Lon belongs to a unique group of AAA(+) proteases that bind DNA. However, the DNA-mediated regulation of Lon remains elusive. Here, the crystal structure of the alpha subdomain of the Lon protease from Brevibacillus thermoruber (Bt-Lon) is presented, together with biochemical data, and the DNA-binding mode is delineated, showing that Arg518, Arg557 and Arg566 play a crucial role in DNA binding. Electrostatic interactions contributed by arginine residues in the AAA(+) module are suggested to be important to DNA binding and allosteric regulation of enzymatic activities. Intriguingly, Arg557, which directly binds DNA in the alpha subdomain, has a dual role in the negative regulation of ATPase stimulation by DNA and in the domain-domain communication in allosteric regulation of Bt-Lon by substrate. In conclusion, structural and biochemical evidence is provided to show that electrostatic interaction in the AAA(+) module is important for DNA binding by Lon and allosteric regulation of its enzymatic activities by DNA and substrate.
