Methylation Dependent Functional Switch Mechanism of the Escherichia coil Ada Protein

NMR studies have revealed the mechanism of a functional switch in the Escherichia coli Ada protein, which converts the DNA methyltransferase to a transcriptional regulator. The Ada protein acquires its ability to bind specific DNA sequences after an irreversible methyl transfer to its own cysteine residue (Cys69) from methyl-phosphotriesters within the alkylated DNA. NMR analysis have revealed that the segment from residues 102 to 123 forms a helix-turn-helix structure, and a site-directed mutagenesis study has identified the second helix to play a crucial role in specific recognition of DNA. NMR experiments on the methylated protein-DNA complex showed that although the major contacts are made by residues within the recognition helix, the S-methyl group at Cys69 come into direct contact with the cognate DNA. Therefore, the direct contact of this region after methylation is the “switch” which converts the Ada protein from a nonspecific DNA binding form to a transcription factor.