Structures of beta-ketoacyl-acyl carrier protein synthase I complexed withfatty acids elucidate its catalytic machinery

Background: beta -ketoacyl-acyl carrier protein synthase (KAS) I is vital f or the construction of the unsaturated fatty acid carbon skeletons characte rizing E. coli membrane lipids. The new carbon-carbon bonds are created by KAS I in a Claisen condensation performed in a three-step enzymatic reactio n. KAS I belongs to the thiolase fold enzymes, of which structures are know n for five other enzymes. Results: Structures of the catalytic Cys-Ser KAS I mutant with covalently b ound C10 and C12 acyl substrates have been determined to 2.40 and 1.85 Angs trom resolution, respectively. The KAS I dimer is not changed by the format ion of the complexes but reveals an asymmetric binding of the two substrate s bound to the dimer. A detailed model is proposed for the catalysis of KAS I. Of the two histidines required for decarboxylation, one donates a hydro gen bond to the malonyl thioester oxo group, and the other abstracts a prot on from the leaving group. Conclusions: The same mechanism is proposed for KAS II, which also has a Cy s-His-His active site triad. Comparison to the active site architectures of other thiolase fold enzymes carrying out a decarboxylation step suggests t hat chalcone synthase and KAS III with Cys-His-Asn triads use another mecha nism in which both the histidine and the asparagine interact with the thioe ster oxo group. The acyl binding pockets of KAS I and KAS II are so similar that they alone cannot provide the basis for their differences in substrat e specificity.