ArticleThe Journal of biological chemistry2015
Mechanistic Studies Reveal Similar Catalytic Strategies for Phosphodiester Bond Hydrolysis by Protein-only and RNA-dependent Ribonuclease P.
Article in The Journal of biological chemistry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 38 citations in OpenAlex.
- Structural and functional insights into Pseudomonas aeruginosa ApaH, a diadenosine tetraphosphatase crucial for bacterial virulence.Protein science : a publication of the Protein Society · 2026Article
- Three-metal-ion catalysis by ribonuclease P holoenzyme: a new mechanistic insight into transfer RNA maturation.Research square · 2026Article
- Structural basis for protein-free catalysis by ribonuclease P ribozyme.Nature communications · 2026Article
- Substrate and enzyme determinants for recognition by human mitochondrial RNase P.Nucleic acids research · 2025Article
- Discovery, structure, mechanisms, and evolution of protein-only RNase P enzymes.The Journal of biological chemistry · 2024Review
- Cleavage kinetics of human mitochondrial RNase P and contribution of its non-nuclease subunits.Nucleic acids research · 2023Article
- How RNases Shape Mitochondrial Transcriptomes.International journal of molecular sciences · 2022Review
- Pentatricopeptide repeats of protein-only RNase P use a distinct mode to recognize conserved bases and structural elements of pre-tRNA.Nucleic acids research · 2020Article
- Interplay between substrate recognition, 5' end tRNA processing and methylation activity of human mitochondrial RNase P.RNA (New York, N.Y.) · 2019Article
- Biochemical Studies Provide Insights into the Necessity for Multiple Arabidopsis thaliana Protein-Only RNase P Isoenzymes.Journal of molecular biology · 2019Article
- Molecular recognition of pre-tRNA byRNA (New York, N.Y.) · 2017Article
- Comprehensive classification of the PIN domain-like superfamily.Nucleic acids research · 2017Article
- Mechanistic and Structural Studies of Protein-Only RNase P Compared to Ribonucleoproteins Reveal the Two Faces of the Same Enzymatic Activity.Biomolecules · 2016Review
- Use of chemical modification and mass spectrometry to identify substrate-contacting sites in proteinaceous RNase P, a tRNA processing enzyme.Nucleic acids research · 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
- Substrate recognition and cleavage-site selection by a single-subunit protein-only RNase P.Nucleic acids research · 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
- Cleavage of Model Substrates by Arabidopsis thaliana PRORP1 Reveals New Insights into Its Substrate Requirements.PloS one · 2016Article
- Structure of the nuclease subunit of human mitochondrial RNase P.Nucleic acids research · 2015Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Ribonuclease P (RNase P) is an endonuclease that catalyzes the essential removal of the 5' end of tRNA precursors. Until recently, all identified RNase P enzymes were a ribonucleoprotein with a conserved catalytic RNA component. However, the discovery of protein-only RNase P (PRORP) shifted this paradigm, affording a unique opportunity to compare mechanistic strategies used by naturally evolved protein and RNA-based enzymes that catalyze the same reaction. Here we investigate the enzymatic mechanism of pre-tRNA hydrolysis catalyzed by the NYN (Nedd4-BP1, YacP nuclease) metallonuclease of Arabidopsis thaliana, PRORP1. Multiple and single turnover kinetic data support a mechanism where a step at or before chemistry is rate-limiting and provide a kinetic framework to interpret the results of metal alteration, mutations, and pH dependence. Catalytic activity has a cooperative dependence on the magnesium concentration (nH = 2) under kcat/Km conditions, suggesting that PRORP1 catalysis is optimal with at least two active site metal ions, consistent with the crystal structure. Metal rescue of Asp-to-Ala mutations identified two aspartates important for enhancing metal ion affinity. The single turnover pH dependence of pre-tRNA cleavage revealed a single ionization (pKa ∼ 8.7) important for catalysis, consistent with deprotonation of a metal-bound water nucleophile. The pH and metal dependence mirrors that observed for the RNA-based RNase P, suggesting similar catalytic mechanisms. Thus, despite different macromolecular composition, the RNA and protein-based RNase P act as dynamic scaffolds for the binding and positioning of magnesium ions to catalyze phosphodiester bond hydrolysis.
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