Photoreceptor cGMP phosphodiesterases (PDE6 1 family) function as effector proteins in the vertebrate visual transduction, which is mediated by the rhodopsin-coupled G protein, transducin (1-3). Retinal rod PDE6 is composed of two catalytic PDE6␣ subunits each tightly associated with the smaller inhibitory ␥ subunit (P␥) (4 -6). Cone PDE consists of two identical PDE␣Ј subunits complexed with two copies of the cone-specific P␥ subunit (7-9). The catalytic subunits of rod and cone PDE, as well as the respective P␥ subunits, share a high degree of homology (9 -10). The key role of P␥ is to inhibit cGMP hydrolysis by the catalytic subunits in the dark. Upon light stimulation of photoreceptors, PDE6 is activated by GTPbound transducin-␣, which displaces P␥ from the enzyme catalytic core.Two regions of P␥ are principally involved in the interaction with the PDE6 catalytic subunits, the central polycationic region (residues 24 -45 of rod P␥) and the P␥ C terminus. The C terminus of P␥ constitutes the key inhibitory domain, whereas the polycationic region enhances the overall affinity of P␥ toward PDE6 catalytic subunits (11)(12)(13)(14). A cross-linking study localized the P␥ C-terminal binding site on PDE6␣ to residues 751-763 (residues 749 -761 of PDE6 or PDE6␣Ј) within the broader PDE6 catalytic domain (15). Our further analysis of the interaction between fluorescently labeled P␥ and PDE6␣ suggests that the C terminus of P␥ inhibits PDE6 activity by physically blocking the PDE catalytic site (16).Progress in the investigation of the structure/function of PDE6 and the mechanism of PDE6 inhibition by P␥ has been slowed by the lack of an efficient expression system for PDE6 (17, 18). Our approach to developing a system for PDE6 expression and mutagenesis included the construction of chimeras between PDE6␣Ј and cGMP-binding, cGMP-specific PDE (PDE5 family) (19). PDE5 and PDE6 share a common domain organization, i.e. two noncatalytic cGMP-binding sites located N-terminally to the conserved PDE catalytic domain (20). Furthermore, PDE5 and PDE6 display a high homology (45-48% identity) between catalytic domains, a strong substrate preference for cGMP, and similar patterns of inhibition by competitive inhibitors such as zaprinast, dipyridamole, and sildenafil (20 -23). Unlike PDE6, PDE5 is readily expressed using the baculovirus/insect cell system (24, 25). Earlier, we reported (19) the functional expression and characterization of a chimeric PDE6␣Ј/PDE5 enzyme containing the PDE6␣Ј noncatalytic cGMP-binding sites and the PDE5 catalytic domain. In this study, we generated chimeric PDE6␣Ј/PDE5 enzymes that contain the P␥ C-terminal binding site and that are potently inhibited by P␥. Ala-scanning mutational analysis of the P␥-binding site, using chimeric PDE as a template, revealed the key interaction residues and provided structural justification for the mechanism of PDE6 inhibition.