Mammalian synapse-associated protein SAP97, a structural and functional homolog of Drosophila Dlg, is a membrane-associated guanylate kinase (MAGUK) that is present at pre-and postsynaptic sites as well as in epithelial cell-cell contact sites. It is a multidomain scaffolding protein that shares with other members of the MAGUK protein family a characteristic modular organization composed of three sequential protein interaction motifs known as PDZ domains, followed by an Src homology 3 (SH3) domain, and an enzymatically inactive guanylate kinase (GK)-like domain. Specific binding partners are known for each domain, and different modes of intramolecular interactions have been proposed that particularly involve the SH3 and GK domains and the so-called HOOK region located between these two domains. We identified the HOOK region as a specific site for calmodulin binding and studied the dynamics of complex formation of recombinant calmodulin and SAP97 by surface plasmon resonance spectroscopy. Binding of various SAP97 deletion constructs to immobilized calmodulin was strictly calciumdependent. From the rate constants of association and dissociation we determined an equilibrium dissociation constant K d of 122 nM for the association of calcium-saturated calmodulin and a SAP97 fragment, which encompassed the entire SH3-HOOK-GK module. Comparative structure-based sequence analysis of calmodulin binding regions from various target proteins predicts variable affinities for the interaction of calmodulin with members of the MAGUK protein family. Our findings suggest that calmodulin could regulate the intramolecular interaction between the SH3, HOOK, and GK domains of SAP97.Membrane-associated guanylate kinase homologs (MAGUKs) 1 have been implicated in the assembly of synapses and tight junctions. These are multidomain proteins consisting of one or more PDZ domains, an Src homology 3 (SH3) domain, and a guanylate kinase (GK)-like domain (for reviews, see Refs. 1-4). Rat SAP97 belongs to the MAGUK subfamily comprising Drosophila Dlg, SAP97/hDlg, SAP90/PSD-95, SAP102/NE-Dlg, and PSD93/Chapsyn110. SAP97 has earlier been reported to be presynaptic (5), but it has recently been shown also to be present at postsynaptic sites in cerebral cortex (6); it is found both at the post-synaptic density (PSD) region and in the cytoplasm of hippocampal synapses, suggesting a role for SAP97 in ionotropic glutamate receptor trafficking (7). Recently it was discovered that SAP97, via its guanylate kinase (GK)-like domain, directly regulates the function of an inwardly rectifier potassium channel (8). In addition to its crucial role as a scaffolding protein in neuronal cells, SAP97 is an essential component of the basolateral membrane cytoskeleton in a variety of epithelial cells (5).Each domain in the SAP subfamily of MAGUKs is highly conserved and has been shown to be a site of protein-protein interaction: PDZ domains bind voltage-and ligand-gated ion channels (3, 9); SH3 domains interact with proline-rich, PXXPR-like sequences (3, 4, 10) as w...