ArticleJournal of molecular biology2013
Active-site monovalent cations revealed in a 1.55-Å-resolution hammerhead ribozyme structure.
Article in Journal of molecular biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 42 citations in OpenAlex.
- Cat_Wiz: a stereochemistry-guided toolkit for locating, diagnosing, and annotating Mg2+ ions in RNA structures.Nucleic acids research · 2026Article
- Critical structural perturbations of ribozyme active sites induced by 2'-O-methylation commonly used in structural studies.Nucleic acids research · 2026Article
- Enhanced hammerhead ribozyme turnover rates: Reevaluating therapeutic space for small catalytic RNAs.Molecular therapy. Nucleic acids · 2025Article
- Structural investigation of an RNA device that regulates PD-1 expression in mammalian cells.Nucleic acids research · 2025Article
- Self-cleaving ribozymes: substrate specificity and synthetic biology applications.RSC chemical biology · 2021Review
- Mechanisms of catalytic RNA molecules.Biochemical Society transactions · 2021Review
- RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers.RNA (New York, N.Y.) · 2020Article
- Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme.Nature chemistry · 2020Article
- Comparison of the Structures and Mechanisms of the Pistol and Hammerhead Ribozymes.Journal of the American Chemical Society · 2019Article
- Nucleobase carbonyl groups are poor MgRNA (New York, N.Y.) · 2019Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Divalent Metal Ion Activation of a Guanine General Base in the Hammerhead Ribozyme: Insights from Molecular Simulations.Biochemistry · 2017Article
- Mg2+ ions: do they bind to nucleobase nitrogens?Nucleic acids research · 2017Article
- Ligation of RNA Oligomers by the Schistosoma mansoni Hammerhead Ribozyme in Frozen Solution.Journal of molecular evolution · 2016Article
- Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue.Biochemistry · 2016Article
- Chemistry and Biology of Self-Cleaving Ribozymes.Trends in biochemical sciences · 2015Review
- Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction.Biochemistry · 2015Article
- Minimal Hammerhead Ribozymes with Uncompromised Catalytic Activity.Journal of molecular biology · 2015Article
- Structural and catalytic effects of an invariant purine substitution in the hammerhead ribozyme: implications for the mechanism of acid-base catalysis.Acta crystallographica. Section D, Biological crystallography · 2014Article
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4 authors at 1 institution in 1 country.
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Abstract
We have obtained a 1.55-Å crystal structure of a hammerhead ribozyme derived from Schistosoma mansoni under conditions that permit detailed observations of Na(+) ion binding in the ribozyme's active site. At least two such Na(+) ions are observed. The first Na(+) ion binds to the N7 of G10.1 and the adjacent A9 phosphate in a manner identical with that previously observed for divalent cations. A second Na(+) ion binds to the Hoogsteen face of G12, the general base in the hammerhead cleavage reaction, thereby potentially dissipating the negative charge of the catalytically active enolate form of the nucleotide base. A potential but more ambiguous third site bridges the A9 and scissile phosphates in a manner consistent with that of previous predictions. Hammerhead ribozymes have been observed to be active in the presence of high concentrations of monovalent cations, including Na(+), but the mechanism by which monovalent cations substitute for divalent cations in hammerhead catalysis remains unclear. Our results enable us to suggest that Na(+) directly and specifically substitutes for divalent cations in the hammerhead active site. The detailed geometry of the pre-catalytic active-site complex is also revealed with a new level of precision, thanks to the quality of the electron density maps obtained from what is currently the highest-resolution ribozyme structure in the Protein Data Bank.
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