The molybdenum cofactor (Moco) sulfurase C-terminal domain (MOSC) family plays a key role in the detoxification of mutagenic chemicals and the activation of prodrugs by catalyzing a nitrogen-reducing reaction. MOSC proteins are functionally required to bind Moco for their enzymatic reactions. However, the structural features and Moco-recognition mechanism of the MOSC family have not been revealed in detail. YiiM belongs to the MOSC family and is involved in reducing mutagenic 6-N-hydroxylaminopurine to yield nontoxic adenine in bacteria. Here, we report the crystal structure of YiiM. YiiM consists of three domains (a β-barrel and two α-helix bundles) that collectively generate a cavity in the center of the structure. Structural features critical for Moco-mediated enzymatic catalysis were observed in the cavity, including an oxidized invariant cysteine residue and positive electrostatic potentials. Furthermore, our modeling study, combined with our observation of a phosphate ion that emulates a part of a Moco molecule in the cavity, strongly supports the cavity of YiiM as the Moco-binding site where catalysis occurs.