ArticleNature2011
A two-step chemical mechanism for ribosome-catalysed peptide bond formation.
Article in Nature, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
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Who cites it
25 citing papers in PubMed, 84 citations in OpenAlex.
- Mechanism of release factor-mediated peptidyl-tRNA hydrolysis on the ribosome.Science (New York, N.Y.) · 2025Article
- Indirect Formation of Peptide Bonds as a Prelude to Ribosomal Transpeptidation.Journal of the American Chemical Society · 2025Article
- Article
- Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis.Journal of the American Chemical Society · 2023Article
- Translation factor accelerating peptide bond formation on the ribosome: EF-P and eIF5A as entropic catalysts and a potential drug targets.BBA advances · 2023Article
- Insights into the ribosome function from the structures of non-arrested ribosome-nascent chain complexes.Nature chemistry · 2023Article
- Flexizyme-catalyzed synthesis of 3'-aminoacyl-NH-tRNAs.Nucleic acids research · 2019Article
- Translation in Prokaryotes.Cold Spring Harbor perspectives in biology · 2018Review
- Mechanistic alternatives for peptide bond formation on the ribosome.Nucleic acids research · 2018Article
- Distal Proton Shuttle Mechanism of Ribosome Catalysed Peptide Bond Formation-A Theoretical Study.Molecules (Basel, Switzerland) · 2017Article
- DNA Three Way Junction Core Decorated with Amino Acids-Like Residues-Synthesis and Characterization.Molecules (Basel, Switzerland) · 2016Article
- Human DNMT1 transition state structure.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Activities of the peptidyl transferase center of ribosomes lacking protein L27.RNA (New York, N.Y.) · 2015Article
- Heavy atom labeled nucleotides for measurement of kinetic isotope effects.Biochimica et biophysica acta · 2015Review
- Peptide Bond Formation Mechanism Catalyzed by Ribosome.Journal of the American Chemical Society · 2015Article
- Outwitting EF-Tu and the ribosome: translation with d-amino acids.Nucleic acids research · 2015Article
- Determination of relative rate constants for in vitro RNA processing reactions by internal competition.Analytical biochemistry · 2014Article
- Natural isotopic signatures of variations in body nitrogen fluxes: a compartmental model analysis.PLoS computational biology · 2014Article
- A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.Nature structural & molecular biology · 2014Article
- EF-G and EF4: translocation and back-translocation on the bacterial ribosome.Nature reviews. Microbiology · 2014Review
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The chemical step of natural protein synthesis, peptide bond formation, is catalysed by the large subunit of the ribosome. Crystal structures have shown that the active site for peptide bond formation is composed entirely of RNA. Recent work has focused on how an RNA active site is able to catalyse this fundamental biological reaction at a suitable rate for protein synthesis. On the basis of the absence of important ribosomal functional groups, lack of a dependence on pH, and the dominant contribution of entropy to catalysis, it has been suggested that the role of the ribosome is limited to bringing the substrates into close proximity. Alternatively, the importance of the 2'-hydroxyl of the peptidyl-transfer RNA and a Brønsted coefficient near zero have been taken as evidence that the ribosome coordinates a proton-transfer network. Here we report the transition state of peptide bond formation, based on analysis of the kinetic isotope effect at five positions within the reaction centre of a peptidyl-transfer RNA mimic. Our results indicate that in contrast to the uncatalysed reaction, formation of the tetrahedral intermediate and proton transfer from the nucleophilic nitrogen both occur in the rate-limiting step. Unlike in previous proposals, the reaction is not fully concerted; instead, breakdown of the tetrahedral intermediate occurs in a separate fast step. This suggests that in addition to substrate positioning, the ribosome is contributing to chemical catalysis by changing the rate-limiting transition state.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.