Crystal structure of the restriction-modification system control element C.Bcll and mapping of its binding site

Protection from DNA invasion is afforded by restriction-modification systems in many bacteria. The efficiency of protection depends crucially on the relative expression levels of restriction versus methytransferase genes. This regulation is provided by a controller protein, named C protein. Studies of the BcII system in E. coli suggest that C.BcII functions as a negative regulator for M.BcII expression, implying that it plays a role in defense against foreign DNA during virus infection. C.BcII binds (K-d = 14.3 nM) to a 2-fold symmetric C box DNA sequence that overlaps with the putative -35 promoter region upstream of the bcIIM and bcIIC genes. The C.BcII fold comprises five alpha helices: two helices form a helix-turn-helix motif, and the remaining three helices form the extensive dimer interface. The C.BcII-DNA model proposed suggests that DNA bending might play an important role in gene regulation, and that Glu27 and Asp31 in C.BcII might function critically in the regulation.