Carnitine acyltransferases have crucial functions in fatty acid metabolism. Members of this enzyme family show distinctive substrate preferences for short-, medium-or long-chain fatty acids. The molecular mechanism for this substrate selectivity is not clear as so far only the structure of carnitine acetyltransferase has been determined. To further our understanding of these important enzymes, we report here the crystal structures at up to 2.0-Å resolution of mouse carnitine octanoyltransferase alone and in complex with the substrate octanoylcarnitine. The structures reveal significant differences in the acyl group binding pocket between carnitine octanoyltransferase and carnitine acetyltransferase. Amino acid substitutions and structural changes produce a larger hydrophobic pocket that binds the octanoyl group in an extended conformation. Mutation of a single residue (Gly-553) in this pocket can change the substrate preference between short-and medium-chain acyl groups. The side chains of Cys-323 and Met-335 at the bottom of this pocket assume dual conformations in the substrate complex, and mutagenesis studies suggest that the Met-335 residue is important for catalysis.Carnitine acyltransferases catalyze the reversible transfer of acyl groups between carnitine and coenzyme A (see Fig. 1A) (1-4). Members of this family of enzymes include carnitine palmitoyltransferases (CPTs) 1 I and II (CPT-I, CPT-II), carnitine octanoyltransferase (CrOT), and carnitine acetyltransferase (CrAT) with substrate preferences for long-chain, medium-chain, and short-chain acyl groups, respectively. The catalytic domains of these enzymes contain about 600 amino acid residues (see Fig. 1B), and share ϳ30% amino acid sequence identity (see supplemental Fig. 1).Carnitine acyltransferases are of crucial importance for the transport of fatty acids among different cellular compartments (2-4). The CPTs are associated with the mitochondrial compartment and are essential for the import of long-chain fatty acids into the mitochondria for -oxidation. The CoA esters of long-chain fatty acids are impermeable to the mitochondrial membrane. They must first be converted to carnitine esters by CPT-I, which is integrally associated with the outer membrane of the mitochondria through a unique N-terminal segment (see Fig. 1B) (5). Upon transport into the mitochondria, the carnitine esters are converted back to CoA esters by CPT-II, which is located in the mitochondrial matrix. The CoA esters can then undergo -oxidation for energy production.The CPTs are therefore key enzymes for the transport of longchain fatty acids. Inherited mutational defects of these enzymes are the cause of many human diseases (2, 3). CPT-I deficiency is linked to serious episodes of hypoketonic hypoglycemia, whereas autosomal recessive deficiency of CPT-II is one of the most common inherited muscle lipid metabolism disorders (6). Both missense and deletion mutations have been described for these enzymes, and the defect of the mutated enzymes is most often caused by their reduce...