ArticleRNA (New York, N.Y.)2006
Chemical rescue, multiple ionizable groups, and general acid-base catalysis in the HDV genomic ribozyme.
Article in RNA (New York, N.Y.), 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 48 citations in OpenAlex.
- Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis.Journal of the American Chemical Society · 2023Article
- Small Molecule Rescue and Glycosidic Conformational Analysis of the Twister Ribozyme.Biochemistry · 2019Article
- Evidence That Nucleophile Deprotonation Exceeds Bond Formation in the HDV Ribozyme Transition State.Biochemistry · 2018Article
- Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM.RNA (New York, N.Y.) · 2015Article
- Transition State Features in the Hepatitis Delta Virus Ribozyme Reaction Revealed by Atomic Perturbations.Journal of the American Chemical Society · 2015Article
- Role of tautomerism in RNA biochemistry.RNA (New York, N.Y.) · 2015Review
- New tools provide a second look at HDV ribozyme structure, dynamics and cleavage.Nucleic acids research · 2014Article
- Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape.RNA (New York, N.Y.) · 2014Article
- Thio effects and an unconventional metal ion rescue in the genomic hepatitis delta virus ribozyme.Biochemistry · 2013Article
- The glmS ribozyme cofactor is a general acid-base catalyst.Journal of the American Chemical Society · 2012Article
- Charged nucleobases and their potential for RNA catalysis.Accounts of chemical research · 2011Article
- DNA as a versatile chemical component for catalysis, encoding, and stereocontrol.Angewandte Chemie (International ed. in English) · 2010Review
- Modulating RNA structure and catalysis: lessons from small cleaving ribozymes.Cellular and molecular life sciences : CMLS · 2009Review
- General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility.The journal of physical chemistry. B · 2008Article
- Mechanistic characterization of the HDV genomic ribozyme: the cleavage site base pair plays a structural role in facilitating catalysis.RNA (New York, N.Y.) · 2008Article
- An important role of G638 in the cis-cleavage reaction of the Neurospora VS ribozyme revealed by a novel nucleotide analog incorporation method.RNA (New York, N.Y.) · 2008Article
- Hammerhead redux: does the new structure fit the old biochemical data?RNA (New York, N.Y.) · 2008Review
- A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization.RNA (New York, N.Y.) · 2007Article
- Evidence for proton transfer in the rate-limiting step of a fast-cleaving Varkud satellite ribozyme.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis.Nucleic acids research · 2007Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
In the ribozyme from the hepatitis delta virus (HDV) genomic strand RNA, a cytosine side chain is proposed to facilitate proton transfer in the transition state of the reaction and, thus, act as a general acid-base catalyst. Mutation of this active-site cytosine (C75) reduced RNA cleavage rates by as much as one million-fold, but addition of exogenous cytosine and certain nucleobase or imidazole analogs can partially rescue activity in these mutants. However, pH-rate profiles for the rescued reactions were bell shaped, and only one leg of the pH-rate curve could be attributed to ionization of the exogenous nucleobase or buffer. When a second potential ionizable nucleobase (C41) was removed, one leg of the bell-shaped curve was eliminated in the chemical-rescue reaction. With this construct, the apparent pK(a) determined from the pH-rate profile correlated with the solution pK(a) of the buffer, and the contribution of the buffer to the rate enhancement could be directly evaluated in a free-energy or Brønsted plot. The free-energy relationship between the acid dissociation constant of the buffer and the rate constant for cleavage (Brønsted value, beta, = approximately 0.5) was consistent with a mechanism in which the buffer acted as a general acid-base catalyst. These data support the hypothesis that cytosine 75, in the intact ribozyme, acts as a general acid-base catalyst.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.