1L-myo-inositol 1-phosphate (MIP) synthase catalyzes the conversion of D-glucose 6-phosphate to 1L-myo-inositol 1-phosphate, the first and rate-limiting step in the biosynthesis of all inositol-containing compounds. It involves an oxidation, enolization, intramolecular aldol cyclization, and reduction. Here we present the structure of MIP synthase in complex with NAD ؉ and a high-affinity inhibitor, 2-deoxy-D-glucitol 6-(E)-vinylhomophosphonate. This structure reveals interactions between the enzyme active site residues and the inhibitor that are significantly different from that proposed for 2-deoxy-Dglucitol 6-phosphate in the previously published structure of MIP synthase-NAD ؉ -2-deoxy-D-glucitol 6-phosphate. There are several other conformational changes in NAD ؉ and the enzyme active site as well. Based on the new structural data, we propose a new and completely different mechanism for MIP synthase.Inositol-containing compounds play critical and diverse biological roles, including signal transduction, stress response, and cell wall biogenesis (1-4). Though large quantities of inositol are available from the diet, significant biosynthesis of inositol has been detected in organs where a significant blood barrier exists, such as the testes and brain (5-9). In fact, reduction of the brain inositol pool by inhibition of myo-inositol (MI) 1 monophosphatase has been suggested to be the mode of action for lithium in the treatment of bipolar disorder (10 -13). Recent in vivo results in yeast (14) and dictyostelium (15) suggest that Valproate, a drug used in the treatment of depression, bipolar disorder, and seizure disorder, may act by inhibition of MIP synthase, thus lowering neuronal inositol pools similar to the action of lithium (14). Regulation of inositol biosynthesis itself may, therefore, play an important role in the regulation of second messenger signaling.MIP synthase is remarkably conserved in eukaryotes, with better than 45% identity from yeast to humans (3, 16 -25). In all cases, the enzyme displays modest catalytic activity, with turnover numbers ranging from 3 to 13 M/min/mg enzyme and with substrate K m values in the 100 M to 1 mM range (3, 17). The reaction path first proposed by Loewus et al. (shown in Fig. 1) remains the most likely (3, 26 -29). A series of inhibitor studies indicates that the enzyme first binds the open acyclic tautomer of the substrate D-glucose 6-phosphate, followed by oxidation to the C5 keto intermediate (30). Frost and coworkers propose that enolization is promoted by proton extraction by means of the substrate phosphate, which is consistent with the phosphate binding in a transoid conformation (30). They base this conclusion on the ability of 2-deoxy-D-glucitol 6-(E)-vinylhomophosphonate, a substrate mimic of the enzyme that fixes the phosphonate trans to C5, to strongly inhibit the enzyme, whereas the equivalent Z-mimic displays no affinity for the enzyme. 2-Deoxy-D-glucitol 6-(E)-vinylhomophosphonate is, in fact, the most potent inhibitor of the enzyme known, having ...