNA then moves the... 

Krayevsky, A. A., Kukhanova, M. K. The peptidyltransferase center of ribosomes, in Progress in Nucleic Acid Research and Molecular Biology, Vol. 23, p. 1, New York, Academic Press 1979... 

Presumably, the incubation at 80 C acts by ultimately shaping the assembly product formed at 65°C into a spatial design capable of efficiently interacting with the other translational components. This conformational adjustment, in fact a fine tuning of the particle shape, is absolutely dependent on spermine. This observation, and the evidence that spermine is essential to activate the peptidyltransferase center of crenarchaeal ribosomes (see section 3.4), suggest that spermine-like polyamines (notably thermine) are an integral and essential constituent of the large subunits of crenarchaeal ribosomes. 

The LSU rRNA can be divided into six domains [62,73,76,77]. Domain II contains the GTPase center, certain regions of Domains IV and V are part of the peptidyltransferase center and Domain VI is involved in elongation [73,77],... 

Fig. 2. The peptidyltransferase center. The structure of the central loop of Domain V of E. coli 23S rRNA is shown. Nucleotides involved in resistance against different inhibitors are indicated. Closed symbols indicate resistance and open symbols protection against chemical modification by bound antibiotic. Mutations that confer resistance to anisomycin in archaea are indicated [87] (Hcu, Halobacterium cutirubrum Hha, H. halobium). The presence of either a G or U at position 2058 in archaea is also indicated. As a consequence of this change archaea are resistant to erythromycin (Hmo, Halococcus morrhuae, Mva, Methanococcus vannielii Tte, Thermoproteus lenax Dmo, Desulfurococcus wofirfo) [29,30,88,90]. Positions where crosslinking to photoreactive derivatives of Phe-tRNA and puromycin have been observed as well as nucleotides protected by bound tRNA are also indicated. Modified from ref [73].

Protein sequence comparisons are a powerful tool to determine the evolutionary relationship between homologous proteins in the various organisms. The sequence of these proteins, even from distantly related organisms, is often very similar. For example, the primary sequence of r-protein L2, believed to be part of the peptidyltransferase center [108], is identical in humans and hamsters. On the other hand some r-proteins, such as L4, appear to be of more structural importance and are so distantly related between eucarya and bacteria, that a relationship could only be established with the aid of the archaeal protein sequenees[107]. 

Femandez-Munoz, R., Monro, R. E., Torres-Pinedo, R., and Vazquez, D. (1971). Substrate-and antibiotic-binding sites at the peptidyltransferase center of Escherichia coli ribosomes. Studies on the chloramphenicol, lincomycin and erythromycin sites. Eur. J. Biochem. 23, 185-193. 

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