P2 functions as a spacer in the Tetrahymena ribozyme.

The function of the P2 stem-loop region in the group I catalytic intron from Tetrahymena thermophila has been investigated. A comprehensive mutation analysis suggests that the bottom base pair of the P2 stem and nucleotides in the loop L2 are involved in interactions elsewhere on the intron. In addition, the P2 stem can be varied only between 9 and 11 base pairs in length. Phylogenetic evidence (3) from a sub-class of group I introns supports a model in which the P1 and P2 stems are coaxially stacked. We found that variation of the length of P2 does not shift the sites of intron-catalyzed cleavage in P1 (9). This suggests that coaxial stacking of the P1 and P2 stems is unlikely in the Tetrahymena intron. A narrowing of the window for cleavage activity and a drop in cleavage efficiency are observed when substrates with an insertion in P2 are compared with those with a deletion. A possible explanation for this phenomenon is an unfavorable movement of P1 away from the active site as a result of the the lengthening of P2.