Glycogen synthase kinase-3 (GSK-3) isoforms, GSK-3␣ and GSK-3, are serine/threonine kinases involved in numerous cellular processes and diverse diseases, including Alzheimer disease, cancer, and diabetes. GSK-3 isoforms function redundantly in some settings, while, in others, they exhibit distinct activities. Despite intensive investigation into the physiological roles of GSK-3 isoforms, the basis for their differential activities remains unresolved. A more comprehensive understanding of the mechanistic basis for GSK-3 isoform-specific functions could lead to the development of isoform-specific inhibitors. Here, we describe a structure-function analysis of GSK-3␣ and GSK-3 in mammalian cells. We deleted the noncatalytic N and C termini in both GSK-3 isoforms and generated point mutations of key regulatory residues. We examined the effect of these mutations on GSK-3 activity toward Tau, activity in Wnt signaling, interaction with Axin, and GSK-3␣/ Tyr 279/216 phosphorylation. We found that the N termini of both GSK-3 isoforms were dispensable, whereas progressive C-terminal deletions resulted in protein misfolding exhibited by deficient activity, impaired ability to interact with Axin, and a loss of Tyr 279/216 phosphorylation. Our data predict that small molecules targeting the divergent C terminus may lead to isoform-specific GSK-3 inhibition through destabilization of the GSK-3 structure.Glycogen synthase kinase-3 (GSK-3) 2 enzymes are serine/ threonine kinases originally identified based on their activity toward glycogen synthase (1). Two mammalian GSK-3 isoforms exist as products of distinct genes, GSK-3␣ and GSK-3 (2), which are highly homologous within their internal kinase domains but diverge in sequence outside this region. Aberrant regulation and subsequent hyperactivity of GSK-3 has been linked to diseases such as Alzheimer disease, cancer, and diabetes (3). Thus, tight regulation of ubiquitous (4) and constitutive (5) GSK-3 activity is important for maintaining normal cellular function. Control of GSK-3 activity occurs by a combination of mechanisms, including prerequisite phosphorylation of GSK-3 substrates (priming), phosphorylation of GSK-3 itself, and localization of GSK-3 activity through protein interactions.With Ͼ40 putative substrates (6, 7), GSK-3 isoforms are broadly influential, and their activity toward substrates is commonly influenced by a priming phosphorylation mechanism (8). Recognition of a primed substrate by GSK-3 requires a triad of conserved residues, Arg 159/96 , Arg 243/180 , and Lys 268/205 of GSK-3␣/, which form a phosphate-binding pocket and facilitate optimal alignment of GSK-3 into a catalytically active conformation (9 -11). Although priming enhances the efficiency of GSK-3 phosphorylation, it is not a strict requirement. For example, the microtubule-associated protein Tau has both primed and unprimed sites targeted by GSK-3 activity (12).Phosphorylation of Tyr 279 in GSK-3␣ and Tyr 216 in GSK-3 has been reported to facilitate GSK-3 activity by inducing rotation of ...