Point mutations in either of the two nucleotide-binding domains (NBD) of Hsp104 (NBD1 and NBD2) eliminate its thermotolerance function in vivo. In vitro, NBD1 mutations virtually eliminate ATP hydrolysis with little effect on hexamerization; analogous NBD2 mutations reduce ATPase activity and severely impair hexamerization. We report that high protein concentrations overcome the assembly defects of NBD2 mutants and increase ATP hydrolysis severalfold, changing Vmax with little effect on Km. In a complementary fashion, the detergent 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate inhibits hexamerization of wildtype (WT) Hsp104, lowering Vmax with little effect on Km. ATP hydrolysis exhibits a Hill coefficient between 1.5 and 2, indicating that it is influenced by cooperative subunit interactions. To further analyze the effects of subunit interactions on Hsp104, we assessed the effects of mutant Hsp104 proteins on WT Hsp104 activities. An NBD1 mutant that hexamerizes but does not hydrolyze ATP reduces the ATPase activity of WT Hsp104 in vitro. In vivo, this mutant is not toxic but specifically inhibits the thermotolerance function of WT Hsp104. Thus, interactions between subunits influence the ATPase activity of Hsp104, play a vital role in its biological functions, and provide a mechanism for conditionally inactivating Hsp104 function in vivo.T he HSP100͞Clp family of chaperone proteins plays a wide variety of important cellular roles in different organisms, including survival of environmental stress, regulation of genetic competence, transposition, proteolysis, and control of a proteinbased genetic element (prion). These seemingly unrelated roles are unified by a common remarkable biochemical mechanism; the proteins promote the disassembly of aggregated proteins and higher-order protein complexes (reviewed in refs. 1 and 2). Several biochemical properties are shared by HSP100 proteins and are required for their biological functions, suggesting that these properties are important to the complex phenomenon of protein disassembly. These properties include an ATPhydrolyzing activity (3-10) and the ability to self-assemble into oligomers, primarily hexamers (11-13).A member of the HSP100 family from Saccharomyces cerevisiae, Hsp104, is critical for survival after exposure to extreme temperatures (50°C) (14) or high concentrations of ethanol (20%) (15). These stresses cause protein denaturation, and Hsp104 promotes survival by facilitating the resolubilization of heat-damaged, aggregated proteins (reviewed in refs. 1 and 2). At normal temperatures, Hsp104 plays a critical role in the inheritance of the novel proteinaceous genetic element [PSIϩ] (often called a yeast prion), an ordered aggregate of the translation terminator, Sup35 (16).Hsp104 is a member of the class 1 HSP100 proteins, with two distinct but highly conserved nucleotide-binding domains (NBDs) (1, 17). NBD1 and NBD2 of Hsp104 show only 22% amino acid identity with each other, yet each shares 40-60% identity with the corresponding domains of t...