A three-dimensional perspective on exon binding by a group II self-splicing intron

We have used chemical footprinting, kinetic dissection of reactions and com parative 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 o ne 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-dimensio nal 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 s everal close contacts between domain V and one of the intron-exon pairings, These contacts, whose existence is supported by hydroxyl radical footprint ing, provide a structural framework for the known role of domain V in catal ysis and its recently demonstrated involvement in binding of the 5' exon.