The pyruvate dehydrogenase complex (PDC) is a central metabolic enzyme in all living cells composed majorly of E1, E2, and E3. Tight coupling of their reactions makes each component essential, so that loss impacts oxidative metabolism pathologically. E3 retention is mediated by the E3-binding protein (E3BP), which has not previously been clearly resolved within the PDC. Here, the structure of the fungal E3BP in complex with the PDC core from N.crassa is resolved to 3.2Å, showing its mode of binding. Fungal and mammalian E3BP are shown to be orthologs, arguing E3BP as a broadly eukaryotic gene. Fungal E3BP architectures predicted from sequence data and computational models further bridge the evolutionary distance between N. crassa and humans, and suggest discriminants for E3-specificity. This is confirmed by similarities in their respective E3-binding domains, where a novel interaction is also predicted that may affect the interaction of its lipoyl substrate with recruited E3.Competing Interest StatementThe authors have declared no competing interest.