ArticleRNA (New York, N.Y.)2004
The three-dimensional architecture of the class I ligase ribozyme.
Article in RNA (New York, N.Y.), 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- A universal Fab targeting a conserved U1A-RNA epitope for RNA structure determination by cryo-EM.Nucleic acids research · 2026Article
- Molecular Anatomy of the Class I Ligase Ribozyme for Elucidation of the Activity-Generating Unit.Biology · 2023Article
- In vitro selection of ribozyme ligases that use prebiotically plausible 2-aminoimidazole-activated substrates.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Nucleic Acid Catalysis under Potential Prebiotic Conditions.Chemistry, an Asian journal · 2020Review
- Article
- Consistent global structures of complex RNA states through multidimensional chemical mapping.eLife · 2015Article
- Three-dimensional RNA structure refinement by hydroxyl radical probing.Nature methods · 2012Article
- ModeRNA: a tool for comparative modeling of RNA 3D structure.Nucleic acids research · 2011Article
- Characterization of the B6.61 polymerase ribozyme accessory domain.RNA (New York, N.Y.) · 2011Article
- A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination.Nature structural & molecular biology · 2011Article
- Closing the circle: replicating RNA with RNA.Cold Spring Harbor perspectives in biology · 2010Review
- Quasispecies-like behavior observed in catalytic RNA populations evolving in a test tube.BMC evolutionary biology · 2010Article
- A class I ligase ribozyme with reduced Mg2+ dependence: Selection, sequence analysis, and identification of functional tertiary interactions.RNA (New York, N.Y.) · 2009Article
- Crystal structure of the catalytic core of an RNA-polymerase ribozyme.Science (New York, N.Y.) · 2009Article
- Darwinian evolution on a chip.PLoS biology · 2008Article
- Selection of an improved RNA polymerase ribozyme with superior extension and fidelity.RNA (New York, N.Y.) · 2007Article
- Article
- Topological rearrangement yields structural stabilization and interhelical distance constraints in the Kin.46 self-phosphorylating ribozyme.RNA (New York, N.Y.) · 2006Article
- RNA-directed construction of structurally complex and active ligase ribozymes through recombination.RNA (New York, N.Y.) · 2005Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The class I ligase ribozyme catalyzes a Mg(++)-dependent RNA-ligation reaction that is chemically analogous to a single step of RNA polymerization. Indeed, this ribozyme constitutes the catalytic domain of an accurate and general RNA polymerase ribozyme. The ligation reaction is also very rapid in both single- and multiple-turnover contexts and thus is informative for the study of RNA catalysis as well as RNA self-replication. Here we report the initial characterization of the three-dimensional architecture of the ligase. When the ligase folds, several segments become protected from hydroxyl-radical cleavage, indicating that the RNA adopts a compact tertiary structure. Ribozyme folding was largely, though not completely, Mg(++) dependent, with a K(1/2[Mg]) < 1 mM, and was observed over a broad temperature range (20 degrees C -50 degrees C). The hydroxyl-radical mapping, together with comparative sequence analyses and analogy to a region within 23S ribosomal RNA, were used to generate a three-dimensional model of the ribozyme. The predictive value of the model was tested and supported by a photo-cross-linking experiment.
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