Autocatalytic activity and substrate specificity of the pestivirus N-terminal protease Npro

Pestivirus Npro is the first protein translated in the viral polypeptide, and cleaves itself off co-translationally generating the N-terminus of the core protein. Once released, Npro blocks the host׳s interferon response by inducing degradation of interferon regulatory factor-3. Npro׳s intracellular autocatalytic activity and lack of trans-activity have hampered in vitro cleavage studies to establish its substrate specificity and the roles of individual residues. We constructed Npro-GFP fusion proteins that carry the authentic cleavage site and determined the autoproteolytic activities of Npro proteins containing substitutions at the predicted catalytic sites Glu22 and Cys69, at Arg100 that forms a salt bridge with Glu22, and at the cleavage site Cys168. Contrary to previous reports, we show that Npro׳s catalytic activity does not involve Glu22, which may instead be involved in protein stability. Furthermore, Npro does not have specificity for Cys168 at the cleavage site even though this residue is conserved throughout the pestivirus genus.