Rat mammary gland acetyl-CoA carboxylase (acetyl-CoA:carbon dioxide ligase (ADP forming), EC 18.104.22.168) is rapidly and irreversibly inactivated by micromolar concentrations of S-(4-bromo-2,3-dioxobutyl)-CoA (BDB-CoA) or p-hydroxymercuribenzoate (PHMB). Inhibition of both half reactions (i.e., the biotin carboxylation and the carboxyltransferase) catalyzed by acetyl-CoA carboxylase closely parallels loss in overall activity (malonyl-CoA synthesis). The presence of a substrate or product (acetyl-CoA, ATP, ADP, Pi) or inhibitor (palmitoyl-CoA) does not protect the enzyme from inhibition caused by BDB-CoA or PHMB. On the other hand, citrate, an activator of acetyl-CoA carboxylase, affords substantial protection against inhibition by BDB-CoA and PHMB. Covalent modification by BDB-CoA or PHMB appears to lock acetyl-CoA carboxylase in an inactive conformation (15-30 S) that is unable to undergo citrate-induced self-association into the catalytically competent polymeric form.