The molybdenum cofactor (Moco) forms the catalytic site in all eukaryotic molybdenum enzymes and is synthesized by a multistep biosynthetic pathway. The mechanism of transfer, storage, and insertion of Moco into the appropriate apo-enzyme is poorly understood. In Chlamydomonas reinhardtii, a Moco carrier protein (MCP) has been identified and characterized recently. Here we show biochemical evidence that MCP binds Moco as well as the tungstate-substituted form of the cofactor (Wco) with high affinity, whereas molybdopterin, the ultimate cofactor precursor, is not bound. This binding selectivity points to a specific metal-mediated interaction with MCP, which protects Moco and Wco from oxidation with t1 ⁄ 2 of 24 and 96 h, respectively. UV-visible spectroscopy showed defined absorption bands at 393, 470, and 570 nm pointing to ene-diothiolate and protein side-chain charge transfer bonds with molybdenum. We have determined the crystal structure of MCP at 1.6 Å resolution using seleno-methionated and native protein. The monomer constitutes a Rossmann fold with two homodimers forming a symmetrical tetramer in solution. Based on conserved surface residues, charge distribution, shape, in silico docking studies, structural comparisons, and identification of an anionbinding site, a prominent surface depression was proposed as a Moco-binding site, which was confirmed by structure-guided mutagenesis coupled to substrate binding studies.Molybdenum is used in the active center of all molybdenum enzymes (1), catalyzing key metabolic reactions in the global sulfur, nitrogen, and carbon cycles in organisms ranging from bacteria to human. With the exception of nitrogenase, in all molybdenum enzymes, molybdenum is found as molybdenum cofactor (Moco) 3 (2) that consists of molybdenum covalently bound to the dithiolate moiety of a tricyclic pterin referred to as molybdopterin or metal-binding pterin (MPT), whose structure is conserved in eukaryotes, eubacteria, and archaea (3). This pterin molecule is also responsible for metal chelation in all tungsten-containing enzymes analyzed so far. Molybdenum enzymes are essential for diverse metabolic processes such as nitrate assimilation in autotrophs and phytohormone synthesis in plants (4) or sulfur detoxification and purine catabolism in mammals (5). Loss of Moco results in the pleiotropic loss of all molybdenum enzymes. Human Moco deficiency is a severe hereditary metabolic disorder (6), and affected patients die in early childhood.In all organisms studied so far, Moco is synthesized by a conserved pathway that can be divided into four major steps (3), according to the biosynthetic intermediates cyclic pyranopterin monophosphate, (formerly described as precursor Z) (7), MPT, and adenylated MPT. In the final and most diverse step of Moco biosynthesis, a single molybdenum atom is ligated to one (in pro-and eukaryotes) or two MPT dithiolates (in prokaryotes).After completion of biosynthesis, mature cofactor has to be inserted into molybdenum enzymes. In prokaryotes, a complex of proteins ...