The vitamin K-dependent carboxylase modifies and renders active vitamin K-dependent proteins involved in hemostasis, cell growth control, and calcium homeostasis. Using a novel mechanism, the carboxylase transduces the free energy of vitamin K hydroquinone (KH 2) oxygenation to convert glutamate into a carbanion intermediate, which subsequently attacks CO 2, generating the ␥-carboxylated glutamate product. How the carboxylase effects this conversion is poorly understood because the active site has not been identified. Dowd and colleagues [Dowd, P., Hershline, R., Ham, S. W. & Naganathan, S. (1995) Science 269, 1684 -1691] have proposed that a weak base (cysteine) produces a strong base (oxygenated KH 2) capable of generating the carbanion. To define the active site and test this model, we identified the amino acids that participate in these reactions. N-ethyl maleimide inhibited epoxidation and carboxylation, and both activities were equally protected by KH 2 preincubation. Amino acid analysis of 14 C-Nethyl maleimide-modified human carboxylase revealed 1.8 -2.3 reactive residues and a specific activity of 7 ؋ 10 8 cpm͞hr per mg. Tryptic digestion and liquid chromatography electrospray mass spectrometry identified Cys-99 and Cys-450 as active site residues. Mutation to serine reduced both epoxidation and carboxylation, to 0.2% (Cys-99) or 1% (Cys-450), and increased the K ms for a glutamyl substrate 6-to 8-fold. Retention of some activity indicates a mechanism for enhancing cysteine͞serine nucleophilicity, a property shared by many active site thiol enzymes. These studies, which represent a breakthrough in defining the carboxylase active site, suggest a revised model in which the glutamyl substrate indirectly coordinates at least one thiol, forming a catalytic complex that ionizes a thiol to initiate KH 2 oxygenation. T he vitamin K-dependent (VKD) carboxylase is an integral membrane enzyme required for the biological activity of proteins involved in hemostasis (prothrombin, factor X, factor VII, factor IX, protein S, protein C, protein Z), calcium homeostasis (bone gla protein and matrix gla protein), cell growth control (gas 6), and possibly signal transduction (PRGP-1 and PRGP-2) (1, 2). Carboxylation is effected via a homologous Ϸ18-aa sequence in VKD proteins, usually an N-terminal propeptide, which the carboxylase binds with high affinity. Propeptide binding of VKD proteins to the carboxylase leads to the conversion of clusters of glutamyl (Glu) residues to ␥-carboxylated glutamyl (or Gla) residues, in a region adjacent to the propeptide called the Gla domain. This domain serves as a calcium-dependent membrane-binding module for the attached VKD proteins, for example to effect blood coagulation on cell surfaces. Carboxylation requires a continual supply of the reduced form of the vitamin K cofactor, vitamin K hydroquinone (KH 2 ), and when KH 2 is limiting undercarboxylated, inactive VKD proteins are produced. Consequently, understanding the mechanism of carboxylation has important medical ramifications as...