ClpB and Hsp104 are members of the AAA؉ (ATPases associated with various cellular activities) family of proteins and are molecular machines involved in thermotolerance. They are hexameric proteins containing 12 ATP binding sites with two sites per protomer. ClpB and Hsp104 possess some innate protein remodeling activities; however, they require the collaboration of the DnaK/Hsp70 chaperone system to disaggregate and reactivate insoluble aggregated proteins. We investigated the mechanism by which ClpB couples ATP utilization to protein remodeling with and without the DnaK system. When wild-type ClpB, which is unable to remodel proteins alone in the presence of ATP, was mixed with a ClpB mutant that is unable to hydrolyze ATP, the heterohexamers surprisingly gained protein remodeling activity. Optimal protein remodeling by the heterohexamers in the absence of the DnaK system required approximately three active and three inactive protomers. In addition, the location of the active and inactive ATP binding sites in the hexamer was not important. The results suggest that in the absence of the DnaK system, ClpB acts by a probabilistic mechanism. However, when we measured protein disaggregation by ClpB heterohexamers in conjunction with the DnaK system, incorporation of a single inactive ClpB subunit blocked activity, supporting a sequential mechanism of ATP utilization. Taken together, the results suggest that the mechanism of ATP utilization by ClpB is adaptable and can vary depending on the specific substrate and the presence of the DnaK system.B acterial ClpB and yeast Hsp104 are ATP-dependent protein remodeling machines that function to disaggregate protein aggregates and reactivate proteins after extreme stress conditions (1-3). In the cell, ClpB acts in conjunction with the DnaK chaperone system and Hsp104 acts with the Hsp70 chaperone system (4, 5). DnaK and Hsp70 are members of another large, ubiquitous family of ATP-dependent molecular chaperones that mediate protein reactivation and remodeling in concert with two cochaperones, DnaJ and GrpE in prokaryotes and Hsp40 and NEF in eukaryotes (6). Alone, neither the DnaK/Hsp70 chaperone system nor ClpB/Hsp104 has the ability to reactivate large insoluble aggregates.ClpB/Hsp104 exists as a hexameric ring with an axial channel (7-10). Each protomer contains two AAAϩ (ATPases associated with various cellular activities) nucleotide-binding domains separated by a hinge region and preceded by an N-terminal domain (1, 7). The two AAAϩ domains contain characteristic motifs, including Walker A and B and sensor-1 and -2 motifs, as well as an arginine finger (11,12). Situated in the first AAAϩ domain is a long coiled-coil region, referred to as the middle domain, which is unique to ClpB, Hsp104, and their homologs.In vitro ClpB/Hsp104 solubilizes and reactivates protein aggregates in ATP-dependent reactions in collaboration with the DnaK/Hsp70 chaperone system (1-3). Although the roles of the two chaperone systems in disaggregation are not fully understood, it is likely that ...