An immunochemical approach was employed as a direct test for functional activities of isozymes of methylcobamide:coenzyme M methyltransferase (MT2-M and MT2-A) in the metabolic pathways of methane formation from: methanol, acetate, monomethylamine, dimethylamine, and trimethylamine. Specific removal of the MT2 isozymes from buffer soluble cell extracts of Methanosarcina barkeri was accomplished by use of immobilized, affinity-purified, ovine polyclonal antibodies. Extracts of methanol-grown cells depleted of MT2-M lost entirely the ability to carry out conversion of methanol to 2-(methylthio)ethanesulfonate (methyl-CoM). Methanol:CoM methyl transfer activity was completely restored by addition of purified MT2-M, but no activity was recovered by addition of MT2-A. In contrast, the activity of trimethylamine-grown cell extracts to convert monomethylamine and dimethylamine to methyl-CoM was lost almost entirely by immunosorptive removal of MT2-A. Addition of purified MT2-A, but not MT2-M, to the MT2-A-depleted extract fully reconstituted methyl-CoM formation from both mono- and dimethylamine. Interestingly, in extracts resolved of MT2-A, trimethylamine-dependent methylation of coenzyme M was observed at approximately 20% of the rate of controls not treated with antibody. Furthermore, both isozymes were effective in full restoration of trimethylamine conversion. Tests indicated that neither of the two MT2 isozymes are involved in methane formation from acetate. The results establish that MT2-A plays a specific role in metabolism of methylated amine substrates, whereas, MT2-M functions in methane formation from trimethylamine and methanol.