Acetohydroxy acid synthase (EC 4.1.3.18) of the archaebacterium Methanococcus aeolicus was purified 1,150-fold to homogeneity. The molecular weight of the purified enzyme was 125,000, and it contained only one type of subunit (Mr = 58,000). The amino-terminal sequence had 46 to 57% similarity to those of the large subunits of the eubacterial anabolic enzymes and 37 to 43% similarity to those of the yeast and plant enzymes. The methanococcal enzyme had a pH optimum of 7.6. The pl, estimated by chromatofocusing, was 5.6. Activity required Mg2' or Mn2+ ions, thiamine pyrophosphate, and a flavin. Flavin adenine dinucleotide, flavin mononucleotide, and riboflavin plus 10 mM phosphate all supported activity. However, activity was strongly inhibited by these flavins at 0.3 mM. The Michaelis constants for pyruvate, MgCl2, MnCl2, thiamine pyrophosphate, flavin adenine dinucleotide, and flavin mononucleotide were 6.8 mM, 0.3 mM, 0.16 mM, 1.6 ,uM, 0.4 ,uM, and 1.3 ,uM, respectively. In cell extracts, the enzyme was sensitive to 02 (half-life = 2.7 min with 5% 02 in the headspace), but the purified enzyme was less sensitive to 02 (half-life = 78.0 min with 20%Y 02). Reconstitution of the enzyme with flavin adenine dinucleotide increased the sensitivity to 02. Moreover, in the assay the homogeneous enzyme was rapidly inactivated by 02, and the concentration required for 50%o inhibition (I50) was obtained with an atmosphere of 0.11% 02. The methanococcal enzyme has similarities to the eubacterial and eucaryotic enzymes, consistent with the ancient origin of the archaebacterial enzyme.Acetohydroxy acid synthase (AHAS) (EC 4.1.3.18) is a common anabolic enzyme in bacteria, yeasts, and plants. In these organisms, it catalyzes the first common step in the biosynthesis of the branched-chain amino acids, i.e., the formation of acetolactate from two molecules of pyruvate and the formation of 2-acetohydroxybutyrate from pyruvate and 2-ketobutyrate (29,30). Some bacteria also contain a catabolic AHAS whose physiological function is acetolactate synthesis for the acetoin and 2,3-butanediol fermentations (28). Both the catabolic and anabolic enzymes contain thiamine pyrophosphate (TPP), and they have 20 to 30% amino acid sequence similarity (17). However, they differ in a number of important respects. While the pH optima of the anabolic enzymes are greater than 7, the pH optima of the catabolic enzymes are between 6 and 7 (13, 24, 26). The anabolic enzymes also contain flavin adenine dinucleotide (FAD), which is absent from the catabolic enzymes (27). Finally, the anabolic enzymes from bacteria contain a small subunit that is required for feedback inhibition by the branched-chain amino acids. When the catabolic enzymes from the same or closely related bacteria have been examined, this small subunit has not been found (17,38).The function of FAD in the anabolic AHAS is unclear. The enzyme does not catalyze an oxidation-reduction reaction, and FAD, but not other flavins, is essential for activity (21). In the plant enzyme, FAD plays a rol...