ArticleScientific reports2018
Cyclization Reaction Catalyzed by Cyclodipeptide Synthases Relies on a Conserved Tyrosine Residue.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 12 citations in OpenAlex.
- The tRNA moieties of both aminoacyl-tRNA substrates of a cyclodipeptide synthase share a common binding site, as revealed by RNA microhelices mimicking tRNA acceptor arms.Nucleic acids research · 2026Article
- Biosynthesis of Unnatural Cyclodipeptides through Genetic Code Expansion and Cyclodipeptide Synthase Evolution.Journal of the American Chemical Society · 2025Article
- Crystal Structure and Mutagenesis of an XYP Subfamily Cyclodipeptide Synthase Reveal Key Determinants of Enzyme Activity and Substrate Specificity.Biochemistry · 2024Article
- The high-throughput solid-phase extraction ofFrontiers in molecular biosciences · 2024Article
- 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
- 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
- Reprogramming Escherichia coli for the production of prenylated indole diketopiperazine alkaloids.Scientific reports · 2019Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cyclodipeptide synthases (CDPSs) form various cyclodipeptides from two aminoacyl tRNAs via a stepwise mechanism with the formation of a dipeptidyl enzyme intermediate. As a final step of the catalytic reaction, the dipeptidyl group undergoes intramolecular cyclization to generate the target cyclodipeptide product. In this work, we investigated the cyclization reaction in the cyclodipeptide synthase AlbC using QM/MM methods and free energy simulations. The results indicate that the catalytic Y202 residue is in its neutral protonated form, and thus, is not likely to serve as a general base during the reaction. We further demonstrate that the reaction relies on the conserved residue Y202 serving as a proton relay, and the direct proton transfer from the amino group to S37 of AlbC is unlikely. Calculations reveal that the hydroxyl group of tyrosine is more suitable for the proton transfer than hydroxyl groups of other amino acids, such as serine and threonine. Results also show that the residues E182, N40, Y178 and H203 maintain the correct conformation of the dipeptide needed for the cyclization reaction. The mechanism discovered in this work relies on the amino groups conserved among the entire CDPS family and, thus is expected to be universal among CDPSs.
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