ArticleProceedings of the National Academy of Sciences of the United States of America2011
Structural basis for nonribosomal peptide synthesis by an aminoacyl-tRNA synthetase paralog.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 91 citations in OpenAlex.
- Biosynthesis of Unnatural Cyclodipeptides through Genetic Code Expansion and Cyclodipeptide Synthase Evolution.Journal of the American Chemical Society · 2025Article
- Yeast-secreted compounds with antifungal activity-screening, genetic parts, biosynthetic pathways, and regulation.FEMS yeast research · 2025Review
- Pulcherriminic acid biosynthesis and transport: insights from a heterologous system in Saccharomyces cerevisiae.FEMS yeast research · 2025Article
- Crystal Structure and Mutagenesis of an XYP Subfamily Cyclodipeptide Synthase Reveal Key Determinants of Enzyme Activity and Substrate Specificity.Biochemistry · 2024Article
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- Heterologous pulcherrimin production in Saccharomyces cerevisiae confers inhibitory activity on Botrytis conidiation.FEMS yeast research · 2024Article
- Pulcherrimin protects Bacillus subtilis against oxidative stress during biofilm development.NPJ biofilms and microbiomes · 2023Article
- Pulcherriminic acid modulates iron availability and protects against oxidative stress during microbial interactions.Nature communications · 2023Article
- Natural and engineered cyclodipeptides: Biosynthesis, chemical diversity, and engineering strategies for diversification and high-yield bioproduction.Engineering microbiology · 2023Review
- Active site remodelling of a cyclodipeptide synthase redefines substrate scope.Communications chemistry · 2022Article
- Directed evolution of a cyclodipeptide synthase with new activitiesChemical science · 2022Article
- The Use of Raman Spectroscopy to Monitor Metabolic Changes in StressedMicroorganisms · 2021Article
- Bypassing the requirement for aminoacyl-tRNA by a cyclodipeptide synthase enzyme.RSC chemical biology · 2021Article
- Research Progress of the Biosynthesis of Natural Bio-Antibacterial Agent Pulcherriminic Acid inMolecules (Basel, Switzerland) · 2020Review
- Flexizyme-aminoacylated shortened tRNAs demonstrate that only the aminoacylated acceptor arms of the two tRNA substrates are required for cyclodipeptide synthase activity.Nucleic acids research · 2020Article
- Structural basis of the interaction between cyclodipeptide synthases and aminoacylated tRNA substrates.RNA (New York, N.Y.) · 2020Article
- Multistep Metabolic Engineering of Bacillus licheniformis To Improve Pulcherriminic Acid Production.Applied and environmental microbiology · 2020Article
- Strategy for the Biosynthesis of Short Oligopeptides: Green and Sustainable Chemistry.Biomolecules · 2019Review
- Pulcherrimin formation controls growth arrest of theProceedings of the National Academy of Sciences of the United States of America · 2019Article
- Genomic and metagenomic signatures of giant viruses are ubiquitous in water samples from sewage, inland lake, waste water treatment plant, and municipal water supply in Mumbai, India.Scientific reports · 2019Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cyclodipeptides are secondary metabolites biosynthesized by many bacteria and exhibit a wide array of biological activities. Recently, a new class of small proteins, named cyclodipeptide synthases (CDPS), which are unrelated to the typical nonribosomal peptide synthetases, was shown to generate several cyclodipeptides, using aminoacyl-tRNAs as substrates. The Mycobacterium tuberculosis CDPS, Rv2275, was found to generate cyclodityrosine through the formation of an aminoacyl-enzyme intermediate and to have a structure and oligomeric state similar to those of the class Ic aminoacyl-tRNA synthetases (aaRSs). However, the poor sequence conservation among CDPSs has raised questions about the architecture and catalytic mechanism of the identified homologs. Here we report the crystal structures of Bacillus licheniformis CDPS YvmC-Blic, in the apo form and complexed with substrate mimics, at 1.7-2.4-Å resolutions. The YvmC-Blic structure also exhibits similarity to the class Ic aaRSs catalytic domain. Our mutational analysis confirmed the importance of a set of residues for cyclodileucine formation among the conserved residues localized in the catalytic pocket. Our biochemical data indicated that YvmC-Blic binds tRNA and generates cyclodileucine as a monomer. We were also able to detect the presence of an aminoacyl-enzyme reaction intermediate, but not a dipeptide tRNA intermediate, whose existence was postulated for Rv2275. Instead, our results support a sequential catalytic mechanism for YvmC-Blic, with the successive attachment of two leucine residues on the enzyme via a conserved serine residue. Altogether, our findings suggest that all CDPS enzymes share a common aaRS-like architecture and a catalytic mechanism involving the formation of an enzyme-bound intermediate.
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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.