Regulation of Ca2؉ /calmodulin-dependent protein kinase II is likely based on an auto-inhibitory mechanism in which a segment of the kinase occupies the catalytic site in the absence of calmodulin. We analyze potential auto-inhibitory associations by employing charge reversal and hydrophobic-to-charged residue mutagenesis. We identify interacting amino acid pairs by using double mutants to test which modification in the catalytic domain complements a given change in the auto-inhibitory domain. Our studies identify the core pseudosubstrate sequence (residues 297-300) but reveal that distinct sequences centered about the autophosphorylation site at Thr-286 are involved in the critical auto-inhibitory interactions. Individual changes in any of the residues Arg-274, His-282, Arg-283, Lys-291, Arg-297, Phe-293, and Asn-294 in the auto-inhibitory domain or their interacting partners in the catalytic domain produces an enhanced affinity for calmodulin or generates a constitutively active enzyme. A structural model of Ca 2؉ /calmodulin-dependent protein kinase II that incorporates these interactions shows that Thr-286 is oriented inwardly into a hydrophobic channel. The model explains why calmodulin must bind to the auto-inhibitory domain in order for Thr-286 in that domain to be phosphorylated and why introduction of phospho-Thr-286 produces the important Ca 2؉ -independent state of the enzyme.Multifunctional Ca 2ϩ /calmodulin-dependent protein kinase (CaM kinase) 1 II has received considerable attention because of its autoregulatory properties (reviewed in Refs. 1 and 2). Regulation of the kinase is likely based on an auto-inhibitory or pseudosubstrate mechanism in which a segment of the kinase occupies the catalytic site in the basal state. Ca 2ϩ /calmodulin activates the kinase by wrapping around its target sequence on the kinase, a site that overlaps the auto-inhibitory domain (3). The active enzyme not only phosphorylates exogenous substrates but also exhibits a prominent autophosphorylation of Thr-286 within the auto-inhibitory domain. Autophosphorylation is an intersubunit reaction occurring within each holoenzyme and requires that calmodulin activate one subunit serving as kinase, while a second calmodulin is bound to the subunit serving as substrate (4 -6). Autophosphorylation traps bound calmodulin by greatly reducing its dissociation rate and prolonging the active state (7). Even after calmodulin dissociates, the autophosphorylated kinase remains partially active or autonomous of Ca 2ϩ /calmodulin (8 -11). Phospho-Thr-286 may therefore be positioned to interfere with re-establishment of auto-inhibitory contacts. This autophosphorylation is critical for Ca 2ϩ spike frequency-dependent activation of the enzyme (12) and enhances targeting of the kinase to synaptic sites (13-15) that may underlie the role of the kinase in regulation of synaptic strength. Mice defective in this autophosphorylation (␣-CaM kinase II Thr-286 3 Ala mutants) do not exhibit long term potentiation and are defective in spatial learning (...