The extreme amino terminus and, in particular, residue Glu-3 in rat liver (L) carnitine palmitoyltransferase I (CPT I) have previously been shown to be essential for the sensitivity of the enzyme to inhibition by malonylCoA. Using the Pichia pastoris expression system, we now observe that, although mutants E3A (Glu-3 3 Ala) or ⌬(3-18) of L-CPT I have markedly lowered sensitivity to malonyl-CoA compared with the wild-type protein, the mutant ⌬(1-82) generated an enzyme that had regained much of the sensitivity of wild-type CPT I. This suggests that a region antagonistic to malonyl-CoA sensitivity is present within residues 19 -82 of the enzyme. This was confirmed in the construct ⌬(19 -30), which was found to be 50-fold more sensitive than wild-type L-CPT I. Indeed, this mutant was >4-fold more sensitive than even the native muscle (M)-CPT I isoform expressed and assayed under identical conditions. This behavior was dependent on the presence of Glu-3, with the mutant E3A-⌬(19 -30) having kinetic characteristics similar to those of the E3A mutant. The increase in the sensitivity of the L-CPT I-⌬(19 -30) mutant was not due to a change in the mechanism of inhibition with respect to palmitoyl-CoA, nor to any marked change of the K 0.5 for this substrate. Conversely, for M-CPT I, a decrease in malonyl-CoA sensitivity was invariably observed with increasing deletions from ⌬(3-18) to ⌬(1-80). However, deletion of residues 3-18 from M-CPT I affected the K m for carnitine of this isoform, but not of L-CPT I. These observations (i) provide the first evidence for negative determinants of malonyl-CoA sensitivity within the amino-terminal segment of L-CPT I and (ii) suggest a mechanism for the inverse relationship between affinity for malonyl-CoA and for carnitine of the two isoforms of the enzyme.Carnitine palmitoyltransferase I (CPT I, 1 malonyl-CoAsensitive) is an integral membrane protein first identified in the outer membrane and contact sites of mitochondria (1, 2). The enzyme catalyzes the formation of acylcarnitines from long-chain acyl-CoA esters, thus enabling the movement of acyl moieties across intracellular membranes. CPT I exists in two isoforms (Liver and Muscle), which have considerable sequence similarity but differ greatly, and inversely, in their malonyl-CoA sensitivity and K m for carnitine (3, 4). It is a polytopic protein, with two transmembrane (TM) segments and amino and carboxyl segments (approximately 46 and 652 residues, respectively) that are both exposed on the cytosolic aspect of the membrane (5). It has been shown that the extreme amino terminus of the nascent L-CPT I is retained in the mature protein (6) and, moreover, that it is essential for the expression of malonyl-CoA sensitivity (5, 7). Subsequent work with expressed CPT I constructs has confirmed these conclusions by showing that deletion of the amino-terminal highly conserved 6 amino acid residues of the L-isoform results in the loss of high affinity malonyl-CoA sensitivity (8). Glu-3, and to a much lesser extent His-5, have been identi...