The X-linked gene cyclin-dependent kinase-like 5 (CDKL5) is mutated in severe neurodevelopmental disorders, including some forms of atypical Rett syndrome, but the function and regulation of CDKL5 protein in neurons remain to be elucidated. Here, we show that CDKL5 binds to the scaffolding protein postsynaptic density (PSD)-95, and that this binding promotes the targeting of CDKL5 to excitatory synapses. Interestingly, this binding is not constitutive, but governed by palmitate cycling on PSD-95. Furthermore, pathogenic mutations that truncate the C-terminal tail of CDKL5 diminish its binding to PSD-95 and synaptic accumulation. Importantly, downregulation of CDKL5 by RNA interference (RNAi) or interference with the CDKL5-PSD-95 interaction inhibits dendritic spine formation and growth. These results demonstrate a critical role of the palmitoylation-dependent CDKL5-PSD-95 interaction in localizing CDKL5 to synapses for normal spine development and suggest that disruption of this interaction by pathogenic mutations may be implicated in the pathogenesis of CDKL5-related disorders.M utations in the X-linked gene cyclin-dependent kinase-like 5 (CDKL5) have been identified in patients with severe neurodevelopmental disorders, including an early-onset variant of Rett syndrome (1, 2). The predicted protein encoded by CDKL5 gene belongs to the CDKL family that comprises five members, CDKL1 to CDKL5 (3). The expression of CDKL5 is enriched in human and rat brain (4, 5). In murine, CDKL5 is expressed at low levels in embryonic stages and its expression is markedly upregulated during postnatal development (5, 6). Loss-of-function studies using RNA interference (RNAi) revealed that CDKL5 is required for neurite growth and excitatory synapse stability (5, 7). Deficiency of CDKL5 in mice leads to autistic-like phenotypes, indicating a causal role for CDKL5 loss of function in disease (8).Several interacting partners of CDKL5 have been reported, including the Rett syndrome-related protein methyl-CpG binding protein 2 (MeCP2) (9), the DNA methyltransferase Dnmt1 (10), and netrin-G1 ligand (NGL-1) (7). All of the three proteins are potential substrates for CDKL5, at least as demonstrated in vitro, suggesting that CDKL5 elicits its function by phosphorylating target proteins. Although the kinase activity of CDKL5 is required for its function and is impaired by some mutations identified in patients (7, 11), the regulation of CDKL5 seems to be equally important in the pathogenesis of disease, which is suggested by a number of pathogenic mutations identified within its C-terminal region (12). Therefore, further identification of CDKL5-interacting proteins may uncover the regulatory mechanisms for CDKL5, which is an important step toward the understanding of the causes of CDKL5-related disorders.The multidomain protein postsynaptic density (PSD)-95 is a major scaffold in the postsynaptic density (PSD) (13), and has been extensively investigated during the past decade. These studies have established the essential role of PSD-95 in syn...