Journal
EMBO JOURNAL
Volume 19, Issue 18, Pages 5007-5018Publisher
OXFORD UNIV PRESS
DOI: 10.1093/emboj/19.18.5007
Keywords
group II intron; hydroxyl radical probing; intron-exon interactions; ribozyme; RNA structure modeling
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Funding
- NIGMS NIH HHS [R01 GM017129, R37 GM017129, GM17129] Funding Source: Medline
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We have used chemical footprinting, kinetic dissection of reactions and comparative sequence analysis to show that in self-splicing introns belonging to subgroup IIB, the sites that bind the 5' and 3' exons are connected to one another by tertiary interactions. This unanticipated arrangement, which contrasts with the direct covalent linkage that prevails in the other major subdivision of group II (subgroup IIA), results in a unique three-dimensional architecture for the complex between the exons, their binding sites and intron domain V, A key feature of the modeled complex is the presence of several close contacts between domain V and one of the intron-exon pairings, These contacts, whose existence is supported by hydroxyl radical footprinting, provide a structural framework for the known role of domain V in catalysis and its recently demonstrated involvement in binding of the 5' exon.
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