Prostacyclin (PGI₂) synthase is a heme–thiolate (P450) protein which reacts with low levels of peroxynitrite (PN) under tyrosine nitration and inactivation. Studying heme proteins as models, we have found the heme–thiolate protein NADH–NO reductase (P450_NOR) to be highly efficient in decomposing PN under concomitant nitration of phenol. The present study investigates two other P450 proteins, P450_BM-3 and chloroperoxidase, in order to test for the specific role of the thiolate ligand in the reaction with PN. A comparison with horseradish peroxidase and microperoxidase gives evidence of kinetic differences that classify heme–thiolate proteins, but not other heme proteins, as effective inhibitors of PGI₂ synthase nitration and inactivation. P450_BM-3 with PN catalyzes phenol nitration and nitration of its own tyrosine below 10 μM PN, whereas chloroperoxidase and P450_NOR at such concentrations also nitrate phenol but not enzyme-bound tyrosine residues. We conclude that heme–thiolate proteins in general exhibit high reactivity with PN and turnover, probably due to the special electronic structure of the presumed thiolate–ferryl intermediate.