ArticleBiochemistry2013
Identification of the catalytic Mg²⁺ ion in the hepatitis delta virus ribozyme.
Article in Biochemistry, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 37 citations in OpenAlex.
- Structure and mechanism of HDV ribozymes revealing Lewis acid catalysis by a metal ion.Nature communications · 2026Article
- The Three-Dimensional Reference Interaction Site Model Approach as a Promising Tool for Studying Hydrated Viruses and Their Complexes with Ligands.International journal of molecular sciences · 2024Review
- Natural soda lakes provide compatible conditions for RNA and membrane function that could have enabled the origin of life.PNAS nexus · 2024Article
- Self-cleaving ribozymes: substrate specificity and synthetic biology applications.RSC chemical biology · 2021Review
- From general base to general acid catalysis in a sodium-specific DNAzyme by a guanine-to-adenine mutation.Nucleic acids research · 2019Article
- Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study.Nucleic acids research · 2019Article
- Evidence That Nucleophile Deprotonation Exceeds Bond Formation in the HDV Ribozyme Transition State.Biochemistry · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Evidence of a General Acid-Base Catalysis Mechanism in the 8-17 DNAzyme.Biochemistry · 2018Article
- Inner-Sphere Coordination of Divalent Metal Ion with Nucleobase in Catalytic RNA.Journal of the American Chemical Society · 2017Article
- Allosteric Modulation of the Faecalibacterium prausnitzii Hepatitis Delta Virus-like Ribozyme by Glucosamine 6-Phosphate: The Substrate of the Adjacent Gene Product.Biochemistry · 2017Article
- The structure of a nucleolytic ribozyme that employs a catalytic metal ion.Nature chemical biology · 2017Article
- Pressure modulates the self-cleavage step of the hairpin ribozyme.Nature communications · 2017Article
- Assessing the Potential Effects of Active Site MgThe journal of physical chemistry letters · 2016Article
- 'Z-DNA like' fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response.Nucleic acids research · 2016Article
- Secondary structure confirmation and localization of Mg2+ ions in the mammalian CPEB3 ribozyme.RNA (New York, N.Y.) · 2016Article
- A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation.ACS catalysis · 2016Article
- Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction.Biochemistry · 2015Article
- Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM.RNA (New York, N.Y.) · 2015Article
- Inverse thio effects in the hepatitis delta virus ribozyme reveal that the reaction pathway is controlled by metal ion charge density.Biochemistry · 2015Article
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
The hepatitis delta virus ribozyme catalyzes an RNA cleavage reaction using a catalytic nucleobase and a divalent metal ion. The catalytic base, C75, serves as a general acid and has a pK(a) shifted toward neutrality. Less is known about the role of metal ions in the mechanism. A recent crystal structure of the precleavage ribozyme identified a Mg²⁺ ion that interacts through its partial hydration sphere with the G25·U20 reverse wobble. In addition, this Mg²⁺ ion is in position to directly coordinate the nucleophile, the 2'-hydroxyl of U(-1), suggesting it can serve as a Lewis acid to facilitate deprotonation of the 2'-hydroxyl. To test the role of the active site Mg²⁺ ion, we replaced the G25·U20 reverse wobble with an isosteric A25·C20 reverse wobble. This change was found to significantly reduce the negative potential at the active site, as supported by electrostatics calculations, suggesting that active site Mg²⁺ binding could be adversely affected by the mutation. The kinetic analysis and molecular dynamics of the A25·C20 double mutant suggest that this variant stably folds into an active structure. However, pH-rate profiles of the double mutant in the presence of Mg²⁺ are inverted relative to the profiles for the wild-type ribozyme, suggesting that the A25·C20 double mutant has lost the active site metal ion. Overall, these studies support a model in which the partially hydrated Mg²⁺ positioned at the G25·U20 reverse wobble is catalytic and could serve as a Lewis acid, a Brønsted base, or both to facilitate deprotonation of the nucleophile.
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