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.