title: A small structural element, Pc-J5/5a, plays dual roles in a group IC1 intron RNA.
abstract: The P4-P6 domain of group IC1 intron ribozymes such as that of the Tetrahymena autonomously folds into a hairpin-shaped structure in which the J5/5a region serves as a hinge. Phylogenetic comparisons of these IC1 introns suggested that the J5/5a region (termed Pc-J5/5a motif) in a subclass of IC1 introns such as the one from Pneumocystis carinii functions not only as a hinge 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 Pneumocystis 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 positively than the original J5/5a region.
authors.affiliation: Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan.
authors.forename: Y
authors.initials: Y
authors.lastname: Ikawa
authors.forename: H
authors.initials: H
authors.lastname: Shiraishi
authors.forename: T
authors.initials: T
authors.lastname: Inoue
mesh_terms: D000818:Animals; D001483:Base Sequence; D004591:Electrophoresis, Polyacrylamide Gel; D007438:Introns; D008957:Models, Genetic; D008969:Molecular Sequence Data; D016296:Mutagenesis; D009690:Nucleic Acid Conformation; D010957:Plasmids / Q000378:metabolism; D011010:Pneumocystis / Q000235:genetics; D012313:RNA / Q000378:metabolism*; D016337:RNA, Catalytic / Q000737:chemistry* / Q000235:genetics*; D013768:Tetrahymena / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D016337:RNA, Catalytic; D012313:RNA