Platelet-activating factor (PAF) acetylhydrolase is the key enzyme in PAF inactivation. We recently purified one isoform of the enzyme from a bovine brain soluble fraction and revealed it as a heterotrimeric enzyme consisting of 29-, 30-, and 45-kDa subunits. Among them, the 29-kDa subunit possesses an active serine residue since diisopropyl fluorophosphate (DFP), an inhibitor of the enzyme, labeled only this subunit (Hattori, M., Arai, H., and Inoue, K. (1993) J. Biol. Chem. 268, 18748-18753). In the current study, we cloned the cDNA for the 29-kDa catalytic subunit. The predicted sequence of 232 amino acids is unique and is not homologous with those of any other proteins reported so far. When transfected into either Escherichia coli or COS7 cells, the cDNA produced PAF acetylhydrolase activity in both types of cells, indicating that this subunit alone is enough for catalysis. The recombinant 29-kDa protein was also inhibited and labeled by DFP. Furthermore, we isolated and sequenced the [3H]DFP-labeled peptide fragment, revealing that Ser47 is the active serine residue. The sequence surrounding it is different from the consensus sequence of the serine esterase family. Interestingly, the sequence of about 30 amino acids located 6 residues downstream from the active serine site exhibits significant homology to the first transmembrane region of the PAF receptor. These data demonstrate that the catalytic subunit of brain PAF acetylhydrolase is a novel type of serine esterase.