Literature DB >> 21552203

The 2'-OH group of the peptidyl-tRNA stabilizes an active conformation of the ribosomal PTC.

Hani S Zaher1, Jeffrey J Shaw, Scott A Strobel, Rachel Green.   

Abstract

The ribosome accelerates the rate of peptidyl transfer by >10(6)-fold relative to the background rate. A widely accepted model for this rate enhancement invokes entropic effects whereby the ribosome and the 2'-OH of the peptidyl-tRNA substrate precisely position the reactive moieties through an extensive network of hydrogen bonds that allows proton movement through them. Some studies, however, have called this model into question because they find the 2'-OH of the peptidyl-tRNA to be dispensable for catalysis. Here, we use an in vitro reconstituted translation system to resolve these discrepancies. We find that catalysis is at least 100-fold slower with the dA76-substituted peptidyl-tRNA substrate and that the peptidyl transferase centre undergoes a slow inactivation when the peptidyl-tRNA lacks the 2'-OH group. Additionally, the 2'-OH group was found to be critical for EFTu binding and peptide release. These findings reconcile the conflict in the literature, and support a model where interactions between active site residues and the 2'-OH of A76 of the peptidyl-tRNA are pivotal in orienting substrates in this active site for optimal catalysis.

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Year:  2011        PMID: 21552203      PMCID: PMC3116277          DOI: 10.1038/emboj.2011.142

Source DB:  PubMed          Journal:  EMBO J        ISSN: 0261-4189            Impact factor:   11.598


  39 in total

1.  The active site of the ribosome is composed of two layers of conserved nucleotides with distinct roles in peptide bond formation and peptide release.

Authors:  Elaine M Youngman; Julie L Brunelle; Anna B Kochaniak; Rachel Green
Journal:  Cell       Date:  2004-05-28       Impact factor: 41.582

2.  Substrate-assisted catalysis of peptide bond formation by the ribosome.

Authors:  Joshua S Weinger; K Mark Parnell; Silke Dorner; Rachel Green; Scott A Strobel
Journal:  Nat Struct Mol Biol       Date:  2004-10-10       Impact factor: 15.369

3.  Mechanism of peptide bond synthesis on the ribosome.

Authors:  Stefan Trobro; Johan Aqvist
Journal:  Proc Natl Acad Sci U S A       Date:  2005-08-22       Impact factor: 11.205

4.  Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes.

Authors:  D Moazed; H F Noller
Journal:  Cell       Date:  1986-12-26       Impact factor: 41.582

5.  An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA.

Authors:  T Martin Schmeing; Kevin S Huang; Scott A Strobel; Thomas A Steitz
Journal:  Nature       Date:  2005-11-24       Impact factor: 49.962

6.  Inhibition of ribosomal translocation by peptidyl transfer ribonucleic acid analogues.

Authors:  T Wagner; M Sprinzl
Journal:  Biochemistry       Date:  1983-01-04       Impact factor: 3.162

7.  Activity of the 2' and 3' isomers of aminoacyl transfer ribonucleic acid in the in vitro peptide elongation on Escherichia coli ribosomes.

Authors:  T Wagner; F Cramer; M Sprinzl
Journal:  Biochemistry       Date:  1982-03-30       Impact factor: 3.162

8.  Nucleoside triphosphate regeneration decreases the frequency of translation errors.

Authors:  P C Jelenc; C G Kurland
Journal:  Proc Natl Acad Sci U S A       Date:  1979-07       Impact factor: 11.205

9.  Complete kinetic mechanism of elongation factor Tu-dependent binding of aminoacyl-tRNA to the A site of the E. coli ribosome.

Authors:  T Pape; W Wintermeyer; M V Rodnina
Journal:  EMBO J       Date:  1998-12-15       Impact factor: 11.598

10.  Chemical engineering of the peptidyl transferase center reveals an important role of the 2'-hydroxyl group of A2451.

Authors:  Matthias D Erlacher; Kathrin Lang; Nisha Shankaran; Brigitte Wotzel; Alexander Hüttenhofer; Ronald Micura; Alexander S Mankin; Norbert Polacek
Journal:  Nucleic Acids Res       Date:  2005-03-14       Impact factor: 16.971

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  19 in total

Review 1.  Slicing tRNAs to boost functional ncRNA diversity.

Authors:  Jennifer Gebetsberger; Norbert Polacek
Journal:  RNA Biol       Date:  2013-11-21       Impact factor: 4.652

Review 2.  Structural aspects of translation termination on the ribosome.

Authors:  Andrei A Korostelev
Journal:  RNA       Date:  2011-06-23       Impact factor: 4.942

3.  The chemical versatility of RNA.

Authors:  David A Hiller; Scott A Strobel
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2011-10-27       Impact factor: 6.237

4.  The ribosome can discriminate the chirality of amino acids within its peptidyl-transferase center.

Authors:  Michael T Englander; Joshua L Avins; Rachel C Fleisher; Bo Liu; Philip R Effraim; Jiangning Wang; Klaus Schulten; Thomas S Leyh; Ruben L Gonzalez; Virginia W Cornish
Journal:  Proc Natl Acad Sci U S A       Date:  2015-04-27       Impact factor: 11.205

5.  Decoding on the ribosome depends on the structure of the mRNA phosphodiester backbone.

Authors:  Hannah E Keedy; Erica N Thomas; Hani S Zaher
Journal:  Proc Natl Acad Sci U S A       Date:  2018-07-02       Impact factor: 11.205

6.  Speciation of a group I intron into a lariat capping ribozyme.

Authors:  Mélanie Meyer; Henrik Nielsen; Vincent Oliéric; Pierre Roblin; Steinar D Johansen; Eric Westhof; Benoît Masquida
Journal:  Proc Natl Acad Sci U S A       Date:  2014-05-12       Impact factor: 11.205

7.  The juxtaposition of ribose hydroxyl groups: the root of biological catalysis and the RNA world?

Authors:  Harold S Bernhardt
Journal:  Orig Life Evol Biosph       Date:  2015-02-27       Impact factor: 1.950

8.  Peptide Bond Formation Mechanism Catalyzed by Ribosome.

Authors:  Katarzyna Świderek; Sergio Marti; Iñaki Tuñón; Vicent Moliner; Juan Bertran
Journal:  J Am Chem Soc       Date:  2015-09-10       Impact factor: 15.419

9.  A Role for the 2' OH of peptidyl-tRNA substrate in peptide release on the ribosome revealed through RF-mediated rescue.

Authors:  Jeffrey J Shaw; Stefan Trobro; Shan L He; Johan Åqvist; Rachel Green
Journal:  Chem Biol       Date:  2012-08-24

10.  Uniformity of Peptide Release Is Maintained by Methylation of Release Factors.

Authors:  William E Pierson; Eric D Hoffer; Hannah E Keedy; Carrie L Simms; Christine M Dunham; Hani S Zaher
Journal:  Cell Rep       Date:  2016-09-27       Impact factor: 9.423

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