RNA recognition and base flipping by the toxin sarcin.

Sarcin is a member of a fungal toxin family that enters cells and specifically cleaves one of the thousands of RNA phosphodiester bonds in the ribosome. As a result, elongation factor binding is disrupted, translation is inhibited and apoptosis is triggered. The toxin targets a universal RNA structure in the ribosome called the sarcin/ricin loop (SRL). A 1.11 A resolution structure of a minimal SRL RNA substrate (approximately 30-mer) shows that the loop portion of the substrate folds into two common building blocks of RNA structure: a bulged-G motif (recognition site) and a GAGA tetraloop (cleavage site). To elucidate the structural basis of toxin action, we determined two co-crystal structures of the sarcin homologue restrictocin bound to different analogs of a minimal SRL RNA substrate. Our studies argue that site selection by the toxin depends on direct base and shape recognition of the SRL RNA, and that cleavage by the toxin depends on a base flipping mechanism that positions the nucleophile for in-line attack on the scissile bond.