ArticleProceedings of the National Academy of Sciences of the United States of America2010
Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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49 citing papers in PubMed, 74 citations in OpenAlex.
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- The Role of General Acid Catalysis in the Mechanism of an Alkyl Transferase Ribozyme.ACS catalysis · 2024Article
- Conjugation of RNAChemical communications (Cambridge, England) · 2022Article
- Self-cleaving ribozymes: substrate specificity and synthetic biology applications.RSC chemical biology · 2021Review
- Synthesis of Oligoribonucleotides Containing a 2'-Amino-5'-The Journal of organic chemistry · 2021Article
- Beyond the Plateau: pL Dependence of Proton Inventories as a Tool for Studying Ribozyme and Ribonuclease Catalysis.Biochemistry · 2021Article
- The Positively Charged Active Site of the Bacterial Toxin RelE Causes a Large Shift in the General Base pBiochemistry · 2020Article
- Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme.Nature chemistry · 2020Article
- Novel ribozymes: discovery, catalytic mechanisms, and the quest to understand biological function.Nucleic acids research · 2019Article
- The abundant DNA adductThe Journal of biological chemistry · 2019Article
- Comparison of the Structures and Mechanisms of the Pistol and Hammerhead Ribozymes.Journal of the American Chemical Society · 2019Article
- Classification of the nucleolytic ribozymes based upon catalytic mechanism.F1000Research · 2019Review
- Adenine protonation enables cyclic-di-GMP binding to cyclic-GAMP sensing riboswitches.RNA (New York, N.Y.) · 2018Article
- Evidence That Nucleophile Deprotonation Exceeds Bond Formation in the HDV Ribozyme Transition State.Biochemistry · 2018Article
- Synthesis of 5'-Thio-3'-O-ribonucleoside Phosphoramidites.The Journal of organic chemistry · 2017Article
- Insights into RNA structure and dynamics from recent NMR and X-ray studies of the Neurospora Varkud satellite ribozyme.Wiley interdisciplinary reviews. RNA · 2017Review
- The structure of a nucleolytic ribozyme that employs a catalytic metal ion.Nature chemical biology · 2017Article
- Structural and Biochemical Properties of Novel Self-Cleaving Ribozymes.Molecules (Basel, Switzerland) · 2017Review
- Crystal structure of Pistol, a class of self-cleaving ribozyme.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Rational engineering of the Neurospora VS ribozyme to allow substrate recognition via different kissing-loop interactions.Nucleic acids research · 2016Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
Existing evidence suggests that the Varkud satellite (VS) ribozyme accelerates the cleavage of a specific phosphodiester bond using general acid-base catalysis. The key functionalities are the nucleobases of adenine 756 in helix VI of the ribozyme, and guanine 638 in the substrate stem loop. This results in a bell-shaped dependence of reaction rate on pH, corresponding to groups with pK(a) = 5.2 and 8.4. However, it is not possible from those data to determine which nucleobase is the acid, and which the base. We have therefore made substrates in which the 5' oxygen of the scissile phosphate is replaced by sulfur. This labilizes the leaving group, removing the requirement for general acid catalysis. This substitution restores full activity to the highly impaired A756G ribozyme, consistent with general acid catalysis by A756 in the unmodified ribozyme. The pH dependence of the cleavage of the phosphorothiolate-modified substrates is consistent with general base catalysis by nucleobase at position 638. We conclude that cleavage of the substrate by the VS ribozyme is catalyzed by deprotonation of the 2'-O nucleophile by G638 and protonation of the 5'-O leaving group by A756.
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