ArticleJournal of the American Chemical Society2012
The glmS ribozyme cofactor is a general acid-base catalyst.
Article in Journal of the American Chemical Society, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Phosphonate and Thiasugar Analogues of Glucosamine-6-phosphate: Activation of theACS chemical biology · 2023Article
- Carba-Sugar Analogs of Glucosamine-6-Phosphate: New Activators for the glmS Riboswitch.Chemistry (Weinheim an der Bergstrasse, Germany) · 2023Article
- Structural basis for substrate binding and catalysis by a self-alkylating ribozyme.Nature chemical biology · 2022Article
- The case of the missing allosteric ribozymes.Nature chemical biology · 2021Review
- Comprehensive sequence-to-function mapping of cofactor-dependent RNA catalysis in the glmS ribozyme.Nature communications · 2020Article
- Riboswitches and Translation Control.Cold Spring Harbor perspectives in biology · 2018Review
- Elucidation of Catalytic Strategies of Small Nucleolytic Ribozymes From Comparative Analysis of Active Sites.ACS catalysis · 2018Article
- 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 GlcN6P cofactor plays multiple catalytic roles in the glmS ribozyme.Nature chemical biology · 2017Article
- A divalent cation-dependent variant of theRNA (New York, N.Y.) · 2017Article
- Many Activities, One Structure: Functional Plasticity of Ribozyme Folds.Molecules (Basel, Switzerland) · 2016Review
- Assessing the Potential Effects of Active Site MgThe journal of physical chemistry letters · 2016Article
- In vitro evolution of coenzyme-independent variants from the glmS ribozyme structural scaffold.Methods (San Diego, Calif.) · 2016Article
- VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions.The Journal of chemical physics · 2016Article
- Chemistry and Biology of Self-Cleaving Ribozymes.Trends in biochemical sciences · 2015Review
- Chemical feasibility of the general acid/base mechanism of glmS ribozyme self-cleavage.Biopolymers · 2015Article
- Role of the active site guanine in the glmS ribozyme self-cleavage mechanism: quantum mechanical/molecular mechanical free energy simulations.Journal of the American Chemical Society · 2015Article
- Role of tautomerism in RNA biochemistry.RNA (New York, N.Y.) · 2015Review
- Phosphatase-inert glucosamine 6-phosphate mimics serve as actuators of the glmS riboswitch.ACS chemical biology · 2014Article
- An in vitro evolved glmS ribozyme has the wild-type fold but loses coenzyme dependence.Nature chemical biology · 2013Article
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2 authors.
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Abstract
The glmS ribozyme is the first natural self-cleaving ribozyme known to require a cofactor. The d-glucosamine-6-phosphate (GlcN6P) cofactor has been proposed to serve as a general acid, but its role in the catalytic mechanism has not been established conclusively. We surveyed GlcN6P-like molecules for their ability to support self-cleavage of the glmS ribozyme and found a strong correlation between the pH dependence of the cleavage reaction and the intrinsic acidity of the cofactors. For cofactors with low binding affinities, the contribution to rate enhancement was proportional to their intrinsic acidity. This linear free-energy relationship between cofactor efficiency and acid dissociation constants is consistent with a mechanism in which the cofactors participate directly in the reaction as general acid-base catalysts. A high value for the Brønsted coefficient (β ~ 0.7) indicates that a significant amount of proton transfer has already occurred in the transition state. The glmS ribozyme is the first self-cleaving RNA to use an exogenous acid-base catalyst.
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