The flavoprotein iodotyrosine deiodinase (IYD) salvages iodide from mono-and diiodotyrosine formed during the biosynthesis of the thyroid hormone thyroxine. Expression of a soluble domain of this membrane-bound enzyme provided sufficient material for crystallization and characterization by x-ray diffraction. The structures of IYD and two co-crystals containing substrates, mono-and diiodotyrosine, alternatively, were solved at resolutions of 2.0, 2.45, and 2.6 Å , respectively. The structure of IYD is homologous to others in the NADH oxidase/ flavin reductase superfamily, but the position of the active site lid in IYD defines a new subfamily within this group that includes BluB, an enzyme associated with vitamin B 12 biosynthesis. IYD and BluB also share key interactions involving their bound flavin mononucleotide that suggest a unique catalytic behavior within the superfamily. Substrate coordination to IYD induces formation of an additional helix and coil that act as an active site lid to shield the resulting substrate⅐flavin complex from solvent. This complex is stabilized by aromatic stacking and extensive hydrogen bonding between the substrate and flavin. The carbon-iodine bond of the substrate is positioned directly over the C-4a/N-5 region of the flavin to promote electron transfer. These structures now also provide a molecular basis for understanding thyroid disease based on mutations of IYD.The micronutrient iodide is essential for the biosynthesis of thyroxine (3,3Ј,5,5Ј-tetraiodothyronine), a hormone used by a wide range of organisms as a master control of metabolic rate. In mammals, iodide homeostasis in the thyroid gland is critical for generating thyroxine and is achieved by sequestering and salvaging iodide. Both of these functions are critical for human health, and congenital defects in either may lead to hypothyroidism (1, 2). Sequestration of iodide from the circulatory system is accomplished by a Na ϩ /I Ϫ symporter located in the plasma membrane of thyroid follicular cells (2). Salvage of iodide is accomplished by iodotyrosine deiodinase (IYD) 3 located in the apical plasma membrane surrounding the thyroid colloid in which thyroglobulin is stored and processed (3). Proteolysis of mature thyroglobulin releases thyroxine as well as mono-and diiodotyrosine (MIT and DIT, respectively). IYD catalyzes a reductive deiodination of MIT and DIT selectively to prevent loss of iodide that would otherwise occur by excretion of these amino acids. The gene encoding IYD has recently been identified (3, 4) and has provided an initial basis for correlating its mutation with hypothyroidism and goiter observed in certain patients (1). The crystal structure described in this work now supersedes the previous structural models.IYD represents one of only two enzymes known to promote reductive dehalogenation in mammals (Fig. 1). The other enzyme, iodothyronine deiodinase, acts alternatively to activate and deactivate thyroxine by deiodinating the outer or inner ring, respectively (5). Interestingly two distinct strateg...