Mechanism of counterattack against eIF2α kinase immune signalling by viral pseudo-kinase PK2

Viral infection triggers the activation of host innate immune responses, including the integrated stress response (ISR). The antiviral response is mediated by the phosphorylation of eukaryotic translation initiation factor 2 alpha (eIF2) catalyzed by host eIF2 kinase, resulting in suppression of global protein synthesis and induction of selected genes in the cell. To evade and/or subvert the host antiviral signalling pathway, viruses have evolved and harnessed elaborate counter-attack mechanisms to repress the activation of host eIF2 kinase. In insects, eIF2 kinase-mimic protein PK2 encoded in baculovirus directly binds to and inhibits host eIF2 kinase for viral propagation. However, the mechanism underlying how viral PK2 recognizes host eIF2 kinase and interrupts its activity has remained unclear. Here we present a series of crystal structures of apo PK2 and its complex with eIF2 kinase, revealing a conformational transition mechanism of PK2 for eIF2 kinase inhibition. PK2 alone, comprised of an N-terminal extension (NTE) and eIF2 kinase C-lobe mimic (EKCM), adopted a two-fold symmetric homotetramer assembled mainly by the NTE region. Pull-down assay identified a region of Bombyx mori HRI-like kinase (BmHRI) that binds to PK2, and its complex structure revealed that the PK2-binding region of BmHRI, subdomain III-IV, is entrapped in a newly formed groove between the NTE region and EKCM of PK2. The structural data, together with biochemical analyses, indicated that PK2 suppresses eIF2 kinase activity by the pullout and subsequent blockade of the subdomain III-IV, a regulatory element essential for its kinase activity. These results not only provide the molecular mechanisms for the inhibition of host eIF2 kinase by viral pseudo-kinase, but also unveil the viral evolutionary strategy to shut-off host immunity via horizontal gene transfer from host to virus.