β-Ketoacyl-CoA thiolase catalyzes the last step in the β-oxidation of long chain fatty acids, the catabolic process by which fatty acid molecules are broken down in the mitochondria to generate acetyl-CoA. In the mechanism of β-ketoacyl CoA thiolase, β-ketoacyl CoA is cleaved by an enzyme cysteine thiol group. Inserted between carbon-2 and carbon-3, addition of the cysteine thiol leads to fragmentation of the substrate into two parts, an acetyl-enzyme portion and an acyl CoA molecule now two carbons shorter than the original substrate. Transthioesterification passes the acetyl portion to coenzyme A to yield acetyl CoA.
Fragmentation occurs in the mechanism because the acyl CoA portion is released as a resonance stabilized enolate. The β-Ketoacyl-CoA thiolase mechanism is
akin to aldol addition in reverse (a favorite of MCAT writers), a retro-aldol addition. However, aldol addition occurs between aldehydes and ketones, so Claisen condensation is a better reference point, the ester analog to the aldol addition reaction. In Claisen condensation, one ester acts as a nucleophile while a second ester acts as the electrophile. In the case of the β-Ketoacyl-CoA thiolase mechanism, in summary, what we have is a retro-Claisen condensation, but with thioesters instead of normal esters. While carboxylic acids don't form stable enolates, some carboxylic acid derivatives can form stable enolates such as acyl-bromides as well as esters in Claisen condensation and thioesters in the β-Ketoacyl-CoA thiolase mechanism.