ArticleNature chemical biology2017
The structure of a nucleolytic ribozyme that employs a catalytic metal ion.
Article in Nature chemical biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Structure and mechanism of HDV ribozymes revealing Lewis acid catalysis by a metal ion.Nature communications · 2026Article
- Exploring GNRA tetraloop-like motifs in nucleic acid 3D structures.Scientific reports · 2025Article
- Transferability of MACE Graph Neural Network for Range Corrected Δ-Machine Learning Potential QM/MM Applications.The journal of physical chemistry. B · 2025Article
- Article
- The Role of General Acid Catalysis in the Mechanism of an Alkyl Transferase Ribozyme.ACS catalysis · 2024Article
- Structure-based investigation of a DNA aptamer targeting PTK7 reveals an intricate 3D fold guiding functional optimization.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- RNA Control via Redox-Responsive Acylation.Angewandte Chemie (International ed. in English) · 2024Article
- The 8-17 DNAzyme can operate in a single active structure regardless of metal ion cofactor.Nature communications · 2024Article
- RNA structure determination: From 2D to 3D.Fundamental research · 2023Review
- RNA 3D Modeling with FARFAR2, Online.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Coordination Chemistry of Nucleotides and Antivirally Active Acyclic Nucleoside Phosphonates, including Mechanistic Considerations.Molecules (Basel, Switzerland) · 2022Review
- Modeling Noncanonical RNA Base Pairs by a Coarse-Grained IsRNA2 Model.The journal of physical chemistry. B · 2021Article
- FARFAR2: Improved De Novo Rosetta Prediction of Complex Global RNA Folds.Structure (London, England : 1993) · 2020Article
- RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers.RNA (New York, N.Y.) · 2020Article
- Accurate inference of the full base-pairing structure of RNA by deep mutational scanning and covariation-induced deviation of activity.Nucleic acids research · 2020Article
- Crucial Roles of Two Hydrated MgAngewandte Chemie (International ed. in English) · 2020Article
- The L-platform/L-scaffold framework: a blueprint for RNA-cleaving nucleic acid enzyme design.RNA (New York, N.Y.) · 2020Article
- RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools.Nucleic acids research · 2020Article
- Novel ribozymes: discovery, catalytic mechanisms, and the quest to understand biological function.Nucleic acids research · 2019Article
- Cleaning Up Mechanistic Debris Generated by Twister Ribozymes Using Computational RNA Enzymology.ACS catalysis · 2019Article
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3 authors.
Funding
Abstract
The TS ribozyme (originally called "twister sister") is a catalytic RNA. We present a crystal structure of the ribozyme in a pre-reactive conformation. Two co-axial helical stacks are organized by a three-way junction and two tertiary contacts. Five divalent metal ions are directly coordinated to RNA ligands, making important contributions to the RNA architecture. The scissile phosphate lies in a quasihelical loop region that is organized by a network of hydrogen bonding. A divalent metal ion is directly bound to the nucleobase 5' to the scissile phosphate, with an inner-sphere water molecule positioned to interact with the O2' nucleophile. The rate of ribozyme cleavage correlated in a log-linear manner with divalent metal ion pK
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