The PDE5 enzyme has a molecular mass of 200 kDa and its active state is a homodimer. PDE5 consists of monomers and each contains two major functional domains: the regulatory domain (R domain) which is located in the N-terminal portion of the protein and the catalytic domain (C domain) located in the more C-terminal portion of the protein.
The R domain contains specific allosteric cGMP binding site that controls the enzymes function. This specific binding site consists of subdomain GAF (cGMP-specific cGMP-stimulated PDE, adenylate cyclase, and FhlA) which is located in the N-terminal section of the specific proteins. The allosteric binding site GAF consists of GAFa and GAFb where GAFa has a higher binding affinity. The importance and functional role of the two homologous binding sites are unknown.
Conformational change occurs when cGMP binds to the allosteric site that exposes serine and permits phosphorylation. The results for the phosphorylation of serine leads to increased cGMP hydrolysis at the catalytic domain. The affinity of the catalytic domain for cGMP increases and further increases the PDE5 catalytic domain activity.
Through the C domain, intracellular cGMP is degraded rapidly by PDE5 which minimizes the activity of cGMP on its PKG1 substrate by cleaving the cyclic phosphate part of cGMP to GMP. GMP is an inactive molecule with no second messenger activity.
Phosphorylation of a single serine by PKG1 and the allosteric cGMP binding site activates the PDE5 catalytic activity and the result is a negative feedback regulation of cGMP/NO/PKG1 signalling. cGMP therefore interacts with both allosteric and catalytic domain of the PDE5 enzyme and PDE5 inhibitors compete with cGMP for binding at the catalytic domain resulting in higher cGMP levels. PDE5 domains are demonstrated in .