ArticleJournal of molecular biology2007
Requirement of helix P2.2 and nucleotide G1 for positioning the cleavage site and cofactor of the glmS ribozyme.
Article in Journal of molecular biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 79 citations in OpenAlex.
- DesiRNA: structure-based design of RNA sequences with a replica exchange Monte Carlo approach.Nucleic acids research · 2025Article
- Optimized periphery-core interface increases fitness of the Bacillus subtilis glmS ribozyme.Nucleic acids research · 2024Article
- Biological Catalysis and Information Storage Have Relied onBiomolecules · 2023Review
- Carba-Sugar Analogs of Glucosamine-6-Phosphate: New Activators for the glmS Riboswitch.Chemistry (Weinheim an der Bergstrasse, Germany) · 2023Article
- Riboswitches as Drug Targets for Antibiotics.Antibiotics (Basel, Switzerland) · 2021Review
- EPR Distance Measurements on Long Non-coding RNAs Empowered by Genetic Alphabet Expansion Transcription.Angewandte Chemie (International ed. in English) · 2020Article
- Comprehensive sequence-to-function mapping of cofactor-dependent RNA catalysis in the glmS ribozyme.Nature communications · 2020Article
- Effects of Noncanonical Base Pairing on RNA Folding: Structural Context and Spatial Arrangements of G·A Pairs.Biochemistry · 2019Article
- Self-cleavage of theProceedings of the National Academy of Sciences of the United States of America · 2018Article
- Small-Molecule-Binding Riboswitches.Microbiology spectrum · 2018Review
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- The GlcN6P cofactor plays multiple catalytic roles in the glmS ribozyme.Nature chemical biology · 2017Article
- A divalent cation-dependent variant of theRNA (New York, N.Y.) · 2017Article
- Assessing the Potential Effects of Active Site MgThe journal of physical chemistry letters · 2016Article
- In vitro evolution of coenzyme-independent variants from the glmS ribozyme structural scaffold.Methods (San Diego, Calif.) · 2016Article
- Chemical feasibility of the general acid/base mechanism of glmS ribozyme self-cleavage.Biopolymers · 2015Article
- Role of the active site guanine in the glmS ribozyme self-cleavage mechanism: quantum mechanical/molecular mechanical free energy simulations.Journal of the American Chemical Society · 2015Article
- Phosphatase-inert glucosamine 6-phosphate mimics serve as actuators of the glmS riboswitch.ACS chemical biology · 2014Article
- Dramatic improvement of crystals of large RNAs by cation replacement and dehydration.Structure (London, England : 1993) · 2014Article
- New molecular engineering approaches for crystallographic studies of large RNAs.Current opinion in structural biology · 2014Review
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
Abstract
The glmS ribozyme is a catalytic RNA that self-cleaves at its 5'-end in the presence of glucosamine 6-phosphate (GlcN6P). We present structures of the glmS ribozyme from Thermoanaerobacter tengcongensis that are bound with the cofactor GlcN6P or the inhibitor glucose 6-phosphate (Glc6P) at 1.7 A and 2.2 A resolution, respectively. The two structures are indistinguishable in the conformations of the small molecules and of the RNA. GlcN6P binding becomes apparent crystallographically when the pH is raised to 8.5, where the ribozyme conformation is identical with that observed previously at pH 5.5. A key structural feature of this ribozyme is a short duplex (P2.2) that is formed between sequences just 3' of the cleavage site and within the core domain, and which introduces a pseudoknot into the active site. Mutagenesis indicates that P2.2 is required for activity in cis-acting and trans-acting forms of the ribozyme. P2.2 formation in a trans-acting ribozyme was exploited to demonstrate that N1 of the guanine at position 1 contributes to GlcN6P binding by interacting with the phosphate of the cofactor. At neutral pH, RNAs with adenine, 2-aminopurine, dimethyladenine or purine substitutions at position 1 cleave faster with glucosamine than with GlcN6P. This altered cofactor preference provides biochemical support for the orientation of the cofactor within the active site. Our results establish two features of the glmS ribozyme that are important for its activity: a sequence within the core domain that selects and positions the cleavage-site sequence, and a nucleobase at position 1 that helps position GlcN6P.
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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.