ArticleNucleic acids research2007
The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 32 citations in OpenAlex.
- An intricate balance of hydrogen bonding, ion atmosphere and dynamics facilitates a seamless uracil to cytosine substitution in the U-turn of the neomycin-sensing riboswitch.Nucleic acids research · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Determination of hepatitis delta virus ribozyme N(-1) nucleobase and functional group specificity using internal competition kinetics.Analytical biochemistry · 2015Article
- Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics.Physical chemistry chemical physics : PCCP · 2015Article
- Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape.RNA (New York, N.Y.) · 2014Article
- Structural insights into substrate recognition by the Neurospora Varkud satellite ribozyme: importance of U-turns at the kissing-loop junction.Biochemistry · 2014Article
- Secondary structure of bacteriophage T4 gene 60 mRNA: implications for translational bypassing.RNA (New York, N.Y.) · 2013Article
- Characterization of the Structure and Dynamics of the HDV Ribozyme at Different Stages Along the Reaction Path.The journal of physical chemistry letters · 2011Article
- Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations.RNA (New York, N.Y.) · 2010Article
- Efficient inhibition of hepatitis B virus replication by hepatitis delta virus ribozymes delivered by targeting retrovirus.Virology journal · 2010Article
- Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in.Accounts of chemical research · 2010Article
- Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme.RNA (New York, N.Y.) · 2009Article
- The Small Ribozymes: Common and Diverse Features Observed through the FRET Lens.Springer series in biophysics · 2009Article
- RNA dynamics: it is about time.Current opinion in structural biology · 2008Article
- Review
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4 authors at 1 institution in 1 country.
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Abstract
The genome of the human hepatitis delta virus (HDV) harbors a self-cleaving catalytic RNA motif, the genomic HDV ribozyme, whose crystal structure shows the dangling nucleotides 5' of the cleavage site projecting away from the catalytic core. This 5'-sequence contains a clinically conserved U-1 that we find to be essential for fast cleavage, as the order of activity follows U-1 > C-1 > A-1 > G-1, with a >25-fold activity loss from U-1 to G-1. Terbium(III) footprinting detects conformations for the P1.1 stem, the cleavage site wobble pair and the A-minor motif of the catalytic trefoil turn that depend on the identity of the N-1 base. The most tightly folded catalytic core, resembling that of the reaction product, is found in the U-1 wild-type precursor. Molecular dynamics simulations demonstrate that a U-1 forms the most robust kink around the scissile phosphate, exposing it to the catalytic C75 in a previously unnoticed U-turn motif found also, for example, in the hammerhead ribozyme and tRNAs. Strikingly, we find that the common structural U-turn motif serves distinct functions in the HDV and hammerhead ribozymes.
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