Plant fatty acids can be completely degraded within the peroxisomes. Fatty acid degradation plays a role in several plant processes including plant hormone synthesis and seed germination. Two multifunctional peroxisomal isozymes, MFP2 and AIM1, both with 2-trans-enoyl-CoA hydratase and L-3-hydroxyacyl-CoA dehydrogenase activities, function in mouse ear cress (Arabidopsis thaliana) peroxisomal -oxidation, where fatty acids are degraded by the sequential removal of two carbon units. A deficiency in either of the two isozymes gives rise to a different phenotype; the biochemical and molecular background for these differences is not known. Structure determination of Arabidopsis MFP2 revealed that plant peroxisomal MFPs can be grouped into two families, as defined by a specific pattern of amino acid residues in the flexible loop of the acylbinding pocket of the 2-trans-enoyl-CoA hydratase domain. This could explain the differences in substrate preferences and specific biological functions of the two isozymes. The in vitro substrate preference profiles illustrate that the Arabidopsis AIM1 hydratase has a preference for short chain acyl-CoAs compared with the Arabidopsis MFP2 hydratase. Remarkably, neither of the two was able to catabolize enoyl-CoA substrates longer than 14 carbon atoms efficiently, suggesting the existence of an uncharacterized long chain enoyl-CoA hydratase in Arabidopsis peroxisomes.Fatty acids are degraded by the sequential removal of two carbon units in a process known as -oxidation (Fig. 1). This process is ubiquitous and takes its name from the oxidation taking place at the carbon atom  to the carboxyl group. The discovery of a peroxisomal -oxidation system was made in plants (1), and whereas peroxisomal -oxidation in animals appears to be merely a fatty acid chain-shortening machine feeding mitochondrial -oxidation, plant and fungal -oxidation takes place almost entirely in the peroxisomes. The products of the reaction are H 2 O 2 , acetyl-CoA, reducing equivalents, and a variety of chain length-shortened acyl-containing molecules like the plant hormones jasmonic acid (2) and indole-3-acetic acid (3, 4).The conversion of storage triacylglycerols by -oxidation provides metabolic energy and carbon skeletons for germination and early post-germinative seedling growth in oil seed plants (5) and metabolic energy and carbon for the production of hydrolytic enzymes in cereals (6). It is a salvage pathway for fatty acids during foliar senescence (7), supplies respiratory substrates to carbohydrate-deprived tissue (8), and at a lower level, is a constitutive property of all plant tissues most likely involved with membrane lipid turnover (7).Three proteins (each present as several isozymes) that host a total of four enzyme activities constitute the core of peroxisomal -oxidation. Acyl-CoA oxidase (ACX) 6 oxidizes acyl-CoA to 2-trans-enoyl-CoA using FAD as co-enzyme. A multifunctional protein (MFP) adds water over the 2-trans-enoyl-CoA double bond and oxidizes the resultant L-3-hydroxyacylCoA usin...