A small structural element, Pc-J5/5a, plays dual roles in a group IC1 intron RNA

The P4-P6 domain of group IC1 intron ribozymes such as that of the Tetrahym ena autonomously folds into a hairpin-shaped structure in which the J5/5a r egion serves as a hinge. Phylogenetic comparisons of these IC1 introns sugg ested that the J5/5a region (termed Pc-J5/5a motif) in a subclass of IC1 in trons such as the one from Pneumocystis carinii functions not only as a hin ge but also as a receptor for a GAAA-tetraloop. We investigated the role of this motif by transplanting the structural unit, Pc-J5/5a motif, of Pneumo cystis carinii into the P4-P6 domain of the Tetrahymena intron. The results showed that the Pc-J5/5a motif binds to a GAAA loop with high affinity and also facilitates the bending of the Tetrahymena P4-P6 domain more positive ly than the original J5/5a region. (C) 2000 Academic Press.