Tandem RNA-binding domain architecture drives PKR activation through an intramolecular interface.

Abstract

Tandem repeats of RNA-binding domains (RBDs), often linked by intrinsically disordered sequences, are prevalent among RNA-binding proteins (RBPs). The inherent flexibility of these arrangements, however, raises the question of whether such domains can adopt defined configurations critical for function. Here, we reveal that in Protein Kinase R (PKR)-an RBP that triggers the innate immune response upon sensing double-stranded RNAs (dsRNAs)-its two dsRNA-binding domains (dsRBDs) assemble into a unique architecture through intramolecular interactions. This dsRBD1:dsRBD2 interface allows PKR to convert diffusive, transient contacts with RNA into a stabilized complex on the duplex, establishing a scaffold required for downstream protein dimerization and phosphorylation. Disrupting this dsRBD1:dsRBD2 interface dismantles the tandem dsRBD architecture and severely impairs PKR activity both in vitro and in cells. Together, these findings uncover an exceptional advantage of the tandem dsRBD arrangement and underscore intramolecular RBD coupling as a mechanism for regulating RBP activity.