The 39-kDa Ada protein that carries two distinct methyltransferase activities and an activity to promote transcription of the ada and alkA genes is cleaved to smaller polypeptides in the case of incubation with a crude extract of Escherichia coli. A protease that specifically cleaves the Ada protein was partially purified and characterized. The enzyme showed maximal activity at pH 7.8-8.0 and did not require specific ions or ATP for the reaction. The activity was inhibited by p-chloromercuribenzoic acid, thereby suggesting that it is a thiol protease. When a purified preparation of Ada protein was incubated with the protease preparation, definite sizes of cleavage products were formed; at the initial stage of proteolysis, the 20- and 19-kDa proteins were formed as the major products. When each of these products was purified by successive column chromatography, the 20-kDa protein was found to catalyze transfer of a methyl group from methylphosphotriester of methylated polynucleotides, whereas the 19-kDa protein transfers a methyl group from O6-methylguanine of methylated DNA to each of the molecules. Neither the 20- nor 19-kDa protein, even after methyl acceptance, exhibited an activity to promote transcription of the ada gene. However, alkA transcription was promoted by the 20-kDa protein provided that it was methylated.