ArticlePLoS biology2005
Functional identification of catalytic metal ion binding sites within RNA.
Article in PLoS biology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 74 citations in OpenAlex.
- Structure and mechanism of HDV ribozymes revealing Lewis acid catalysis by a metal ion.Nature communications · 2026Article
- Article
- Nucleic Acid Catalysis under Potential Prebiotic Conditions.Chemistry, an Asian journal · 2020Review
- Elucidation of Catalytic Strategies of Small Nucleolytic Ribozymes From Comparative Analysis of Active Sites.ACS catalysis · 2018Article
- Inner-Sphere Coordination of Divalent Metal Ion with Nucleobase in Catalytic RNA.Journal of the American Chemical Society · 2017Article
- Debranchase-resistant labeling of RNA using the 10DM24 deoxyribozyme and fluorescent modified nucleotides.Chemical communications (Cambridge, England) · 2017Article
- 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
- Force Field for Mg(2+), Mn(2+), Zn(2+), and Cd(2+) Ions That Have Balanced Interactions with Nucleic Acids.The journal of physical chemistry. B · 2015Article
- Probing the kinetic and thermodynamic consequences of the tetraloop/tetraloop receptor monovalent ion-binding site in P4-P6 RNA by smFRET.Biochemical Society transactions · 2015Review
- Calcium inhibition of ribonuclease H1 two-metal ion catalysis.Journal of the American Chemical Society · 2014Article
- Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme.Journal of the American Chemical Society · 2014Article
- Exploring purine N7 interactions via atomic mutagenesis: the group I ribozyme as a case study.RNA (New York, N.Y.) · 2012Article
- Metal-ion rescue revisited: biochemical detection of site-bound metal ions important for RNA folding.RNA (New York, N.Y.) · 2012Article
- Synthesis, properties, and applications of oligonucleotides containing an RNA dinucleotide phosphorothiolate linkage.Accounts of chemical research · 2011Article
- 2'-Fluoro substituents can mimic native 2'-hydroxyls within structured RNA.Chemistry & biology · 2011Article
- Article
- Mechanistic strategies in the HDV ribozyme: chelated and diffuse metal ion interactions and active site protonation.The journal of physical chemistry. B · 2011Article
- Tightening of active site interactions en route to the transition state revealed by single-atom substitution in the guanosine-binding site of the Tetrahymena group I ribozyme.Journal of the American Chemical Society · 2011Article
- Metal binding and substrate positioning by evolutionarily invariant U6 sequences in catalytically active protein-free snRNAs.RNA (New York, N.Y.) · 2010Article
- A rearrangement of the guanosine-binding site establishes an extended network of functional interactions in the Tetrahymena group I ribozyme active site.Biochemistry · 2010Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
The viability of living systems depends inextricably on enzymes that catalyze phosphoryl transfer reactions. For many enzymes in this class, including several ribozymes, divalent metal ions serve as obligate cofactors. Understanding how metal ions mediate catalysis requires elucidation of metal ion interactions with both the enzyme and the substrate(s). In the Tetrahymena group I intron, previous work using atomic mutagenesis and quantitative analysis of metal ion rescue behavior identified three metal ions (MA, MB, and MC) that make five interactions with the ribozyme substrates in the reaction's transition state. Here, we combine substrate atomic mutagenesis with site-specific phosphorothioate substitutions in the ribozyme backbone to develop a powerful, general strategy for defining the ligands of catalytic metal ions within RNA. In applying this strategy to the Tetrahymena group I intron, we have identified the pro-SP phosphoryl oxygen at nucleotide C262 as a ribozyme ligand for MC. Our findings establish a direct connection between the ribozyme core and the functionally defined model of the chemical transition state, thereby extending the known set of transition-state interactions and providing information critical for the application of the recent group I intron crystallographic structures to the understanding of catalysis.
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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.