ArticleJournal of the American Chemical Society2017
Structural Basis for Substrate Helix Remodeling and Cleavage Loop Activation in the Varkud Satellite Ribozyme.
Article in Journal of the American Chemical Society, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 23 citations in OpenAlex.
- RNA targeting and cleavage by the type III-Dv CRISPR effector complex.Nature communications · 2024Article
- Acquisition of Dual Ribozyme-Functions in Nonfunctional Short Hairpin RNAs through Kissing-Loop Interactions.Life (Basel, Switzerland) · 2022Article
- How does RNA fold dynamically?Journal of molecular biology · 2022Review
- Regulation of Gene Expression Through Effector-dependent Conformational Switching by Cobalamin Riboswitches.Journal of molecular biology · 2022Review
- RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis.The journal of physical chemistry. B · 2022Article
- An integrative NMR-SAXS approach for structural determination of large RNAs defines the substrate-free state of a trans-cleaving Neurospora Varkud Satellite ribozyme.Nucleic acids research · 2021Article
- Beyond the Plateau: pL Dependence of Proton Inventories as a Tool for Studying Ribozyme and Ribonuclease Catalysis.Biochemistry · 2021Article
- A unified dinucleotide alphabet describing both RNA and DNA structures.Nucleic acids research · 2020Article
- In vitro selection of ribozyme ligases that use prebiotically plausible 2-aminoimidazole-activated substrates.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme.Nature chemistry · 2020Article
- The L-platform/L-scaffold framework: a blueprint for RNA-cleaving nucleic acid enzyme design.RNA (New York, N.Y.) · 2020Article
- Evidence for a Catalytic Strategy to Promote Nucleophile Activation in Metal-Dependent RNA-Cleaving Ribozymes and 8-17 DNAzyme.ACS catalysis · 2019Article
- A multi-axial RNA joint with a large range of motion promotes sampling of an active ribozyme conformation.Nucleic acids research · 2019Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The Varkud satellite (VS) ribozyme catalyzes site-specific RNA cleavage and ligation reactions. Recognition of the substrate involves a kissing loop interaction between the substrate and the catalytic domain of the ribozyme, resulting in a rearrangement of the substrate helix register into a so-called "shifted" conformation that is critical for substrate binding and activation. We report a 3.3 Å crystal structure of the complete ribozyme that reveals the active, shifted conformation of the substrate, docked into the catalytic domain of the ribozyme. Comparison to previous NMR structures of isolated, inactive substrates provides a physical description of substrate remodeling, and implicates roles for tertiary interactions in catalytic activation of the cleavage loop. Similarities to the hairpin ribozyme cleavage loop activation suggest general strategies to enhance fidelity in RNA folding and ribozyme cleavage.
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