The Arabidopsis FAE1 b-ketoacyl-CoA synthase (FAE1 KCS) catalyzes the condensation of malonyl-CoA with longchain acyl-CoAs. Sequence analysis of FAE1 KCS predicted that this condensing enzyme is anchored to a membrane by two adjacent N-terminal membrane-spanning domains. In order to characterize the FAE1 KCS and analyze its mechanism, FAE1 KCS and its mutants were engineered with a His 6 -tag at their N-terminus, and expressed in Saccharomyces cerevisiae. The membrane-bound enzyme was then solubilized and purified to near homogeneity on a metal affinity column. Wild-type recombinant FAE1 KCS was active with several acyl-CoA substrates, with highest activity towards saturated and monounsaturated C16 and C18. In the absence of an acyl-CoA substrate, FAE1 KCS was unable to carry out decarboxylation of [3][4][5][6][7][8][9][10][11][12][13][14] C]malonyl-CoA, indicating that it requires binding of the acyl-CoA for decarboxylation activity. Site-directed mutagenesis was carried out on the FAE1 KCS to assess if this condensing enzyme was mechanistically related to the well characterized soluble condensing enzymes of fatty acid and flavonoid syntheses. A C223A mutant enzyme lacking the acylation site was unable to carry out decarboxylation of malonyl-CoA even when 18:1-CoA was present. Mutational analyses of the conserved Asn424 and His391 residues indicated the importance of these residues for FAE1-KCS activity. The results presented here provide the initial analysis of the reaction mechanism for a membrane-bound condensing enzyme from any source and provide evidence for a mechanism similar to the soluble condensing enzymes.Keywords: very long chain fatty acids; fatty acid elongation; condensation mechanism.Fatty acids with greater than 18 carbon atoms (very long chain fatty acids, VLCFA) are precursors of many biologically important compounds such as sphingolipids [1,2], waxes [3], and triacylglycerols in many seed oils [4]. Biosynthesis of VLCFA in plants and animals, is dependent on the activity of a membrane-bound fatty acid elongation system which consists of four component reactions similar to fatty acid synthase. The first reaction of elongation involves condensation of malonyl-CoA with a long chain acyl substrate producing a b-ketoacyl-CoA. Subsequent reactions are reduction to b-hydroxyacyl-CoA, dehydration to an enoyl-CoA, followed by a second reduction to form the elongated acyl-CoA [5]. In both animals and plants, the initial condensation reaction is believed to be the ratelimiting step [6,7].In Arabidopsis, FAE1 codes for a b-ketoacyl-CoA synthase (FAE1 KCS) which is expressed exclusively in the seed and catalyzes the initial condensation step in the elongation pathway [8]. Based on fatty acid profiles of transgenic plants and yeast, it has been reported that FAE1 KCS has a substrate preference for C18:1, producing eicosenoic (C20:1) acid as the major product and erucic acid (C22:1) as a minor product [7].A prominent feature of b-ketoacyl-CoA synthases involved in VLCFA biosynthesis is their membrane-bound...