Involved in transport of phospholipids. Contributes to transmembrane flipping of lipids. Required for secretory processes during plant development. Requires an interaction with an ALIS protein for activity. Has activity with phosphatidylserine, phosphatidylcholine and phosphatidylethanolamine, but not with lysolipid (PubMed:18344284, PubMed:19566596, PubMed:20053675). Modifies endomembranes in multiple cell types, enabling structural changes, or signaling functions that are critical for normal development and adaptation to varied growth environments (PubMed:23667493). Required for the trafficking and endocytic recycling of ABCG36/PEN3 between the trans-Golgi network and the plasma membrane; thus promoting ABCG36/PEN3 recruitment to the host-pathogen interface upon infection by powdery mildews (e.g. Blumeria graminis) and bacteria (e.g. Pseudomonas syringae), or upon the detection of pathogen-associated molecular patterns (PAMPs) (e.g. flg22 and chitin) (PubMed:28434950). ATP + H2O + phospholipidSide 1 = ADP + phosphate + phospholipidSide 2. Associates with ALIS1 to form a stable and active complex. Interacts with ALIS3 and ALIS5 in a heterologous system. Requires the presence of an ALIS protein to exit the endoplasmic reticulum to the Golgi. Expressed in petals and sepals, but not in reproductive tissues. In siliques, detected in the upper part of the seed pod and in the area between the seed pod and the stem, but not in developing seeds. Strong expression in vascular shoot tissues and in stomatal guard cells of young rosettes leaves. In roots, expressed in cells surrounding the xylem and in central and peripheral columella cells. Detected in developing and mature trichomes, roots, pollen and growing pollen tubes. Impaired growth of roots and shoots (PubMed:18344284, PubMed:23667493, PubMed:28434950). Roots devoided of the characteristic trans-Golgi proliferation of slime vesicles containing polysaccharides and enzymes for secretion (PubMed:18344284). Aberrant trichome expansion, reduced primary root growth and longer root hairs (PubMed:19566596, PubMed:28434950). Impaired pollen growth (PubMed:19566596, PubMed:23667493, PubMed:28434950). Impaired ovule development (PubMed:23667493, PubMed:28434950). Reduced adaptability to temperature stresses (PubMed:23667493). Abnormal accumulation of ABCG36/PEN3 in endomembrane compartments, likely in the trans-Golgi network, instead of plasma membrane (PM), due to an impaired endocytic trafficking of the ABCG36/PEN3 transporter, thus causing delays in ABCG36/PEN3 recruitment to the host-pathogen interface upon infection by powdery mildews (e.g. Blumeria graminis) within papillae and in response to pathogenic bacteria (e.g. Pseudomonas syringae) or pathogen-associated molecular patterns (PAMPs) (e.g. flg22 and chitin) (PubMed:28434950). The intracellular targeting signals and lipid specificity determinants reside in the catalytic ALA subunit. Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IV subfamily.