Figure 6.

Modes of Interaction of RNase E with RNA

RNase E (purple) can recognize RNA (red) via the 5′ sensing route (top right panel) or direct entry (middle right panel), or can utilize both 5′ end and structural elements (mixed mode, bottom right panel). 5′ end recognition involves 5′ monophosphate binding by the 5′ sensing pocket (blue). The direct entry mode requires RNA fold recognition by the identified RNA duplex binding surface localized between RNase H, DNase I, and small domains. The cleavage of the substrate can occur both upstream and downstream of the structural element, depending on the overall fold and alignment of the RNA on RNase E.