ArticleNucleic acids research2019
Mechanistic insights into the slow peptide bond formation with D-amino acids in the ribosomal active site.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
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Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Cell-Free Approach for Non-canonical Amino Acids Incorporation Into Polypeptides.Frontiers in bioengineering and biotechnology · 2020Pooled it
- Enhancing ribosomal translation of backbone-altering nonproteinogenic amino acids via YebC and YeeN.Nucleic acids research · 2026Article
- The Alteromonas macleodii ribosome enables consecutive incorporation of bulky D-amino acids into peptides.Nucleic acids research · 2026Article
- Co-Translational Incorporation ofJournal of the American Chemical Society · 2026Article
- Engineering of tRNAPro1E2 anticodon stem enhances multiple/consecutive ribosomal incorporation of N-methyl-l-α-amino acids and d-α-amino acids.Nucleic acids research · 2026Article
- Mammalian Tolerance to Amino Acid Heterochirality.Chembiochem : a European journal of chemical biology · 2025Review
- Promoting ribosomal incorporation of backbone-modifying nonproteinogenic amino acids into nascent peptides by ATP-binding cassette family-F proteins and EF-P.Nucleic acids research · 2025Article
- Reprogramming the genetic code with flexizymes.Nature reviews. Chemistry · 2024Review
- β-Amino Acids Reduce Ternary Complex Stability and Alter the Translation Elongation Mechanism.ACS central science · 2024Article
- Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers.Chemical reviews · 2024Review
- β-amino acids reduce ternary complex stability and alter the translation elongation mechanism.bioRxiv : the preprint server for biology · 2024Article
- Tuning tRNAs for improved translation.Frontiers in genetics · 2024Review
- Synthesis of Peptidyl-tRNA Mimics for Structural Biology Applications.Accounts of chemical research · 2023Review
- Ribosomal proteins can hold a more accurate record of bacterial thermal adaptation compared to rRNA.Nucleic acids research · 2023Article
- Aminobenzoic Acid Derivatives Obstruct Induced Fit in the Catalytic Center of the Ribosome.ACS central science · 2023Article
- Rational design of the genetic code expansion toolkit forFrontiers in genetics · 2023Article
- Ribosome-mediated biosynthesis of pyridazinone oligomers in vitro.Nature communications · 2022Article
- Ribosome selectivity and nascent chain context in modulating the incorporation of fluorescent non-canonical amino acid into proteins.Scientific reports · 2022Article
- Structural basis for the context-specific action of the classic peptidyl transferase inhibitor chloramphenicol.Nature structural & molecular biology · 2022Article
- Fundamental Clock of Biological Aging: Convergence of Molecular, Neurodegenerative, Cognitive and Psychiatric Pathways: Non-Equilibrium Thermodynamics Meet Psychology.International journal of molecular sciences · 2021Review
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8 authors.
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Abstract
During protein synthesis, ribosomes discriminate chirality of amino acids and prevent incorporation of D-amino acids into nascent proteins by slowing down the rate of peptide bond formation. Despite this phenomenon being known for nearly forty years, no structures have ever been reported that would explain the poor reactivity of D-amino acids. Here we report a 3.7Å-resolution crystal structure of a bacterial ribosome in complex with a D-aminoacyl-tRNA analog bound to the A site. Although at this resolution we could not observe individual chemical groups, we could unambiguously define the positions of the D-amino acid side chain and the amino group based on chemical restraints. The structure reveals that similarly to L-amino acids, the D-amino acid binds the ribosome by inserting its side chain into the ribosomal A-site cleft. This binding mode does not allow optimal nucleophilic attack of the peptidyl-tRNA by the reactive α-amino group of a D-amino acid. Also, our structure suggests that the D-amino acid cannot participate in hydrogen-bonding with the P-site tRNA that is required for the efficient proton transfer during peptide bond formation. Overall, our work provides the first mechanistic insight into the ancient mechanism that helps living cells ensure the stereochemistry of protein synthesis.
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