NMR solution structure of AlcR (1-60) provides insight in the unusual DNA binding properties of this zinc binuclear cluster protein

The three-dimensional structure of the DNA-binding domain (residues 1-60) o f the ethanol regulon transcription factor AlcR from Aspergillus nidulans h as been solved by NMR. This domain belongs to the zinc binuclear cluster cl ass. Although the core of the protein is similar to previously characterize d structures, consisting of two helices organized around a Zn,Cys, motif, t he present structure presents important variations, among them the presence of two supplementary helices. This structure gives new insight into the un derstanding of the AlcR specificities in DNA binding such as longer consens us half-sites, in vitro monomeric binding but in vivo multiple repeat trans criptional activation, either in direct or inverse orientations. The presen ce of additional contacts of the protein with its DNA target can be predict ed from a model proposed for the interaction with the consensus DNA target. The clustering of accessible negative charges on helix 2 delineates a poss ible interaction site for other determinants of the transcriptional machine ry, responsible for the fine tuning of the selection of the AlcR cognate si tes. (C) 2000 Academic Press.