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

J Mol Biol. 2000 Jan 28;295(4):729-36. doi: 10.1006/jmbi.1999.3417.


The three-dimensional structure of the DNA-binding domain (residues 1-60) of the ethanol regulon transcription factor AlcR from Aspergillus nidulans has been solved by NMR. This domain belongs to the zinc binuclear cluster class. Although the core of the protein is similar to previously characterized structures, consisting of two helices organized around a Zn(2)Cys(6 )motif, the present structure presents important variations, among them the presence of two supplementary helices. This structure gives new insight into the understanding of the AlcR specificities in DNA binding such as longer consensus half-sites, in vitro monomeric binding but in vivo multiple repeat transcriptional activation, either in direct or inverse orientations. The presence of additional contacts of the protein with its DNA target can be predicted from a model proposed for the interaction with the consensus DNA target. The clustering of accessible negative charges on helix 2 delineates a possible interaction site for other determinants of the transcriptional machinery, responsible for the fine tuning of the selection of the AlcR cognate sites.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Aspergillus nidulans / metabolism
  • Cysteine
  • DNA / chemistry
  • DNA / metabolism
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / metabolism
  • Fungal Proteins / chemistry*
  • Fungal Proteins / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Nuclear Magnetic Resonance, Biomolecular / methods
  • Nucleic Acid Conformation
  • Protein Conformation
  • Solutions
  • Transcription Factors / chemistry
  • Transcription Factors / metabolism
  • Zinc Fingers


  • ALCR protein, Aspergillus nidulans
  • DNA-Binding Proteins
  • Fungal Proteins
  • Solutions
  • Transcription Factors
  • DNA
  • Cysteine

Associated data

  • PDB/2ALC
  • PDB/3ALC