Replication of positive-strand RNA viruses involves translation of polyproteins which are proteolytically processed into functional peptides. These maturation steps often involve virus-encoded autoproteases specialized in generating their own N or C termini. Nonstructural protein 2 (NS2) of the pestivirus bovine viral diarrhea virus represents such an enzyme. Bovine viral diarrhea virus NS2 creates in cis its own C terminus and thereby releases an essential viral replication factor. As a unique feature, this enzyme requires for proteolytic activity stoichiometric amounts of a cellular chaperone termed Jiv (J-domain protein interacting with viral protein) or its fragment Jiv90. To obtain insight into the structural organization of the NS2 autoprotease, the basis for its restriction to cis cleavage, as well as its activation by Jiv, we dissected NS2 into functional domains. Interestingly, an N-terminal NS2 fragment covering the active center of the protease, cleaved in trans an artificial substrate composed of a C-terminal NS2 fragment and two downstream amino acids. In the authentic NS2, the 4 Cterminal amino acids interfered with binding and cleavage of substrates offered in trans. These findings strongly suggest an intramolecular product inhibition for the NS2 autoprotease. Remarkably, the chaperone fragment Jiv90 independently interacted with protease and substrate domain and turned out to be essential for the formation of a protease͞substrate complex that is required for cleavage. Thus, the function of the cell-derived protease cofactor Jiv in proteolysis is regulation of protease͞substrate interaction, which ultimately results in positioning of active site and substrate peptide into a cleavage-competent conformation.hepacivirus ͉ J-domain chaperone ͉ pestivirus ͉ protease cofactor T he pestiviruses, together with the flaviviruses and hepatitis C virus, form the family Flaviviridae (1). Replication of these positive-strand RNA viruses involves translation of one polyprotein that is processed by cellular and virus-encoded proteases (2). These processing events generate the proteins required for viral RNA replication and the production of infectious progeny.Recently in nonstructural protein 2 (NS2) of the pestivirus bovine viral diarrhea virus (BVDV) an autoprotease was identified (3). In the polyprotein of BVDV strain NCP7, NS2 encompasses amino acids 1137-1589 and thus has a length of 453 aa (4). The N terminus of NS2 is generated by cellular signal peptidases, and the protein remains associated to intracellular membranes, presumably at the endoplasmatic reticulum. The N-terminal half of NS2 is highly hydrophobic and therefore likely to be involved in membrane association. However, so far no experimental data on membrane topology or protein structure are available, in part because of its biochemical properties as well as its toxicity for bacteria. A recent study revealed that NS2 is a cysteine protease (3); the obtained data indicated a catalytic role for histidine at position 1447 (H1447) and cysteine at pos...