DNA Methylphosphotriester Repair Domain, or N-Ada 10

The non-enzymatic methylation of DNA can give rise to the base O6-methylguanine (O6-meG), which then base pairs with thymine (T) instead of adenine (A) thus causing GC to AT transition mutations. To ensure that this damaging process does not occur throughout the genome, there is a repair protein that seeks out and recognizes methylated DNA. E. coli Ada removes the methyl group from the O6 position on guanine by transferring the reactive group to one of its own cysteine residues on the C terminal of the protein. This is known as a suicide reaction because once the transfer of the methyl group has taken place, the enzyme becomes irreversibly inactivated. The protein thus functions more like a reagent in the reaction than as the catalyst of the reaction. Also, this protein will repair O4-methylthymine (O4-meT) by methyl transfer to an internal cysteine residue. Another function of the Ada protein is to repair the Sp diastereomer of DNA methylphosphotriesters by transferring a methyl group to a particular cysteine residue, Cys69, which resides in the N terminus of the protein. This particular methyl transfer induces a sequence-specific DNA-binding ability in the protein's N terminal domain (N-Ada 20) which activates many methylation-resistant genes.
N-Ada 10, which comprises amino acid residues 1-92 of the N terminal domain of the E. coli Ada protein, binds Zinc (Zn) as a metal ligand. Zinc is bound tetrahedrally among four cysteine residues: Cys33, Cys42, Cys69, and Cys72. However, the active site nucleophile is Cys69 which is ligated to and directly interacts with the Zn ion.

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