The ability of an organism or cell to maintain intracellular inorganic ion concentrations when challenged by extracellular fluctuations is among the most ancient and fundamental cellular processes. Despite the importance of inorganic ions in physiology, little is known of the molecular mechanisms by which the predominant inorganic ions of the cellular environment are detected. Here we describe work on the identification and characterization of an intramolecular signalling complex responsive to sodium ion. The ubiquitous GAF domain is an important site of signal perception in eukaryotes and prokaryotes. GAF domains from diverse species have equally diverse ligands including NO in the NorR sensor of Escherichia coli, 2-oxoglutarate in NifA of Azotobacter vinelandii, and the cyclic nucleotides cAMP and cGMP in cyanobacteria, unicellular parasitic eukaryotes, and mammals. The mammalian cyclic nucleotide phosphodiesterases (PDE) are integral to the regulation of cellular levels of cAMP and cGMP by controlling the rate of degradation. Eleven families of PDE whose activity can be regulated by their N-termini are known. Of these regulatory domains PDEs types 2, 5, 6, 10, and 11 possess GAF domains regulated by cyclic nucleotides. The CyaB1 and CyaB2 adenylyl cyclases (AC) of the model cyanobacterium Anabaena PCC 7120 also bind cAMP through one (CyaB1) or two (CyaB2) N-terminal GAF domains to mediate positive feedback regulation of the AC domain. Na⁺ but not other monovalent cations regulates the function of CyaB1 by blocking cAMP mediated autoregulation. Mutation of the cAMP binding GAF domain of CyaB1 (GAF-B) blocks Na⁺ regulation while mutation of GAF-A has no effect. A chimera of the GAF domain motif of CyaB2 with the AC domain of CyaB1 shows a similar response to Na⁺. Na⁺ bound recombinant GAF domains with substantially greater affinity than K⁺. Exogenous cAMP blocked Na⁺ binding to GAF domains but Na⁺ had no effect on cAMP binding. Circular dichroism spectroscopy revealed that Na⁺ maintains the domain in a conformation unable to signal and cAMP removes this constraint. Genetic ablation of the cyaB1 and cyaB2 genes gives strains defective in homeostasis at limiting Na⁺ due to compromised Na⁺/H⁺ antiporter activity. To investigate whether Na+ regulation of GAF domain function is of more global relevance we investigated a chimera of the cGMP regulated GAF domain motif of mammalian PDE2 contiguous with the CyaB1 AC catalytic domain. This experiment revealed that Na⁺ inhibition of AC specific activity was now dependent upon cGMP and that Na⁺ regulation of GAF domain function has been conserved since the eukaryotic/bacterial divergence. The GAF domain is the first identified protein domain able to functionally sense and signal changes in environmental Na⁺.