Apoptosis, NF-κB activation, and IRF3 activation are a triad of intrinsic immune responses that play crucial roles in the pathogenesis of infectious diseases, cancer, and autoimmunity. FLIPs are a family of viral and cellular proteins initially found to inhibit apoptosis and more recently to either up-or down-regulate NF-κB. As such, a broad role for FLIPs in disease regulation is postulated, but exactly how a FLIP performs such multifunctional roles remains to be established. Here we examine FLIPs (MC159 and MC160) encoded by the molluscum contagiosum virus, a dermatotropic poxvirus causing skin infections common in children and immunocompromised individuals, to better understand their roles in viral pathogenesis. While studying their molecular mechanisms responsible for NF-κB inhibition, we discovered that each protein inhibited IRF3-controlled luciferase activity, identifying a unique function for FLIPs. MC159 and MC160 each inhibited TBK1 phosphorylation, confirming this unique function. Surprisingly, MC159 coimmunoprecipitated with TBK1 and IKKe but MC160 did not, suggesting that these homologs use distinct molecular mechanisms to inhibit IRF3 activation. Equally surprising was the finding that the FLIP regions necessary for TBK1 inhibition were distinct from those MC159 or MC160 regions previously defined to inhibit NF-κB or apoptosis. These data reveal previously unappreciated complexities of FLIPs, and that subtle differences within the conserved regions of FLIPs possess distinct molecular and structural fingerprints that define crucial differences in biological activities. A future comparison of mechanistic differences between viral FLIP proteins can provide new means of precisely manipulating distinct aspects of intrinsic immune responses.host-pathogen interactions | immune evasion I FN-β provides an important defense against viral infections (1, 2). The pathway leading to IFN-β production is well characterized. By-products of viral infection, such as dsRNA, are detected by upstream cellular sensors, including retinoic acidinducible gene 1 (RIG-I), melanoma differentiation-associated factor gene 5 (MDA5), and STING. RIG-I and MDA5 proteins then interact with mitochondrial antiviral signaling (MAVS) adaptor protein to trigger MAVS activation (3-8). The TNF receptor-associated factor 3 (TRAF3) adaptor protein is recruited to this complex, resulting in the activation of the kinase complex TANK-binding kinase 1 (TBK1)-IκB kinase e (IKKe) (9-11). Alternatively, the STING molecule activates TBK1-IKKe (12, 13). In either case, TBK1-IKKe phosphorylates and activates IFN regulatory factor (IRF) transcription factor proteins (11), which migrate to the nucleus to bind to the IFN-β enhancer. IFN-β is secreted and binds to the IFN receptor (IFNR). This initiates a second signaling cascade in infected and neighboring cells, which promotes expression of IFN-α and IFN-stimulated genes whose products contribute to an antiviral state.Identification of the above members of the IFN-β signal transduction pathway also resul...