The crystal structure of the PB2 cap-binding domain of influenza B virus reveals a novel cap recognition mechanism

Abstract

The influenza RNA-dependent RNA polymerase is a core enzyme required for both transcription and replication of the virus RNA genome, making it a potential drug target for the influenza virus. To detect the feature of cap-dependent transcription of influenza B virus (FluB) polymerase, we determined the crystal structures of the wild-type FluB polymerase PB2 subunit cap-binding domain (PB2 cap) with bound GDP and the mutant FluB Q325F PB2 cap with bound m 7 GDP or GDP. These structures revealed that, distinct from influenza A virus (FluA) PB2 cap, the guanine and ribose moieties of substrates invert in FluB PB2 caps. Moreover, we characterized the substrate specificity and affinity of the PB2 caps using isothermal titration calorimetry. FluB PB2 cap has a weaker affinity for m 7 GDP than FluA PB2 cap. Unlike FluA PB2 cap that has a preference for m 7 GDP in comparison with GDP, FluB PB2 cap shows an analogous affinity for both substrates. Replacement of FluB PB2 Glu 325 by Phe, the corresponding residue of FluA PB2, increased the binding affinity of FluB PB2 cap for m 7 GDP to a level approximate to that of FluA PB2 cap and caused a significant higher affinity to GDP. This study indicated that FluB PB2 cap has a unique cap recognition mechanism compared with FluA PB2 cap, providing molecular insight into inhibitor design targeting FluB PB2 cap.