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Journal of Bacteriology, January 2006, p. 223-230, Vol. 188, No. 1
0021-9193/06/$08.00+0     doi:10.1128/JB.188.1.223-230.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

The AidB Component of the Escherichia coli Adaptive Response to Alkylating Agents Is a Flavin-Containing, DNA-Binding Protein

Cell and Molecular Biology Program,¹ Department of Microbiology and Molecular Genetics,² Department of Biochemistry and Molecular Biology,³ Department of Physics, Michigan State University, East Lansing, Michigan 48824-4320⁴

Received 3 August 2005/ Accepted 4 October 2005

Upon exposure to alkylating agents, Escherichia coli increases expression of aidB along with three genes (ada, alkA, and alkB) that encode DNA repair proteins. In order to begin to identify the role of AidB in the cell, the protein was purified to homogeneity, shown to possess stoichiometric amounts of flavin adenine dinucleotide (FAD), and confirmed to have low levels of isovaleryl-coenzyme A (CoA) dehydrogenase activity. A homology model of an AidB homodimer was constructed based on the structure of a four-domain acyl-CoA oxidase. The predicted structure revealed a positively charged groove connecting the two active sites and a second canyon of positive charges in the C-terminal domain, both of which could potentially bind DNA. Three approaches were used to confirm that AidB binds to double-stranded DNA. On the basis of its ability to bind DNA and its possession of a redox-active flavin, AidB is predicted to catalyze the direct repair of alkylated DNA.

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