A Possible Mechanism of Peptide Bond Formation on Ribosome without Mediation of Peptidyl Transferase

Das, Gourab Kanti; Bhattacharyya, Dhananjay; Burma, D.P.

doi:10.1006/jtbi.1999.0987

Cited by 36 publications

(34 citation statements)

References 38 publications

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“…Hydrogen bonding between the 29-OH of A76 and the nucleophilic a-NH 2 group may help to position the nucleophile. Another attractive explanation for the importance of 29-OH of A76 of the P-site tRNA is its participation in a concerted proton shuttle that bridges the attacking a-NH 2 group and the leaving 39 oxygen of the P-site tRNA (Das et al 1999;Dorner et al 2002;Changalov et al 2005;Schmeing et al 2005a;Trobro and Å qvist 2005) The main role of ribosomal residues in the active site appears to provide a preorganized hydrogen-bond network that stabilizes the charged transition state (Schmeing et al 2005a;Trobro and Å qvist 2005). Additionally, they seem to protect pept-tRNA from premature hydrolysis by water when the A site is not filled by aa-tRNA ( Fig.…”

Section: Peptide Bond Formation and Peptide Releasementioning

confidence: 99%

Modulating the activity of the peptidyl transferase center of the ribosome

Beringer¹

2008

RNA

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The peptidyl transferase (PT) center of the ribosome catalyzes two nucleophilic reactions, peptide bond formation between aminoacylated tRNA substrates and, together with release factor, peptide release. Structure and function of the PT center are modulated by binding of aminoacyl-tRNA or release factor, thus providing the basis for the specificity of catalysis. Another way by which the function of the PT center is controlled is signaling from the peptide exit tunnel. The SecM nascent peptide induces ribosome stalling, presumably by inhibition of peptide bond formation. Similarly, the release factor-induced hydrolytic activity of the PT center can be suppressed by the TnaC nascent peptide contained in the exit tunnel. Thus, local and long-range conformational rearrangements can lead to changes in the reaction specificity and catalytic activity of the PT center.

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Section: Peptide Bond Formation and Peptide Releasementioning

confidence: 99%

Modulating the activity of the peptidyl transferase center of the ribosome

Beringer¹

2008

RNA

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“…Models based on the involvement of a general acidbase have been discounted based on biochemical experiments (Bieling et al 2006) whereas involvement of a metal ion has been discounted primarily because of its promiscuous absence from atomic resolution views of the active site (for review, see Rodnina et al 2006). The proton shuttle model, where a proton from the incoming nucleophilic amine on the aminoacyl-tRNA substrate is transferred to the 39 OH of the peptidyl-tRNA leaving group via the 29 OH of the same substrate, reconciles much of the literature surrounding the molecular mechanism of the PT reaction, including site-directed mutagenesis studies (Dorner et al 2003;Weinger et al 2004;Okuda et al 2005), thermodynamic studies (Sievers et al 2004), and molecular modeling approaches (Das et al 1999;Trobro and Aqvist 2005).…”

Section: Introductionmentioning

confidence: 99%

Peptide release on the ribosome depends critically on the 2′ OH of the peptidyl–tRNA substrate

Brunelle¹,

Shaw²,

Youngman³

et al. 2008

RNA

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Peptide release on the ribosome is catalyzed by protein release factors (RFs) on recognition of stop codons positioned in the A site of the small ribosomal subunit. Here we show that the 29 OH of the peptidyl-tRNA substrate plays an essential role in catalysis of the peptide release reaction. These observations parallel earlier studies of the mechanism of the peptidyl transfer reaction and argue that related mechanisms are at the heart of catalysis for these reactions.

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“…It also determines the location of the oxianion and which functional groups are properly positioned for active roles in the reaction. Previous attempts to determine the stereochemistry of the reaction were based mostly on computational methods and resulted in contradictory arguments for both stereoisomers [10,16,38,39].…”

Section: Stereospecificity Of the Peptidyl Transfer Reactionmentioning

confidence: 99%

Exploring the mechanism of protein synthesis with modified substrates and novel intermediate mimics

Weinger¹,

Strobel²

2007

Blood Cells, Molecules, and Diseases

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Translation, the synthesis of proteins from individual amino acids based on genetic information, is a cornerstone biological process. During ribosomal protein synthesis, new peptide bonds form through aminolysis of the peptidyl-tRNA ester bond by the alpha-amino group of the A-site amino acid. The rate of this reaction is accelerated at least 10 7 -fold in the ribosome, but the catalytic mechanism has remained controversial. We have used a combination of synthetic chemistry, biochemical, and structural biology approaches to characterize the mechanism of the peptidyl transfer reaction and the configuration of the reaction's tetrahedral intermediate. Substitution of the P-site tRNA A76 2′ OH with 2′ H or 2′ F results in at least a 10 6 -fold reduction in the rate of peptide bond formation, but does not affect binding of the modified substrates. This indicates that the 2′-OH is essential to the reaction through participation in substrate assisted catalysis. A series of novel mimics of the tetrahedral intermediate were examined to distinguish between possible regio-and stereoisomeric forms of the intermediate. The determination of these parameters has important implications for the configuration of the substrates and intermediate within the ribosomal active site, and thus which functional groups are properly positioned to play various roles in promoting the reaction. Our results contribute to an emerging model of the peptidyl transfer reaction in which the ribosomal active site positions the substrates in an orientation specifically designed to promote the reaction, wherein the A76 2′-OH serves as a proton shuttle to enable critical proton transfers in the formation of the final peptide product. The peptidyl transfer reactionThe two substrates of the peptidyl transfer reaction are the peptidyl tRNA "P-site substrate," and the aminoacyl-tRNA "A-site substrate." The peptidyl and amino acid moieties of these substrates are covalently connected to the tRNAs via high energy ester bonds to the 2′/3′ hydroxyls of the terminal adenosine (A76). Peptidyl transfer occurs when the A-site α-amino group nucleophilically attacks the ester bond connecting the nascent peptide to the P-site tRNA. The new peptide bond forms between the A-site α-amino group and the P-site carboxyl carbon, resulting in an A-site tRNA acylated with a peptide lengthened by one amino acid and a deacylated P-site tRNA ( figure 1)[1].Based on analogy to solution aminolysis reactions [2], ribosomal peptidyl transfer is believed to go through a tetrahedral intermediate during the reaction (figure 1). In this theoretical

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A Possible Mechanism of Peptide Bond Formation on Ribosome without Mediation of Peptidyl Transferase

Cited by 36 publications

References 38 publications

Modulating the activity of the peptidyl transferase center of the ribosome

Modulating the activity of the peptidyl transferase center of the ribosome

Peptide release on the ribosome depends critically on the 2′ OH of the peptidyl–tRNA substrate

Exploring the mechanism of protein synthesis with modified substrates and novel intermediate mimics

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