First computational evidence for a catalytic bridging hydroxide ion in a phosphodiesterase active site

Phosphodiesterases are clinical targets for a variety of biological disorde rs, because this superfamily of enzymes regulates the intracellular concent ration of cyclic nucleotides that serve as the second messengers playing a critical role in a variety of physiological processes. Understanding the st ructure and mechanism of a phosphodiesterase will provide a solid basis for rational design of the more efficient therapeutics. Although a three-dimen sional X-ray crystal structure of the catalytic domain of human phosphodies terase 4B2B was recently reported, it is uncertain whether a critical bridg ing ligand in the active site is a water molecule or a hydroxide ion. The i dentity of this bridging ligand is theoretically determined by performing f irst-principles quantum chemical calculations on models of the active site. All the results obtained indicate that this critical bridging ligand in th e active site of the reported X-ray crystal structure is a hydroxide ion, r ather than a water molecule, expected to serve as the nucleophile to initia lize the catalytic degradation of the intracellular second messengers.