We have cloned and characterized the first human isozyme in a new family of cyclic nucleotide phosphodiesterases, PDE9A. By sequence homology in the catalytic domain, PDE9A is almost equidistant from all eight known mammalian PDE families but is most similar to PDE8A (34% amino acid identity) and least like PDE5A (28% amino acid identity). We report the cloning of human cDNA encoding a full-length protein of 593 amino acids, including a 261-amino acid region located near the C terminus that is homologous to the ϳ270-amino acid catalytic domain of other PDEs. PDE9A is expressed in all eight tissues examined as a ϳ2.0-kilobase mRNA, with highest levels in spleen, small intestine, and brain. The full-length PDE9A was expressed in baculovirus fused to an N-terminal 9-amino acid FLAG tag. Kinetic analysis of the baculovirus-expressed enzyme shows it to be a very high affinity cGMP-specific PDE with a K m of 170 nM for cGMP and 230 M for cAMP. The K m for cGMP makes PDE9A one of the highest affinity PDEs known. The V max for cGMP (4.9 nmol/min/g recombinant enzyme) is about twice as fast as that of PDE4 for cAMP. The enzyme is about twice as active in vitro in 1-10 mM Mn 2؉ than in the same concentration of Mg 2؉ or Ca 2؉ . PDE9A is insensitive (up to 100 M) to a variety of PDE inhibitors including rolipram, vinpocetine, SKF-94120, dipyridamole, and 3-isobutyl-1-methyl-xanthine but is inhibited (IC 50 ؍ 35 M) by zaprinast, a PDE5 inhibitor. PDE9A lacks a region homologous to the allosteric cGMP-binding regulatory regions found in the cGMP-binding PDEs: PDE2, PDE5, and PDE6.Cyclic nucleotide phosphodiesterases (PDEs), 1 which hydrolyze the intracellular second messengers cAMP and cGMP to their corresponding monophosphates, play an important role in signal transduction by regulating the intracellular concentration of cyclic nucleotides. Eight families of mammalian PDEs have been defined based on sequence similarity, substrate specificity, affinity, sensitivity to cofactors, and sensitivity to inhibitory drugs (1).2 These families are: PDE1, Ca 2ϩ /calmodulin-dependent; PDE2, cGMP-stimulated; PDE3, cGMPinhibited; PDE4, cAMP-specific; PDE5, cGMP-specific; PDE6, photoreceptor cGMP-specific; PDE7, cAMP-specific rolipraminsensitive; and PDE8, cAMP-specific IBMX-insensitive. Within families, there are multiple isozymes and multiple splice variants of those isozymes. PDEs are composed of a catalytic domain of ϳ270 amino acids, an N-terminal regulatory domain responsible for binding cofactors, and in some cases, a C-terminal domain of unknown function. Within the catalytic domain, there is approximately 30% amino acid identity between PDE families and ϳ85-95% identity between isozymes of the same family (e.g. PDE4A versus PDE4B). Furthermore, within a family there is extensive similarity (Ͼ60%) outside the catalytic domain, whereas across families there is little or no sequence similarity. The existence of multiple PDE families, isozymes, and splice variants presents an opportunity for complex regulation of cyclic nucleotide ...