Figure 10. Kinetic scheme for activation and inactivation of cOA production.

In its ground state, Csm adopts a conformation where the HD nuclease and cyclase domains are inactive. On binding cognate target RNA with a non-pairing 3’ end, these domains are allosterically activated, stimulating DNA degradation and cOA synthesis. Backbone cleavage of the target RNA occurs most rapidly at site B1 nearest to the 3’ end, with progressively slower rates of cleavage at sites B2 and B3. Cleaved RNA dissociation is observed with an off rate of 0.07 min⁻¹, suggesting it may be rate limited by cleavage at site B2 and does not require cleavage at site B3. The production of cOA is quickly switched off, consistent with a rapid return to the inactive ground state. Non-target RNAs proceed through the same processing steps, but do not activate the cyclase or HD nuclease domains.