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Peptidyl transfer

Many examples of catalytic nucleic acids obtained by in vitro selection demonstrate that reactions catalyzed by ribozymes are not restricted to phosphodiester chemistry. Some of these ribozymes have activities that are highly relevant for theories of the origin of life. Hager et al. have outlined five roles for RNA to be verified experimentally to show that this transition could have occurred during evolution [127]. Four of these RNA functionalities have already been proven Its ability to specifically complex amino acids [128-132], its ability to catalyze RNA aminoacylation [106, 123, 133], acyl-transfer reactions [76, 86], amide-bond formation [76,77], and peptidyl transfer [65,66]. The remaining reaction, amino acid activation has not been demonstrated so far. [Pg.116]

Fig. 11. Comparison of the peptidyl transfer reaction in the ribosome and in the selected peptidyltransferase ribozyme. The ribosome contains a binding site for the peptidyl-tRNA (P-site) and for the aminoacyl-tRNA (A-site). In the selected ribozyme the binding site for the AMP-Met-Bio substrate would be analogous to the P-site. The attacking a-amino group which is bound in the A-site in the ribosome is covalently attached to the 5 -end in the ribozyme. Catalytically active RNAs preferentially attach the biotin tag onto themselves and can thus be separated from the inactive ones... Fig. 11. Comparison of the peptidyl transfer reaction in the ribosome and in the selected peptidyltransferase ribozyme. The ribosome contains a binding site for the peptidyl-tRNA (P-site) and for the aminoacyl-tRNA (A-site). In the selected ribozyme the binding site for the AMP-Met-Bio substrate would be analogous to the P-site. The attacking a-amino group which is bound in the A-site in the ribosome is covalently attached to the 5 -end in the ribozyme. Catalytically active RNAs preferentially attach the biotin tag onto themselves and can thus be separated from the inactive ones...
Termination Three codons (UAA, UAG and UGA) are stop codons which do not code for any amino acid but, instead of attaching to a tRNA molecule, they bind a protein release factor. When one of these factors is encountered by the ribosome, peptidyl transfer is aborted, the completed polypeptide chain released by hydrolysis and the ribosome subunits separate. The N-terminal methionine unit is then removed from the polypeptide chain. [Pg.468]

Although the details of the catalytic mechanism are still being debated, the peptidyl transfer reaction is clearly catalyzed by RNAs. One of the disad-... [Pg.246]

Peptide bond formation (peptidyl transfer) occurs by reaction of the nascent peptide with the aminoacyl-tRNA properly base-paired in the A site. [Pg.172]

Each synthetase module contains three active site domains The A domain catalyzes activation of the amino acid (or hydroxyacid) by formation of an aminoacyl- or hydroxyacyl-adenylate, just as occurs with aminoacyl-tRNA synthetases. However, in three-dimensional structure the A domains do not resemble either of the classes of aminoacyl-tRNA synthetases but are similar to luciferyl adenylate (Eq. 23-46) and acyl-CoA synthetases.11 The T-domain or peptidyl carrier protein domain resembles the acyl carrier domains of fatty acid and polyketide synthetases in containing bound phos-phopantetheine (Fig. 14-1). Its -SH group, like the CCA-terminal ribosyl -OH group of a tRNA, displaces AMP, transferring the activated amino acid or hydroxy acid to the thiol sulfur of phosphopan-tetheine. The C-domain catalyzes condensation (peptidyl transfer). The first or initiation module lacks a C-domain, and the final termination module contains an extra termination domain. The process parallels that outlined in Fig. 21-11.1... [Pg.1713]

The evaluation of kinetic properties of NRPS systems is a problem of generally underestimated complexity. The basic path was established in 1971, defining activation, thiolation, and peptidyl transfers as basic reactions. The further refinement from structural data to establish the multiple carrier model, and now to tackle domain interactions, has added some precision to the questions asked. However, we have not yet arrived at a complete kinetic description of even the simple tripeptide synthetase. The ACV synthetase operates with four different substrates at six binding sites, releasing 3 moles of AMP and 3 moles of MgPPi for each ACV formed at optimal conditions [51], A sequence of 10 reactions has been... [Pg.12]

It competes with the latter as an acceptor in the peptidyl transfer reaction. The growing chain is transferred to the NH2 group of puromycin and is prematurely terminated. [Pg.507]

Next, fMet-tRNA will deliver the carboxyl terminus of fMet to the amino terminus of the amino acid linked to the tRNA at the A site (a peptidyl transfer reaction), with the subsequent formation of a peptide bond between the two amino acids. At this point, the tRNA at the A site is covalently linked to a dipeptide (Fig. 23-5). [Pg.370]

