ArticleThe EMBO journal2002
The global structure of the VS ribozyme.
Article in The EMBO journal, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Impact of Ion-Mixing Entropy on Orientational Preferences of DNA Helices: FRET Measurements and Computer Simulations.The journal of physical chemistry. B · 2023Article
- Revolving hexameric ATPases as asymmetric motors to translocate double-stranded DNA genome along one strand.iScience · 2023Review
- An integrative NMR-SAXS approach for structural determination of large RNAs defines the substrate-free state of a trans-cleaving Neurospora Varkud Satellite ribozyme.Nucleic acids research · 2021Article
- Self-cleaving ribozymes: substrate specificity and synthetic biology applications.RSC chemical biology · 2021Review
- A structural intermediate pre-organizes the add adenine riboswitch for ligand recognition.Nucleic acids research · 2021Article
- Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme.Nature chemistry · 2020Article
- Ligand recognition and helical stacking formation are intimately linked in the SAM-I riboswitch regulatory mechanism.RNA (New York, N.Y.) · 2017Article
- Insights into RNA structure and dynamics from recent NMR and X-ray studies of the Neurospora Varkud satellite ribozyme.Wiley interdisciplinary reviews. RNA · 2017Review
- MgBiophysical journal · 2017Article
- Crystal structure of the Varkud satellite ribozyme.Nature chemical biology · 2015Article
- The NMR structure of the II-III-VI three-way junction from the Neurospora VS ribozyme reveals a critical tertiary interaction and provides new insights into the global ribozyme structure.RNA (New York, N.Y.) · 2015Article
- Fitness Landscapes of Functional RNAs.Life (Basel, Switzerland) · 2015Review
- A remarkably stable kissing-loop interaction defines substrate recognition by the Neurospora Varkud Satellite ribozyme.RNA (New York, N.Y.) · 2014Article
- Nucleic acid catalysis: metals, nucleobases, and other cofactors.Chemical reviews · 2014Review
- Helix-length compensation studies reveal the adaptability of the VS ribozyme architecture.Nucleic acids research · 2012Article
- Metal-ion-dependent folding of a uranyl-specific DNAzyme: insight into function from fluorescence resonance energy transfer studies.Chemistry (Weinheim an der Bergstrasse, Germany) · 2011Article
- Mechanisms of RNA catalysis.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2011Article
- Constitutive regulatory activity of an evolutionarily excluded riboswitch variant.The Journal of biological chemistry · 2011Article
- NMR structure of the A730 loop of the Neurospora VS ribozyme: insights into the formation of the active site.Nucleic acids research · 2011Article
- Folding of the lysine riboswitch: importance of peripheral elements for transcriptional regulation.Nucleic acids research · 2011Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The VS ribozyme comprises five helical segments (II-VI) in a formal H shape, organized by two three-way junctions. It interacts with its stem-loop substrate (I) by tertiary interactions. We have determined the global shape of the 3-4-5 junction (relating helices III-V) by electrophoresis and FRET. Estimation of the dihedral angle between helices II and V electrophoretically has allowed us to build a model for the global structure of the complete ribozyme. We propose that the substrate is docked into a cleft between helices II and VI, with its loop making a tertiary interaction with that of helix V. This is consistent with the dependence of activity on the length of helix III. The scissile phosphate is well placed to interact with the probable active site of the ribozyme, the loop containing A730.
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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.