Triple bond analogues of natural fatty acids irreversibly inactivate lipoxygenase during their enzymatic conversion [Nieuwenhuizen, W. F., et al. (1995) Biochemistry 34, 10538-10545]. To gain insight into the mechanism of the irreversible inactivation of soybean lipoxygenase-1, we studied the enzymatic conversion of two linoleic acid analogues, 9(Z)-octadec-9-en-12-ynoic acid (9-ODEYA) and 12(Z)-octadec-12-en-9-ynoic acid (12-ODEYA). During the inactivation process, Fe(III)-lipoxygenase converts 9-ODEYA into three products, i.e. 11-oxooctadec-9-en-12-ynoic acid, racemic 9-hydroxy-10(E)-octadec-10-en-12-ynoic acid, and racemic 9-hydroperoxy-10(E)-octadec-10-en-12-ynoic acid. Fe(II)-lipoxygenase does not convert the inhibitor and is not inactivated by 9-ODEYA. Fe(III)-lipoxygenase converts 12-ODEYA into 13-hydroperoxy-11(Z)-octadec-11-en-9-ynoic acid (34/66 R/S), 13-hydroperoxy11(E)-octadec-11-en-9-ynoic acid (36/64 R/S), 11-hydroperoxyoctadec-12-en-9-ynoic acid (11-HP-12-ODEYA, enantiomeric composition of 33/67), and 11-oxooctadec-12-en-9-ynoic acid (11-oxo-12-ODEYA) during the inactivation process. Also, Fe(II)-lipoxygenase is inactivated by 12-ODEYA. It converts the inhibitor into the same products as Fe(III)-lipoxygenase does, but two additional products are formed, viz. 13-oxo-11(E)-octadec-11-en-9-ynoic acid and 13-oxo-11(Z)-octadec-11-en-9-ynoic acid. The purified reaction products were tested for their lipoxygenase inhibitory activities. The oxo compounds, formed in the reaction of 9-ODEYA and 12-ODEYA, do not inhibit Fe(II)- or Fe(III)-lipoxygenase. The 9- and 13-hydroperoxide products that are formed from 9-ODEYA and 12-ODEYA, respectively, oxidize Fe(II)-lipoxygenase to its Fe(III) state and are weak lipoxygenase inhibitors. 11-HP-12-ODEYA is, however, the most powerful inhibitor and is able to oxidize Fe(II)-lipoxygenase to Fe(III)-lipoxygenase. 11-HP-12-ODEYA is converted into 11-oxo-12-ODEYA by Fe(III)-lipoxygenase. We propose a mechanism for the latter reaction in which Fe(III)-lipoxygenase abstracts the bisallylic hydrogen H-11 from 11-HP-12-ODEYA, yielding a hydroperoxyl radical which is subsequently cleaved into 11-oxo-ODEYA and a hydroxyl radical which may inactivate the enzyme.