ArticleRNA (New York, N.Y.)2007
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.
Article in RNA (New York, N.Y.), 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 53 citations in OpenAlex.
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- Crucial Roles of Two Hydrated MgAngewandte Chemie (International ed. in English) · 2020Article
- Multiscale methods for computational RNA enzymology.Methods in enzymology · 2015Article
- Strand-specific (asymmetric) contribution of phosphodiester linkages on RNA polymerase II transcriptional efficiency and fidelity.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path.Journal of the American Chemical Society · 2014Article
- Intermolecular domain docking in the hairpin ribozyme: metal dependence, binding kinetics and catalysis.RNA biology · 2013Article
- A transition-state interaction shifts nucleobase ionization toward neutrality to facilitate small ribozyme catalysis.Journal of the American Chemical Society · 2012Article
- Crystallographic analysis of small ribozymes and riboswitches.Methods in molecular biology (Clifton, N.J.) · 2012Article
- Multistrand RNA secondary structure prediction and nanostructure design including pseudoknots.ACS nano · 2011Article
- QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms.The journal of physical chemistry. B · 2011Article
- Two distinct catalytic strategies in the hepatitis δ virus ribozyme cleavage reaction.Biochemistry · 2011Review
- Base ionization and ligand binding: how small ribozymes and riboswitches gain a foothold in a protein world.Current opinion in structural biology · 2011Review
- The pH dependence of hairpin ribozyme catalysis reflects ionization of an active site adenine.The Journal of biological chemistry · 2011Article
- The glmS ribozyme: use of a small molecule coenzyme by a gene-regulatory RNA.Quarterly reviews of biophysics · 2010Review
- Use of the spliceosomal protein U1A to facilitate crystallization and structure determination of complex RNAs.Methods (San Diego, Calif.) · 2010Review
- Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme.The journal of physical chemistry. B · 2010Article
- Catalytic importance of a protonated adenosine in the hairpin ribozyme active site.Biochemistry · 2010Article
- Exploring ribozyme conformational changes with X-ray crystallography.Methods (San Diego, Calif.) · 2009Review
- Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.Methods (San Diego, Calif.) · 2009Review
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3 authors at 2 institutions in 1 country.
Funding
Abstract
The potential for water to participate in RNA catalyzed reactions has been the topic of several recent studies. Here, we report crystals of a minimal, hinged hairpin ribozyme in complex with the transition-state analog vanadate at 2.05 A resolution. Waters are present in the active site and are discussed in light of existing views of catalytic strategies employed by the hairpin ribozyme. A second structure harboring a 2',5'-phosphodiester linkage at the site of cleavage was also solved at 2.35 A resolution and corroborates the assignment of active site waters in the structure containing vanadate. A comparison of the two structures reveals that the 2',5' structure adopts a conformation that resembles the reaction intermediate in terms of (1) the positioning of its nonbridging oxygens and (2) the covalent attachment of the 2'-O nucleophile with the scissile G+1 phosphorus. The 2',5'-linked structure was then overlaid with scissile bonds of other small ribozymes including the glmS metabolite-sensing riboswitch and the hammerhead ribozyme, and suggests the potential of the 2',5' linkage to elicit a reaction-intermediate conformation without the need to form metalloenzyme complexes. The hairpin ribozyme structures presented here also suggest how water molecules bound at each of the nonbridging oxygens of G+1 may electrostatically stabilize the transition state in a manner that supplements nucleobase functional groups. Such coordination has not been reported for small ribozymes, but is consistent with the structures of protein enzymes. Overall, this work establishes significant parallels between the RNA and protein enzyme worlds.
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