Unique DNA binding specificity of the binuclear zinc AlcR activator of the ethanol utilization pathway in Aspergillus nidulans

AlcR is the transcriptional activator in Aspergillus nidulans, necessary for the induction of the ale gene cluster. It belongs to the Zn(2)Cys(6) zinc cluster protein family, but contains some striking differences compared with other proteins of this group. In this report, we show that no dimerization element is present in the entire AlcR protein which occurs in solution as a monomer and binds also to its cognate sites as a monomer. Another important feature of AlcR is its unique specificity for single sites occurring naturally as inverted or direct repeats and sharing a common motif, 5'-(T/A)GCGG-S', Like most other Zn(2)Cys(6) proteins, AlcR contacts directly with the CGG triplet and, in addition, the upstream adjacent guanine is required for high affinity binding. We also establish that the flanking regions outside the core play an essential role in tight binding. From our in vitro analysis, we propose an optimal AlcR-binding site which is 5'-PuNGCGG-AT rich 3'.