GoxA from Pseudoalteromonas luteoviolaceae belongs to a recently identified family of enzymes (the LodA‐like proteins) that utilize a post‐translationally derived cysteine tryptophylquinone (CTQ) cofactor for catalysis. In contrast to other tryptophylquinone enzymes, GoxA acts as an oxidase rather than a dehydrogenase, using molecular oxygen to catalyze the oxidative deamination of glycine to produce ammonia, glyoxylate and hydrogen peroxide. The crystal structure of this enzyme revealed a homotetramer with a novel alpha helical domain and extensive inter‐subunit interactions, which account for the positive cooperativity observed toward its substrate by steady‐state kinetics. Soaking GoxA crystals in glycine results in a dramatic color change from yellow to blue, indicating the formation of an unusual intermediate at the CTQ site that was also detected in solution. The structure of this intermediate reveals a Schiff‐base formed between the substrate and CTQ that is stabilized by numerous hydrogen bond contacts with residues both in the active site and from a neighboring protomer. The kinetics and structures of active site mutants reveal the roles of specific residues in substrate binding, cooperativity, and catalysis, and allowed for the detection of another intermediate in the GoxA reaction pathway. This combination of kinetics, spectroscopy and X‐ray crystallography has allowed for the construction of a detailed reaction mechanism for this unusual enzyme with high‐resolution structures now available for key intermediates.