8-(Methylsulfonyl)FAD reacts with a single cysteine residue (Cys449) in pig apolipoamide dehydrogenase to generate a flavinylated enzyme containing covalently bound 8-(cysteinyl)FAD. Competitive behavior is observed in reconstitution reactions containing both FAD and 8-(methylsulfonyl)FAD. Covalently bound 8-(cysteinyl)FAD is shielded from solvent, as judged by spectral comparison with model 8-(alkylthio)-flavins in various solvents. Flavinylated lipoamide dehydrogenase is monomeric and catalytically inactive. Cys449 is located in the interface domain, near the active site histidine (His452). As shown previously, Cys449 is oxidized when native enzyme is treated with cupric ions. Cys449 is close to the isoalloxazine ring of FAD in native enzyme, as judged by alignment of the pig sequence with the structure of the homologous enzyme from Azotobacter vinelandii. The residue corresponding to Cys449 in A. vinlandii lipoamide dehydrogenase (Val447) is about 9 A from the carbonyl oxygen at C(2) in the pyrimidine ring of FAD. Approximation of a substituent at position 8 in FAD with Cys449 requires a 180 degrees flip of the isoalloxazine ring as compared with its orientation in the native structure. The different flavin orientation can explain the absence of dimerization and catalytic activity. Using the same method of apoenzyme preparation, noncovalent binding was observed with 8-chloroFAD, a less reactive flavin analogue. Relatively nonspecific covalent incorporation was observed with 8-chloroFAD when apoenzyme was prepared by an older method used in previous studies with this derivative [Moore, E.G., Cardemil, E., & Massey, V. (1978) J. Biol. Chem. 253, 6413-6422].