Phosphodiesterase 4 (PDE4) is an essential contributor to intracellular signaling and an important drug target. The four members of this enzyme family (PDE4A to -D) are functional dimers in which each subunit contains two upstream conserved regions (UCR), UCR1 and -2, which precede the C-terminal catalytic domain. Alternative promoters, transcriptional start sites, and mRNA splicing lead to the existence of over 25 variants of PDE4, broadly classified as long, short, and supershort forms. We report the X-ray crystal structure of long form PDE4B containing UCR1, UCR2, and the catalytic domain, crystallized as a dimer in which a disulfide bond cross-links cysteines engineered into UCR2 and the catalytic domain. Biochemical and mass spectrometric analyses showed that the UCR2-catalytic domain interaction occurs in trans, and established that this interaction regulates the catalytic activity of PDE4. By elucidating the key structural determinants of dimerization, we show that only long forms of PDE4 can be regulated by this mechanism. The results also provide a structural basis for the long-standing observation of high-and low-affinity binding sites for the prototypic inhibitor rolipram.T he diverse, pivotal roles of cAMP and cGMP (1) in mammalian intracellular signaling include acting as "second messengers" of signals delivered through G protein-coupled receptors (2), regulating the opening and closing of ligand-gated ion-channels (3), activating guanine-nucleotide exchange factors (4), and activating kinase signaling cascades (5). Responsibility for degrading these 3′,5′-cyclic nucleotides, and thereby limiting the duration and amplitude of the signals that they convey, falls to enzymes of the intracellular phosphodiesterase family (PDEs). The significance of these enzymes in cellular control makes them important targets of medicinal discovery, and maximizing our understanding of their respective structures and activities is an urgent priority (6).Mammalian PDEs are encoded by 21 genes and divided into 11 families (PDE1 to -11) defined by their amino acid sequences, with supporting distinctions based on pharmacologic and kinetic properties. Among the most intriguing of these families is PDE4, the four members (PDE4A to -D) of which have high selectivity for cAMP over cGMP as substrate and are characteristically sensitive to inhibition by rolipram. PDE4 inhibition has been pursued as a therapeutic target for over 30 y, since the first discovery of the potential efficacy of rolipram in treating clinical depression (7). Two different PDE4 inhibitors, roflumilast (Daxas) and apremilast (Otezla), are Food and Drug Administration-approved therapies for exacerbations of chronic obstructive pulmonary disease and psoriatic arthritis, respectively, and several others are in clinical trials for a variety of indications.Because of alternative promoters/start sites and variable mRNA splicing, transcription from the four PDE4 genes results in the expression of more than 25 different isoforms of PDE4. Each isoform has a unique N...