Lysine 2,3-aminomutase, which catalyzes the interconversion of L-lysine and L-beta-lysine, is S-adenosyl-methionine-dependent, and the adenosyl-C-5' methylene group of this coenzyme mediates the transfer of hydrogen from C-3 of lysine to C-2 of beta-lysine. We here report experiments that address the mechanism by which S-adenosylmethionine activates lysine 2,3-aminomutase. We also describe an updated and improved purification procedure that produces enzyme with a specific activity substantially higher than that previously reported. Activation of the enzyme by less than 1 mol of S-adenosyl[1-14C]methionine/mol of subunits in the presence of lysine leads to the production of [14C] methionine in a kinetically biphasic process. After 1.8 min at 30 degrees C, 10% of the 14C is reisolated as [14C] methionine, and the cleavage increases to 19% after 10 min and to 51% after 40 min. Similar experiments with S-[8-14C]adenosylmethionine produce 5'-deoxy[14C]adenosine in amounts similar to the formation of methionine. The major radioactive products isolated in each case are [14C]methionine or 5'-deoxy[14C]adenosine, respectively, and unchanged 14C-labeled S-adenosylmethionine. These experiments support the hypothesis that activation of lysine 2,3-aminomutase involves a transfer of the 5'-deoxyadenosyl moiety from S-adenosylmethionine to another species associated with the enzyme, presumably another cofactor, to form an adenosyl cofactor that functions as the proximal, hydrogen abstracting species in the mechanism.