The three antibiotic inhibitors of translation that will be used in this experiment are chloramphenicol, cycloheximide, and puromycin (Fig. 23-10). Chloramphenicol is specific for prokaryotic ribosomes, blocking the transfer of the peptide on the tRNA at the P site to the amino acid linked to the tRNA at the A site (the peptidyl transfer reaction). Since the source of the ribosomes used in this experiment is wheat germ (eukaryotic), we would predict that chloramphenicol would not have a great effect on translation. The mechanism of cycloheximide-mediated inhibition is the same as that described above for chloramphenicol, except for the fact that it is specific for the 80S eukaryotic ribosome. Puromycin is a more broad translational inhibitor, effective on both eukaryotic and prokaryotic ribosomes. It acts as a substrate analog of aminoacyl tRNA. When it binds at the A site of the ribosome, it induces premature termination of translation (Fig. [Pg.377]

Figure 7 General chemical scheme for peptidyl transfer by the ribosome. The scheme shows nucleophilic attack by the amine group of the amino acid (with side chain R2) esterified to the tRNA in the ribosomal A site (right) on the ester linkage of the aminoacyl tRNA (with amino acid chain Rl). The 2 OH of the peptidyl tRNA participates in the reaction and seems to transfer a proton to the 3 0 leaving group, either directly or potentially via a solvent bridge. Adapted from Reference 76. Figure 7 General chemical scheme for peptidyl transfer by the ribosome. The scheme shows nucleophilic attack by the amine group of the amino acid (with side chain R2) esterified to the tRNA in the ribosomal A site (right) on the ester linkage of the aminoacyl tRNA (with amino acid chain Rl). The 2 OH of the peptidyl tRNA participates in the reaction and seems to transfer a proton to the 3 0 leaving group, either directly or potentially via a solvent bridge. Adapted from Reference 76.
Erlacher MD, Lang K, Wotzel B, Rieder R, Micura R, Polacek N. Efficient ribosomal peptidyl transfer critically relies on the presence of the ribose 2 -OH at A2451 of 23S rRNA. J. Am. Chem. Soc. 2006 128 4453-4459. [Pg.2031]

With exception of the ribosome that catalyzes peptidyl transfer reactions, aU naturally occurring ribozymes catalyze phosphoryl... [Pg.2340]

Studies on archaeal ribosomes have shown that mutations that confer resistance to the peptidyl-transfer inhibitor anisomycin (an antibiotic that also affects eucaryal ribosomes) also map to this central loop [87]. Sequencing of several archaeal LSU rRNA has also revealed that they have either a G or a U at a position equivalent to A2058, which in bacteria produces sensitivity to erythromycin. As a consequence of this change, archaea are insensitive to this drug [29,30,87,88,95]. [Pg.444]

Since the distance between the nascent chain exit site from the ribosome and the peptidyl-transfer center is about 16 nm, it is possible that the SRP exerts its effect on protein translation by binding to both the signal sequence (near the exit site) and a component of the peptidyl-transfer site (Andrews et al., 1985). [Pg.133]

A few biological catalysts are RNA molecules. Known as ribozymes, these catalytic RNAs are involved in RNA splicing and other forms of RNA processing. A special ribozyme of central importance is the ribosomal peptidyl transferase, the catalyst in ribosomes responsible for peptidyl transfer in protein synthesis. [Pg.172]

Peptidyl transfer from the peptidyl /RNA to newly bound aminoacyl /RNA on the acceptor site. [Pg.239]

Erythromycins bind reversibly with a single high-affinity site on the 50S subunit of susceptible bacterial ribosomes. The site appears to be proteins L-15 and L-16, two of the 34 proteins constituting the ribosomal protein mass of the 50S unit. Removal of several L-16 proteins (by LiCl extraction) from a 50S subunit eliminates its affinity for EM peptidyl transfer ability is also eliminated. Restoring the L-16 protein alone reestablishes both functions. By itself L-16 has no EM binding capacity L-15 possesses both the capacity to bind EM and to effect peptidyl transfer, participated in some way by L-16. Both events occur on the P-site. Whether the bacteriostatic antimicrobial action of EM is due to the drugs inhibition of peptide bond formation or by the prevention of its translocation following peptide formation has not been established. To clarify the picture somewhat, perhaps it should be pointed out which aspects of protein synthesis are not affected by EM. They are amino acid activation, synthesis of the amino acid /RNA derivative, ribosomal association with raRNA, and reassociation of the 30S and 50S subunits to the complete ribosome. [Pg.258]

Monro, R. E., and Vazquez, D. (1967). Ribosome-catalyzed peptidyl transfer Effect of some inhibitors of protein synthesis. J. Mol. Biol. 28, 161-165. [Pg.492]


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See also in sourсe #XX -- [ Pg.234 ]




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