Plants produce a unique peroxisomal short chain-specific acyl-CoA oxidase (ACX4) for -oxidation of lipids. The short chain-specific oxidase has little resemblance to other peroxisomal acyl-CoA oxidases but has an ϳ30% sequence identity to mitochondrial acyl-CoA dehydrogenases. Two biochemical features have been linked to structural properties by comparing the structures of short chain-specific Arabidopsis thaliana ACX4 with and without a substrate analogue bound in the active site to known acyl-CoA oxidases and dehydrogenase structures: (i) a solvent-accessible acyl binding pocket is not required for oxygen reactivity, and (ii) the oligomeric state plays a role in substrate pocket architecture but is not linked to oxygen reactivity. The structures indicate that the acyl-CoA oxidases may encapsulate the electrons for transfer to molecular oxygen by blocking the dehydrogenase substrate interaction site with structural extensions. A small binding pocket observed adjoining the flavin adenine dinucleotide N5 and C4a atoms could increase the number of productive encounters between flavin adenine dinucleotide and O 2 .The central pathway for fatty acid breakdown in higher plants is via peroxisomal -oxidation. Fatty acids enter the cycle in the form of acyl-CoA thioesters, and during one round of -oxidation, the acyl chain is shortened by a two-carbon unit and one acetyl-CoA molecule is produced. The first step in the peroxisomal -oxidation cycle is the introduction of a double bond into the acyl-CoA substrate, resulting in the formation of 2-trans-enoyl-CoA. This reaction is a two-step reaction catalyzed by the family of acyl-CoA oxidases (ACXs) 2 requiring flavin adenine dinucleotide (FAD) as a cofactor. The cofactor gets reduced to FADH Ϫ in the first half-reaction concomitant with acyl-CoA oxidation. FADH Ϫ is reoxidized by molecular oxygen in the second step, thereby generating H 2 O 2 , an intracellular signaling molecule.Unlike plants, two parallel and distinct -oxidation pathways exist in mammals, the peroxisomal -oxidation pathway and a mitochondrial -oxidation pathway. In mitochondrial -oxidation, the first step is catalyzed by the acyl-CoA dehydrogenase family (ACD) (1), which is related to ACXs. The FADH Ϫ in ACDs is not, however, reoxidized by molecular oxygen but rather by another flavoprotein, the electron transfer flavoprotein, which transfers electrons to the electron transport chain. As a result, the oxidation of fatty acids/amino acids and the generation of ATP molecules are linked in mitochondrial -oxidation (2). It is puzzling that natural selection has not forced plants to utilize the mitochondrial electron transport chain for general lipid oxidation despite the apparent ATP advantage of this pathway. This might reflect less stress on the ATP requirement and a higher demand for lipid turnover and excess oxygen management in plants.Six genes for ACX isozymes have been identified in Arabidopsis thaliana. Five encode for proteins of ϳ75 kDa (3-5). The proteins have different but overlapping s...