Many plus-strand RNA viruses encode a viral RNA polymerase and capping enzymes to synthesize a 5’-capped RNA genome. However, how these two activities are coordinated during viral replication is not understood. In flaviviruses, polymerase and capping enzymes are encoded in a single multifunctional protein, where separate domains within the polypeptide are responsible for these activities; flavivirus NS5, composed of the polymerase and methyltransferase domains, carries out viral RNA synthesis, 5’-RNA capping, and RNA cap methylations. Previous NS5 monomer structures were unable to provide mechanistic insight into how the two domains communicate or the quaternary organization of the functional enzyme. We have determined the crystal structure of dengue virus NS5 and show that the NS5 dimer is likely the biological assembly of NS5, and RNA synthesis and RNA capping may be coordinated by the dimer. We found that essential interactions between the two NS5 domains can be maintained either within a monomer or via inter-molecular interactions within a dimer, and thus NS5 can adopt multiple conformations while preserving necessary interactions between the methyltransferase and polymerase domains. Using dengue virus, we additionally determined that such specific interaction between the two NS5 domains is the major determinant of viral replication.
Many plus-strand RNA viruses encode a viral RNA polymerase and capping enzymes to synthesize a 5’-capped RNA genome. However, how these two activities are coordinated during viral replication is not understood. In flaviviruses, polymerase and capping enzymes are encoded in a single multifunctional protein, where separate domains within the polypeptide are responsible for these activities; flavivirus NS5, composed of the polymerase and methyltransferase domains, carries out viral RNA synthesis, 5’-RNA capping, and RNA cap methylations. Previous NS5 monomer structures were unable to provide mechanistic insight into how the two domains communicate or the quaternary organization of the functional enzyme. We have determined the crystal structure of dengue virus NS5 and show that the NS5 dimer is likely the biological assembly of NS5, and RNA synthesis and RNA capping may be coordinated by the dimer. We found that essential interactions between the two NS5 domains can be maintained either within a monomer or via inter-molecular interactions within a dimer, and thus NS5 can adopt multiple conformations while preserving necessary interactions between the methyltransferase and polymerase domains. Using dengue virus, we additionally determined that such specific interaction between the two NS5 domains is the major determinant of viral replication.
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