The
phospholipase D (
PLD) superfamily catalyzes the hydrolysis of cell membrane
phospholipids generating the key intracellular
lipid second messenger
phosphatidic acid. However, there is not yet any resolved structure either from a crystallized
protein or from NMR of any mammalian PLDs. We propose here a 3D model of the PLD2 by combining homology and ab initio 3 dimensional structural modeling methods, and docking conformation. This model is in agreement with the biochemical and physiological behavior of
PLD in cells. For the
lipase activity, the N- and C-terminal histidines of the HKD motifs (His 442/His 756) form a catalytic pocket, which accommodates
phosphatidylcholine head group (but not
phosphatidylethanolamine or
phosphatidyl serine). The model explains the mechanism of the reaction catalysis, with nucleophilic attacks of His 442 and water, the latter aided by His 756. Further, the secondary structure regions superimposed with bacterial
PLD crystal structure, which indicated an agreement with the model. It also explains
protein-
protein interactions, such as PLD2-Rac2 transmodulation (with a 1:2 stoichiometry) and PLD2 GEF activity both relevant for cell migration, as well as the existence of binding sites for
phosphoinositides such as PIP2. These consist of R236/W238 and R557/W563 and a novel PIP2 binding site in the PH domain of PLD2, specifically R210/R212/W233. In each of these, the polar
inositol ring is oriented towards the
basic amino acid Arginine. Since
tumor-aggravating properties have been found in mice overexpressing
PLD2 enzyme, the 3D model of PLD2 will be also useful, to a large extent, in developing
pharmaceuticals to modulate its in vivo activity.