The human neuroendocrine enzyme glutamic acid decarboxylase (GAD) catalyses the synthesis of the neurotransmitter GABA, using pyridoxal-5’-phosphate (PLP) as co-factor. GAD exists as two isoforms named according to their respective molecular weights, GAD65 and GAD67. While cytosolic GAD67 is more saturated with the co-factor PLP and constitutively active to produce basal levels of GABA, the membrane associated GAD65 exists mainly as autoinactivated apoenzyme (no cofactor bound). ApoGAD65 can be reactivated by PLP to form holoGAD65 (co-factor bound), when additional GABA is required, for example in response to stress.  GAD65, but not GAD67, is a major autoantigen and autoantibodies to GAD65 are detected at high frequency in patients with type 1 diabetes and other autoimmune disorders. The series of events responsible for initiation of these autoimmune responses are unknown.  We have used an array of computational and experimental methods in order to understand the nature of apoGAD65, providing insights into the conformational changes associated with holo-apo conversion, and thus GAD65 autoinactivation.  This has important implications for the role of GABA homeostasis in neurological disorders, as well as autoimmune reactivity of GAD65 in type 1 diabetes.