The mitochondrial NAD-dependent methylenetetrahydrofolate dehydrogenase-cyclohydrolase (NMDMC) is believed to have evolved from a trifunctional NADP-dependent methylenetetrahydrofolate dehydrogenase-cyclohydrolase-synthetase. It is unique in its absolute requirement for inorganic phosphate and magnesium ions to support dehydrogenase activity. To enable us to investigate the roles of these ions, a homology model of human NMDMC was constructed based on the structures of three homologous proteins. The model supports the hypothesis that the absolutely required P i can bind in close proximity to the 2-hydroxyl of During embryogenesis and tumorigenesis mammalian mitochondria use a folate-dependent pathway to generate both glycine and one-carbon units to support cytoplasmic purine synthesis (1, 2). One of the enzymes in this pathway, the NAD-dependent methylenetetrahydrofolate dehydrogenase-methenyltetrahydrofolate cyclohydrolase (NMDMC), 5 catalyzes the interconversion of 5,10-methylenetetrahydrofolate (methylene-THF) and 10-formyltetrahydrofolate (formyl-THF) in mammalian mitochondria. The mitochondrial formyl-THF is converted to formate by a monofunctional formyl-THF synthetase and is released to the cytoplasm for reconversion into formyl-THF to support purine biosynthesis (1). NMDMC can use both NAD and NADP as a cofactor in its dehydrogenase activity, although the maximal activity with NADP is only about twenty percent of that with NAD (3). NMDMC is thought to have evolved from a trifunctional NADP-dependent methylene-THF dehydrogenase-methenyl-THF cyclohydrolase-formyl-THF synthetase (DCS) through the loss of the synthetase domain and the change in cofactor specificity from NADP to NAD (4). This change in cofactor specificity is important because the use of NAD rather than NADP in mitochondria shifts the equilibrium of the reaction to favor the production of formyl-THF (5). The increased production of formyl-THF is required to meet the demand for glycine and purines during embryogenesis (1, 2, 6). However, it is not known how this cofactor specificity change was accomplished.NMDMC is unique in its absolute requirement for magnesium and inorganic phosphate ions for NAD-dependent dehydrogenase activity and magnesium ions for NADP-dependent dehydrogenase activity (3, 7). However, neither ion is essential for the cyclohydrolase activity. The role of these ions in the dehydrogenase activity is not clear. The sequence of binding of the cofactors and substrates to NMDMC, as established kinetically by Yang and Mackenzie (3) and Rios-Orlandi and MacKenzie (7), suggests a role for P i and Mg 2ϩ in the binding of the cofactor; the ions bind to the protein first, followed by NAD and then the folate substrate. A preferred order of binding of the ions was not established; either ion appears to be able to bind to the enzyme and affect the binding of the other. These results suggested a possible interaction between the two ions in the binding site. The observation that P i competitively inhibits the cofactor in NADP-dependent de...