Human 5-lipoxygenase is a non-heme iron protein which possesses 5-oxygenase, leukotriene A4 synthase and pseudoperoxidase activities and which undergoes a rapid irreversible inactivation during these reactions. The inactivation of the enzyme was dependent on the structural characteristics of the substrate for the reaction, on O2 concentration and on exposure to phospholipids and calcium. The apparent first-order rate constant for enzyme inactivation (k(in)) was 0.6 min(-1) during the oxygenation of arachidonic acid in air-saturated buffer containing phosphatidylcholine vesicles and Ca2+. The rate of enzyme inactivation was dependent on the substrate for the reaction and was about threefold slower during the oxygenation of 5,8-icosadienoic acid and 12(S)-hydroxyicosatetraenoic acid compared with arachidonic acid. Lowering the 02 concentration to 60 microM during the oxygenation of arachidonic acid also caused a 2.5-fold decrease in k(in) without affecting the initial rate of the reaction resulting in an increase in both 5-hydroperoxyicosatetraenoic acid (5-HPETE) and leukotriene A4 accumulation. The concentration of 02 for half-maximal activity (initial rate and product accumulation) was approximately 10 microM. In contrast, the activity and the rate of inactivation during the leukotriene A4 synthase reaction with exogenous 5-HPETE (k(in)=2.0 min(-1) were independent of 02 concentration. A rapid inactivation of the enzyme was also observed during aerobic incubation with phosphatidylcholine vesicles and Ca2+ in the absence of substrate, with a sequential loss of the oxygenase (t1/2 = 0.5 min) and pseudoperoxidase (t1/2 = 7 min) activities. Protection against this turnover-independent inactivation was observed in the presence of the selective reversible 5-lipoxygenase inhibitor L-739,010 ([1S, 5R] 3-cyano-1-(3-furyl)-6-(6-[3-(3 alpha-hydroxy-6,8-dioxyabicyclo [3.2.11 octanyl)] pyridin-2-ylmethoxy) naphthalene) and by prior treatment of vesicles with sodium borohydride and, to a lesser extent, by glutathione peroxidase. The results show that the inactivation of 5-lipoxygenase in phospholipid vesicles is dependent on the structure of the unsaturated fatty acid substrate for the reaction, on the concentration of oxygen and on a turnover-independent oxidation at the active-site leading to the sequential loss of the oxygenase and pseudoperoxidase activities of the enzyme.