The central effector of visual transduction in retinal rod photoreceptors, cGMP phosphodiesterase (PDE6), is a catalytic heterodimer (␣) to which low molecular weight inhibitory ␥ subunits bind to form the nonactivated PDE holoenzyme (␣␥ 2 ). Although it is known that ␥ binds tightly to ␣, the binding affinity for each ␥ subunit to ␣, the domains on ␥ that interact with ␣, and the allosteric interactions between ␥ and the regulatory and catalytic regions on ␣ are not well understood. We show here that the ␥ subunit binds to two distinct sites on the catalytic ␣ dimer (K D1 < 1 pM, K D2 ؍ 3 pM) when the regulatory GAF domains of bovine rod PDE6 are occupied by cGMP. Binding heterogeneity of ␥ to ␣ is absent when cAMP occupies the noncatalytic sites. Two major domains on ␥ can interact independently with ␣ with the N-terminal half of ␥ binding with 50-fold greater affinity than its C-terminal, inhibitory region. The N-terminal half of ␥ is responsible for the positive cooperativity between ␥ and cGMP binding sites on ␣ but has no effect on catalytic activity. Using synthetic peptides, we identified regions of the amino acid sequence of ␥ that bind to ␣, restore high affinity cGMP binding to low affinity noncatalytic sites, and retard cGMP exchange with both noncatalytic sites. Subunit heterogeneity, multiple sites of ␥ interaction with ␣, and positive cooperativity of ␥ with the GAF domains are all likely to contribute to precisely controlling the activation and inactivation kinetics of PDE6 during visual transduction in rod photoreceptors.The extent and lifetime of activation of the photoreceptor cGMP PDE 1 (PDE6; EC 3.1.4.35) must be precisely regulated in rod and cone cells to control the exquisite sensitivity, speed, and adaptational properties of the visual transduction pathway in vertebrate photoreceptors. The membrane-associated rod photoreceptor PDE6 consists of a dimer of two homologous catalytic subunits (P␣) to which two low molecular weight inhibitory subunits (P␥) bind (holoenzyme stoichiometry, ␣␥ 2 ). The catalytic subunits contain GAF domains that are responsible for high affinity, noncatalytic binding of two cGMP molecules/holoenzyme. It is well established that relief of the inhibitory constraint on PDE6 arises from the binding of activated heterotrimeric G protein (transducin) to P␥ following photoactivation of the visual pigment, rhodopsin (reviewed in Refs. 1-4). However, the strength of the interaction between P␥ and P␣ has been difficult to quantitate, and K D values vary widely (from picomolar (5-7) up to nanomolar values (8, 9)). In addition, it has not been conclusively demonstrated whether both P␥ molecules bind with equal affinity to P␣ to form the nonactivated holoenzyme (although two different binding sites on P␣ have been inferred using mutant P␥ (10)). Finally, recent evidence suggests that binding of activated transducin to PDE6 relieves inhibition at only one of the two active sites, further supporting the idea of catalytic subunit heterogeneity with respect to ...