ArticleRNA (New York, N.Y.)2009
Conformational change in the Bacillus subtilis RNase P holoenzyme--pre-tRNA complex enhances substrate affinity and limits cleavage rate.
Article in RNA (New York, N.Y.), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 49 citations in OpenAlex.
- A minimal RNA substrate with dual fluorescent probes enables rapid kinetics and provides insight into bacterial RNase P active site interactions.RSC chemical biology · 2024Article
- Structural and mechanistic basis for recognition of alternative tRNA precursor substrates by bacterial ribonuclease P.Nature communications · 2022Article
- Structural basis for impaired 5' processing of a mutant tRNA associated with defects in neuronal homeostasis.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- The many faces of RNA-based RNase P, an RNA-world relic.Trends in biochemical sciences · 2021Review
- Protein cofactors and substrate influence Mg2+-dependent structural changes in the catalytic RNA of archaeal RNase P.Nucleic acids research · 2021Article
- Chaperna: linking the ancient RNA and protein worlds.RNA biology · 2021Review
- Nucleic Acid Catalysis under Potential Prebiotic Conditions.Chemistry, an Asian journal · 2020Review
- Inner-Sphere Coordination of Divalent Metal Ion with Nucleobase in Catalytic RNA.Journal of the American Chemical Society · 2017Article
- Analysis of the RNA Binding Specificity Landscape of C5 Protein Reveals Structure and Sequence Preferences that Direct RNase P Specificity.Cell chemical biology · 2016Article
- The Diversity of Ribonuclease P: Protein and RNA Catalysts with Analogous Biological Functions.Biomolecules · 2016Review
- Differential substrate recognition by isozymes of plant protein-only Ribonuclease P.RNA (New York, N.Y.) · 2016Article
- Nuclear Protein-Only Ribonuclease P2 Structure and Biochemical Characterization Provide Insight into the Conserved Properties of tRNA 5' End Processing Enzymes.Journal of molecular biology · 2016Article
- An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions.RNA (New York, N.Y.) · 2016Article
- Differential Assembly of Catalytic Interactions within the Conserved Active Sites of Two Ribozymes.PloS one · 2016Article
- Mechanistic Studies Reveal Similar Catalytic Strategies for Phosphodiester Bond Hydrolysis by Protein-only and RNA-dependent Ribonuclease P.The Journal of biological chemistry · 2015Article
- A real-time fluorescence polarization activity assay to screen for inhibitors of bacterial ribonuclease P.Nucleic acids research · 2014Article
- Alternative substrate kinetics of Escherichia coli ribonuclease P: determination of relative rate constants by internal competition.The Journal of biological chemistry · 2013Article
- Transient kinetic analysis of USP2-catalyzed deubiquitination reveals a conformational rearrangement in the K48-linked diubiquitin substrate.Biochemistry · 2012Article
- Mitochondrial ribonuclease P structure provides insight into the evolution of catalytic strategies for precursor-tRNA 5' processing.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Fidelity of tRNA 5'-maturation: a possible basis for the functional dependence of archaeal and eukaryal RNase P on multiple protein cofactors.Nucleic acids research · 2012Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Ribonuclease P (RNase P) is a ribonucleoprotein complex that catalyzes the 5' maturation of precursor tRNAs. To investigate the mechanism of substrate recognition in this enzyme, we characterize the thermodynamics and kinetics of Bacillus subtilis pre-tRNA(Asp) binding to B. subtilis RNase P holoenzyme using fluorescence techniques. Time courses for fluorescein-labeled pre-tRNA binding to RNase P are biphasic in the presence of both Ca(II) and Mg(II), requiring a minimal two-step association mechanism. In the first step, the apparent bimolecular rate constant for pre-tRNA associating with RNase P has a value that is near the diffusion limit and is independent of the length of the pre-tRNA leader. Following formation of the initial enzyme-substrate complex, a unimolecular step enhances the overall affinity of pre-tRNA by eight- to 300-fold as the length of the leader sequence increases from 2 to 5 nucleotides. This increase in affinity is due to a decrease in the reverse rate constant for the conformational change that correlates with the formation of an optimal leader-protein interaction in the RNase P holoenzyme-pre-tRNA complex. Furthermore, the forward rate constant for the conformational change becomes rate limiting for cleavage under single-turnover conditions at high pH, explaining the origin of the observed apparent pK(a) in the RNase P-catalyzed cleavage reaction. These data suggest that a conformational change in the RNase P*pre-tRNA complex is coupled to the interactions between the 5' leader and P protein and aligns essential functional groups at the cleavage active site to enhance efficient cleavage of pre-tRNA.
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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.