Brain intracellular platelet-activating factor acetylhydrolase (PAF-AH) isoform I is a member of a family of complex enzymes composed of mutually homologous ␣ 1 and ␣ 2 subunits, both of which account for catalytic activity, and the  subunit. We previously demonstrated that the expression of one catalytic subunit, ␣ 1 , is developmentally regulated, resulting in a switching of the catalytic complex from ␣ 1 /␣ 2 to ␣ 2 /␣ 2 during brain development (Manya, H., Aoki, J., Watanabe, M., Adachi, T., Asou, H., Inoue, Y., Arai, H., and Inoue, K. (1998) J. Biol. Chem. 273, 18567-18572). In this study, we explored the biochemical differences in three possible catalytic dimers, ␣ 1 /␣ 1 , ␣ 1 /␣ 2 , and ␣ 2 /␣ 2 . The ␣ 2 /␣ 2 homodimer exhibited different substrate specificity from the ␣ 1 /␣ 1 homodimer and the ␣ 1 /␣ 2 heterodimer, both of which showed similar substrate specificity. The ␣ 2 /␣ 2 homodimer hydrolyzed PAF and 1-O-alkyl-2-acetyl-snglycero-3-phosphorylethanolamine (AAGPE) most efficiently among 1-O-alkyl-2-acetyl-phospholipids. In contrast, both ␣ 1 /␣ 1 and ␣ 1 /␣ 2 hydrolyzed 1-O-alkyl-2-acetyl-sn-glycero-3-phosphoric acid more efficiently than PAF. AAGPE was the poorest substrate for these enzymes. The  subunit bound to all three catalytic dimers but modulated the enzyme activity in a catalytic dimer composition-dependent manner. The  subunit strongly accelerated the enzyme activity of the ␣ 2 /␣ 2 homodimer but rather suppressed the activity of the ␣ 1 /␣ 1 homodimer and had little effect on that of the ␣ 1 /␣ 2 heterodimer. The (His 149 to Arg) mutant , which has been recently identified in isolated lissencephaly sequence patients, lost the ability to either associate with the catalytic complexes or modulate their enzyme activity. The enzyme activity of PAF-AH isoform I may be regulated in multiple ways by switching the composition of the catalytic subunit and by manipulating the  subunit.Brain platelet-activating factor acetylhydrolase (PAF-AH 1 isoform I) was first identified in bovine brain as an oligomeric enzyme consisting of two catalytic ␣ 1 and ␣ 2 subunits and a noncatalytic  subunit (1). The oligomeric brain PAF-AH contains a dimer of two highly homologous catalytic subunits, ␣ 1 and ␣ 2 , that share 63% amino acid sequence identity but are not related to any other known proteins (2, 3). The ␣ 1 and ␣ 2 subunits form a heterodimer in the PAF-AH purified from the bovine brain cortex (1). They can also form a catalytically active homodimer when expressed individually in Escherichia coli (3). Recently, the crystal structure of the ␣ 1 /␣ 1 homodimer was determined (4). Surprisingly, the ␣ 1 subunit has a tertiary fold reminiscent of small GTPases such as p21 ras and harbors a chymotrypsin-like Ser-Asp-His triad in its active site (4). Although the catalytic subunits of PAF acetylhydrolase were first identified as a ␣ 1 /␣ 2 heterodimer from young adult bovine brain (1), recent studies have revealed that the ␣ 2 /␣ 2 homodimers are present in vivo as well (5). We have demonstrated in a pr...