At first, the PDE3s were purified and described as enzymes that hydrolyse both cGMP and cAMP with K values of 0.1–0.8 μM. However the V for cAMP hydrolysis is 4–10 times higher than V for cGMP hydrolysis.
When different PDEs were first identified, two types of PDEs (PDE3 and PDE4) that exhibited high affinities for cAMP were isolated. PDE3 exhibited high affinity for both cGMP and cAMP, but PDE4 had high affinity for only cAMP. For that reason, the PDE3 was called the cGMP-inhibited PDE to distinguish it from PDE4.
The 44-amino acid insertion in the catalytic domain of PDE3s is believed to be involved in PDE3's interaction with its substrate and inhibitors, but that remains to be established.
The proposed molecular mechanism of cyclic nucleotide specificity of PDEs is the so-called glutamine switch mechanism.
In the PDEs that have had their structure solved, there seems to be an invariant glutamine residue that stabilizes the binding of the purine ring in the active site (binding pocket). The g-amino group of the glutamine residue can alternatively adopt two different orientations:
# The hydrogen bond network supports guanine binding – cGMP selectivity
# The hydrogen bond network supports adenine binding – cAMP selectivity.
In PDEs that can hydrolyse both cGMP and cAMP (PDE3s), the glutamine can rotate freely and therefore switch between orientations.