The solution structure of an AlcR-DNA complex sheds light onto the unique tight and monomeric DNA binding of a Zn(2)Cys(6) protein

Background: In Aspergillus nidulans, the transcription activator AlcR media tes specific induction of a number of the genes of the a/c cluster. This cl uster includes genes involved in the oxidation of ethanol and other alcohol s to acetate. The pattern of binding and of transactivation of AlcR is uniq ue within the Zn(2)Cys(delta) family. The structural bases for these specif icities have not been analyzed at the atomic level until now. Results: We have used NMR spectroscopy and restrained molecular dynamics to determine a set of structures of the AlcR DNA binding domain [AlcR(1-60)] in complex with a 10-mer DNA duplex. Analysis of the structures reveals spe cific interactions between AlcR and DNA common to the other known zinc clus ters. In addition, the involvement of the N-terminal residues upstream of t he AlcR zinc cluster in DNA binding is clearly highlighted, and the pivotal role of R6 is confirmed. Totally unprecedented specific and nonspecific co ntacts of two additional regions of the protein with the DNA are demonstrat ed. The differences with the available crystallographic structures of other zinc binuclear cluster proteins-DNA complexes are analyzed. Conclusions: The structures of the AlcR(1-60)-DNA complex provide the basis for a better understanding of some of the specificities of the AlcR system : the DNA consensus recognition sequence-usually the triplet CGG-is extende d to five base pairs, AlcR acts as a monomer, and additional contacts insid e and outside the DNA binding domain in the major and minor groove are obse rved. These extensive interactions stabilize the AlcR monomer to its cognat e DNA site.