ArticleRNA (New York, N.Y.)2009
Mapping metal-binding sites in the catalytic domain of bacterial RNase P RNA.
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 37 papers.
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Who cites it
37 citing papers in PubMed.
- Coevolution of RNase P and the ribosome.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Article
- RNase P cleavage of pseudoknot substrates reveals differences in active site architecture that depend on residue N-1 in the 5' leader.RNA biology · 2025Article
- A small cationic probe for accurate, punctate discovery of RNA tertiary structure.bioRxiv : the preprint server for biology · 2025Article
- The conformational space of RNase P RNA in solution.Nature · 2025Article
- Article
- RNAvigate: efficient exploration of RNA chemical probing datasets.Nucleic acids research · 2024Article
- Determining structures of individual RNA conformers using atomic force microscopy images and deep neural networks.Research square · 2023Article
- Visualizing RNA conformational and architectural heterogeneity in solution.Nature communications · 2023Article
- Identifying proximal RNA interactions from cDNA-encoded crosslinks with ShapeJumper.PLoS computational biology · 2021Article
- Direct Mapping of Higher-Order RNA Interactions by SHAPE-JuMP.Biochemistry · 2021Article
- Time-Resolved, Single-Molecule, Correlated Chemical Probing of RNA.Journal of the American Chemical Society · 2020Article
- Nucleobase carbonyl groups are poor MgRNA (New York, N.Y.) · 2019Article
- Second-Shell Basic Residues Expand the Two-Metal-Ion Architecture of DNA and RNA Processing Enzymes.Structure (London, England : 1993) · 2018Article
- Inner-Sphere Coordination of Divalent Metal Ion with Nucleobase in Catalytic RNA.Journal of the American Chemical Society · 2017Article
- TheJournal of bacteriology · 2017Article
- Structural and Biochemical Properties of Novel Self-Cleaving Ribozymes.Molecules (Basel, Switzerland) · 2017Review
- Structural Roles of Noncoding RNAs in the Heart of Enzymatic Complexes.Biochemistry · 2017Article
- The Diversity of Ribonuclease P: Protein and RNA Catalysts with Analogous Biological Functions.Biomolecules · 2016Review
- Review toward all RNA structures, concisely.Biopolymers · 2015Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ribonuclease P (RNase P) is a ribonucleoprotein enzyme that contains a universally conserved, catalytically active RNA component. RNase P RNA requires divalent metal ions for folding, substrate binding, and catalysis. Despite recent advances in understanding the structure of RNase P RNA, no comprehensive analysis of metal-binding sites has been reported, in part due to the poor crystallization properties of this large RNA. We have developed an abbreviated yet still catalytic construct, Bst P7Delta RNA, which contains the catalytic domain of the bacterial RNase P RNA and has improved crystallization properties. We use this mutant RNA as well as the native RNA to map metal-binding sites in the catalytic core of the bacterial RNase P RNA, by anomalous scattering in diffraction analysis. The results provide insight into the interplay between RNA structure and focalization of metal ions, and a structural basis for some previous biochemical observations with RNase P. We use electrostatic calculations to extract the potential functional significance of these metal-binding sites with respect to binding Mg(2+). The results suggest that with at least one important exception of specific binding, these sites mainly map areas of diffuse association of magnesium ions.
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