Allosteric Functional Switch in Poliovirus 3C Protease

Viral genomes are very efficient; they are typically compact but nevertheless encode numerous elements that are essential for regulation of both its own replication and packaging, and of the host cell's machinery. Viruses have developed successful strategies to overcome their biological information storage problem. For example, the 3C pro protein from the picornavirus family of positive‐strand RNA viruses is responsible for binding of RNA control sequences to regulate translation and replication, interacting with phosphoinositide lipids (PI) to regulate the maturation of virus replication organelles, and acting as the main protease to cleave host and virus proteins to further regulate host and virus processes. 3C pro can also be found as a domain in the 3CD pro polyprotein. 3C pro by itself and 3CD pro have different protease specificities, and likely different RNA and PI binding capabilities. The domains in 3CD pro are tethered by a flexible linker and do not make specific 3C pro ‐3D pol interactions. Surprisingly, we have found that by extending the C‐terminal tail of 3C with just a few amino acid residues, the RNA and PI binding properties alter dramatically. These functional changes are accompanied by changes in the structural dynamics of 3C, as measured by NMR relaxation methods. We propose that these findings have critical bearing on 3C function; proteolytic processing of the C‐terminus is the switch from 3CD pro to 3C pro (by itself) activities. Such a simple, but elegant, mechanism does not require any additional domain‐domain interactions in the 3CD pro polyprotein to regulate 3C pro function, and can help explain functional differences between 3C pro and 3CD pro that have confounded virologists and structural biologists.