Zinc Fingers

A zinc finger is a large superfamily of protein domains that can bind to DNA. A zinc finger consists of two antiparallel β strands, and an α helix. The zinc ion is crucial for the stability of this domain type - in the absence of the metal ion the domain unfolds as it is too small to have a hydrophobic core.
One very well explored subset of zinc-fingers (the C2H2 class) comprises a pair of cysteine residues in the beta strands and two histidine residues in the alpha helix which are responsible for binding a zinc ion. The two other classes of zinc finger proteins are the C4 and C6 classes. Zinc fingers are important in regulation because when interacted with DNA and zinc ion, they provide a unique structural motif for DNA-binding proteins.
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The structure of each individual finger is highly conserved and consists of about 30 amino acid residues, constructed as a ββα fold and held together by the zinc ion. The α-helix occurs at the C-terminal part of the finger, while the β-sheet occurs at the N-terminal part.This is most useful in tanscription process.
The consensus sequence of a single finger is: Cys-X2-4-Cys-X3-Phe-X5-Leu-X2-His-X3-His
The zinc finger protein TFIIIA, a positive transcription factor of the 5S RNA gene, binds to an internal control region of 50 nucleotides. Two modes of binding have been considered for the TFIIIA-DNA complex, one of which has been proposed on the basis of nuclease and chemical protection experiments and the other on model building. Since then, evidence has accumulated on the structures of individual components of the complex--for example, zinc finger polypeptides studied by NMR and a segment of the binding site analyzed by x-ray crystallography, but no high-resolution structural data on the TFIIIA-DNA complex itself are available. Probes used previously to study the TFIIIA-DNA complex do not react with every nucleotide of DNA, unlike hydroxyl radical, which cleaves DNA at every backbone position. We describe here the quantitative analysis of high-resolution hydroxyl radical footprints and suggest how the array of zinc fingers might interact with the double helix.

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