The topography of mitochondrial glycerol-3-phosphate acyltransferase (GPAT) was determined using rat liver mitochondria and mutagenized recombinant rat GPAT (828 aa (amino acids)) expressed in CHO cells. Hydrophobicity analysis of GPAT predicts two transmembrane domains (TMDs), residues 472-493 and 576 -592. Residues 224 -323 correspond to the active site of the enzyme, which is believed to lie on the cytosolic face of the outer mitochondrial membrane. Protease treatment of rat liver mitochondria revealed that GPAT has a membraneprotected segment of 14 kDa that could correspond to the mass of the two predicted TMDs plus a loop between aa 494 and 575. Recombinant GPAT constructs containing tagged epitopes were transiently expressed in Chinese hamster ovary cells and immunolocalized. Both the C and N termini epitope tags could be detected after selective permeabilization of only the plasma membrane, indicating that both termini face the cytosol. A 6 -8-fold increase in GPAT-specific activity in the transfected cells confirmed correct protein folding and orientation. When the C terminus and loop-tagged GPAT construct was immunoassayed, the epitope at the C terminus could be detected when the plasma membrane was permeabilized, but loop-epitope accessibility required disruption of the outer mitochondrial membrane. Similar results were observed when GPAT was truncated before the second TMD, again consistent with an orientation in which the loop faces the mitochondrial intermembrane space. Although protease digestion of the HA-tagged loop resulted in preservation of a 14-kDa fragment, consistent with a membrane protected loop domain, neither the truncated nor loop-tagged enzymes conferred GPAT activity when overexpressed, suggesting that the loop plays a critical structural or regulatory role for GPAT function. Based on these data, we propose a GPAT topography model with two transmembrane domains in which both the N (aa 1-471) and C (aa 593-end) termini face the cytosol and a single loop (aa 494 -575) faces the intermembrane space.Glycerol phosphate acyltransferase (GPAT) 1 (EC 2.3.1.15) catalyzes the first and committed step in de novo cellular glycerolipid synthesis, the formation of 1-acyl-sn-glycerol-3-phosphate (lysophosphatidic acid) from glycerol-3-phosphate and long chain fatty acyl-CoA substrates (1, 2). Mammalian cells contain two GPAT isozymes that have different cellular locations, one in the endoplasmic reticulum and the other in mitochondria, that can be distinguished by sensitivity to inactivation by sulfhydryl reagents. The mitochondrial GPAT is an outer mitochondrial membrane (OMM) protein composing about 10% of the total enzymatic activity in most mammalian tissues. In liver, however, GPAT specific activity is similar in the two subcellular organelles. Only the mitochondrial GPAT isoform has been cloned. Recombinant mouse (3) and rat (4) GPAT open reading frames encode proteins of 827 and 828 amino acids, respectively, with a high degree of homology. Alignment of rat mitochondrial GPAT with other acyl...