FIGURE 6.

Model for A.n. COB pre-RNA/I-AniI assembly. Although important for binding, the P3–P7 domain is not shown for simplicity. Dashed lines indicate single-stranded or destabilized double-stranded regions and the cylinders represent helices. Prior to binding, the P4 and P6 helices in the core are unstable and, as a consequence, P1 and P2 are not properly positioned in the core. In the first step of binding, I-AniI associates with the intron RNA in a weak complex and promotes folding of the catalytic core. Within this complex, P1 and P2 become destabilized and subsequently dock into its intron's catalytic site that leads to the first step in splicing. The P1/P2 docked structure is inferred, since I-AniI binding results in splicing activation (see Discussion). This docking event may cause subtle rearrangements in the I-AniI binding site in P4, resulting in tighter binding and formation of the native complex. The relative orientation of the helices in the free RNA and intermediate complexes is not intended to reflect a specific conformation. I-AniI may dissociate from the RNA in the encounter complexes because of their short half-lives, but once in the native complex, binding is essentially irreversible (Solem et al. 2002).