Catalytic switching and substrate recognition mechanisms of the RNA dependent protein kinase PKR

The RNA dependent protein kinase PKR is a key component of the anti-viral defense mechanism. Upon activation, PKR targets the Ser5l site in the alpha subunit of eukaryotic translation initiation factor, eIF2alpha. Through eIF2alpha phosphorylation, PKR regulates protein synthesis in an effort to promote recovery from and resistance to viral infection. In addition to PKR, the protein kinases, GCN2, HRI and PERK couple diverse stress signals directly to eIF2alpha phosphorylation. One of the main questions that I have addressed in this thesis is the structural basis for the remarkable substrate specificity of PKR and by extension the entire eIF2alpha kinase family. A second theme that I have investigated is the mechanism for the switch that regulates the conversion between the inactive and active states of PKR. Finally, I have explored the connection between the switching and substrate recognition mechanisms of PKR.;In the second chapter, I describe crystal structures of PKR-eIF2alpha complexes. The structures reveal the nature of the PKR dimer interface and also the higher-order targeting mechanism for eIF2alpha recognition. I uncover several unique structural features of PKR, which I relate to PKR's biological function and in particular its ability to target Ser51 in eIF2alpha.;The PKR-eIF2alpha structures reveal the manner in which the PKR kinase domain mediates both dimerization and substrate binding interactions. In the final chapter, I explore an allosteric connection between these interfaces and reveal a mode of regulation that is dependent on autophosphorylation. I test the structural models through mutagenesis and detailed binding analysis. Furthermore, I characterize a mutant of PKR that provides new insights into the PKR activation process. Together, the results of these studies support an exquisite coupling mechanism between PKR dimerization, autophosphorylation, and eIF2alpha substrate recognition.;PKR is targeted for subversion by the vaccinia virus, which produces a structural mimic of eIF2alpha called K3L. In the first data chapter, I describe structural and mutagenesis analysis of K3L. These studies revealed a complex PKR targeting epitope within the globular fold of K3L and eIF2alpha. I also present preliminary experiments that reveal the influence of PKR dimerization on catalytic activation and substrate binding.