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Architecture of a fur binding site: a comparative analysis
Jennifer L Lavrrar1, Mark A McIntosh
1Department of Molecular Microbiology and Immunology, University of Missouri-Columbia School of Medicine, Columbia, Missouri 65212, USA.
Journal of Bacteriology
|March 20, 2003
Summary
The Fur protein, an iron-binding repressor, requires a specific DNA binding site arrangement (F-F-x-R) for high-affinity interactions. This binding involves two overlapping Fur dimers interacting with the DNA sequence.
Area of Science:
- Molecular Biology
- Genetics
- Biochemistry
Background:
- Fur is a transcriptional repressor that binds DNA sequences containing GATAAT hexamers.
- Natural Fur binding sites often exhibit an F-F-x-R configuration, differing from simple adjacent hexamers.
Purpose of the Study:
- To compare Fur's recognition of synthetic DNA sequences with varying hexamer arrangements.
- To elucidate the structural basis for high-affinity Fur-DNA interactions.
Main Methods:
- Gel retardation assays were used to assess Fur-DNA binding affinity.
- Analysis of natural operator sequences from Escherichia coli promoter regions (entS and fepB).
Main Results:
- The F-F-x-R DNA architecture is essential for high-affinity Fur binding, outperforming contiguous hexamers.
- Fur binds to its 19-bp consensus site as two overlapping dimers.
- A model of overlapping-dimer binding, with each dimer recognizing inverted hexamers, was confirmed.
Conclusions:
- High-affinity Fur-DNA interactions depend on the F-F-x-R binding site configuration.
- The Fur protein utilizes an overlapping-dimer binding mechanism at its consensus DNA site.