In the first step of the BER pathway, a lesion-specific DNA N-glycosylase removes the damaged base by cleaving the glycosylic bond between the base and deoxyribose of the DNA backbone. Most single base modifications in DNA are corrected by BER. Cells have devised a number of DNA repair strategies to restore the original DNA structure after a chemical insult, including direct reversal, nucleotide excision repair and base excision repair (BER). These added alkyl groups on the bases block replicative polymerases and/or interfere with the binding of regulatory proteins to DNA ( Friedberg et al., 1995), causing widespread cellular responses ( Jelinsky and Samson, 1999), including the activation of cell cycle checkpoints and/or programmed cell death ( Engelward et al., 1998). A variety of environmental toxins and cellular agents can react with DNA and chemically alkylate the bases. The chemical instability of DNA poses a challenge to the long-term maintenance and inheritance of genetic material. Modeling studies suggest that other HhH glycosylases can bind to DNA in a similar manner. The structure of the AlkA–DNA complex offers the first glimpse of a helix–hairpin–helix (HhH) glycosylase complexed to DNA.

Catalytic selectivity might result from the enhanced stacking of positively charged, alkylated bases against the aromatic side chain of Trp272 in conjunction with the relative ease of cleaving the weakened glycosylic bond of these modified nucleotides. The position of the 1–azaribose in the enzyme active site suggests an S N1-type mechanism for the glycosylase reaction, in which the essential catalytic Asp238 provides direct assistance for base removal. The enzyme flips a 1–azaribose abasic nucleotide out of DNA and induces a 66° bend in the DNA with a marked widening of the minor groove. The 2.5 Å crystal structure of AlkA complexed to DNA shows a large distortion in the bound DNA.

The Escherichia coli AlkA protein is a base excision repair glycosylase that removes a variety of alkylated bases from DNA.

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