Mammalian mitochondrial membranes express two active but distinct carnitine palmitoyltransferases: carnitine palmitoyltransferase I (CPTI), which is malonyl coA-sensitive and detergent-labile; and carnitine palmitoyltransferase II (CPTII), which is malonyl coA-insensitive and detergent-stable. To determine the role of the highly conserved C-terminal acidic residues glutamate 487 (Glu 487 ) and glutamate 500 (Glu 500 ) on catalytic activity in rat liver CPTII, we separately mutated these residues to alanine, aspartate, or lysine, and the effect of the mutations on CPTII activity was determined in the Escherichia coli-expressed mutants. Substitution of Glu 487 with alanine, aspartate, or lysine resulted in almost complete loss in CPTII activity. Because a conservative substitution mutation of this residue, Glu 487 with aspartate (E487D), resulted in a 97% loss in activity, we predicted that Glu 487 would be at the active-site pocket of CPTII. The substantial loss in CPTII activity observed with the E487K mutant, along with the previously reported loss in activity observed in a child with a CPTII deficiency disease, establishes that Glu 487 is crucial for maintaining the configuration of the liver isoform of the CPTII active site. Substitution of the conserved Glu 500 in CPTII with alanine or aspartate reduced the V max for both substrates, suggesting that Glu 500 may be important in stabilization of the enzyme-substrate complex. A conservative substitution of Glu 500 to aspartate resulted in a significant decrease in the V max for the substrates. Thus, Glu 500 may play a role in substrate binding and catalysis. Our site-directed mutagenesis studies demonstrate that Glu 487 in the liver isoform of CPTII is essential for catalysis.Carnitine palmitoyltransferase (CPT) 1 I and CPTII, in conjunction with carnitine translocase, transport long chain fatty acids from the cytoplasm to the mitochondrial matrix for -oxidation (1, 2). Mammalian mitochondrial membranes express two active but distinct carnitine palmitoyltransferases (CPTI and CPTII), a malonyl CoA-sensitive, detergent-labile CPTI, and a malonyl-CoA-insensitive, detergent-stable CPTII. CPTI is an integral membrane enzyme located on the outer mitochondrial membrane, and CPTII is a membrane-associated enzyme loosely bound to the matrix side of the inner mitochondrial membrane. A current model for the membrane topology of CPTI predicts exposure of the N-and C-terminal domains crucial for activity and malonyl-CoA sensitivity on the cytosolic side of the outer mitochondrial membrane (3). As an enzyme that catalyzes the rate-limiting step in fatty acid oxidation, CPTI is tightly regulated by its physiologic inhibitor, malonylCoA, the first intermediate in fatty acid synthesis (1, 2). This is an important regulatory mechanism in fatty acid metabolism and suggests coordinated control of fatty acid oxidation and synthesis. Mammalian tissues express two isoforms of CPTI, a liver isoform of CPTI and a heart/skeletal muscle isoform of CPTI, that are 62% identical in amino ...