ArticleJournal of molecular biology2008
A kinetic intermediate that regulates proper folding of a group II intron RNA.
Article in Journal of molecular biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Dynamic assembly of a large multidomain ribozyme visualized by cryo-electron microscopy.Nature communications · 2025Article
- Review
- Group II intron as cold sensor for self-preservation and bacterial conjugation.Nucleic acids research · 2020Article
- TbFrontiers in chemistry · 2017Article
- Studying metal ion binding properties of a three-way junction RNA by heteronuclear NMR.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2016Article
- Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme.Nucleic acids research · 2016Article
- Crystal structure of group II intron domain 1 reveals a template for RNA assembly.Nature chemical biology · 2015Article
- Principles of ion recognition in RNA: insights from the group II intron structures.RNA (New York, N.Y.) · 2014Article
- RNA helicase proteins as chaperones and remodelers.Annual review of biochemistry · 2014Review
- The structural stabilization of the κ three-way junction by Mg(II) represents the first step in the folding of a group II intron.Nucleic acids research · 2013Article
- Mss116p: a DEAD-box protein facilitates RNA folding.RNA biology · 2013Review
- Toward a molecular understanding of RNA remodeling by DEAD-box proteins.RNA biology · 2013Review
- The brace for a growing scaffold: Mss116 protein promotes RNA folding by stabilizing an early assembly intermediate.Journal of molecular biology · 2012Article
- Folding kinetics for the conformational switch between alternative RNA structures.The journal of physical chemistry. B · 2010Article
- Dual roles for the Mss116 cofactor during splicing of the ai5γ group II intron.Nucleic acids research · 2010Article
- The tertiary structure of group II introns: implications for biological function and evolution.Critical reviews in biochemistry and molecular biology · 2010Review
- Protein-facilitated folding of group II intron ribozymes.Journal of molecular biology · 2010Article
- Compact intermediates in RNA folding.Annual review of biophysics · 2010Review
- Energy barriers, pathways, and dynamics during folding of large, multidomain RNAs.Current opinion in chemical biology · 2008Review
- Selective stabilization of natively folded RNA structure by DNA constraints.Journal of the American Chemical Society · 2008Article
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Authors and funding
2 authors.
Funding
Abstract
The D135 group II intron ribozyme follows a unique folding pathway that is direct and appears to be devoid of kinetic traps. During the earliest stages of folding, D135 collapses slowly to a compact intermediate, and all subsequent assembly events are rapid. Collapse of intron domain 1 (D1) has been shown to limit the rate constant for D135 folding, although the specific substructure of the D1 kinetic intermediate has not yet been identified. Employing time-resolved nucleotide analog interference mapping, we have identified a cluster of atoms within the D1 main stem that control the rate constant for D135 collapse. Functional groups within the kappa-zeta element are particularly important for this earliest stage of folding, which is intriguing given that this same motif also serves later as the docking site for catalytic domain 5. More important, the kappa-zeta element is shown to be a divalent ion binding pocket, indicating that this region is a Mg(2+)-dependent switch that initiates the cascade of D135 folding events. By measuring the Mg(2+) dependence of the compaction rate constant, we conclude that the actual rate-limiting step in D1 compaction involves the formation of an unstable folding intermediate that is captured by the binding of Mg(2+). This carefully orchestrated folding pathway, in which formation of an active-site docking region is early and rate limiting, ensures proper folding of the intron core and faithful splicing. It may represent an important paradigm for the folding of large, multidomain RNA molecules.
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