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Encyclopedia > Zinc finger
Cartoon representation of the protein Zif268 (blue) containing three zinc fingers in complex with DNA (orange). The coordinating amino acid residues of the middle zinc ion (green) are highlighted.
Cartoon representation of the protein Zif268 (blue) containing three zinc fingers in complex with DNA (orange). The coordinating amino acid residues of the middle zinc ion (green) are highlighted.

A zinc finger is a protein domain that can bind to DNA. A zinc finger consists of two antiparallel β sheets, and an α helix. The zinc ion is crucial for the stability of this domain type - in absence of the metal ion the domain unfolds as it is too small to have a hydrophobic core. Image File history File links Download high-resolution version (1188x1114, 410 KB) File links The following pages on the English Wikipedia link to this file (pages on other projects are not listed): Zinc finger Zif268 ... Image File history File links Download high-resolution version (1188x1114, 410 KB) File links The following pages on the English Wikipedia link to this file (pages on other projects are not listed): Zinc finger Zif268 ... --RAG 01:54, 16 March 2007 (UTC) The concept of the domain was first proposed in 1973 by Wetlaufer after X-ray crystallographic studies of hen lysozyme (Phillips, 1966), papain (Drenth et al. ... The structure of part of a DNA double helix Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the development and function of living organisms. ... Diagram of β-pleated sheet with H-bonding between protein strands The β sheet (also β-pleated sheet) is the second form of regular secondary structure in proteins — the first is the alpha helix — consisting of beta strands connected laterally by three or more hydrogen bonds, forming a generally twisted, pleated sheet. ... Side view of an α-helix of alanine residues in atomic detail. ... General Name, Symbol, Number zinc, Zn, 30 Chemical series transition metals Group, Period, Block 12, 4, d Appearance bluish pale gray Standard atomic weight 65. ...

Contents

Classes

One very well explored sub-set of zinc-fingers (the C2H2 class) comprises a pair of cysteine residues in the beta sheets 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. Cysteine is a naturally occurring, sulfur-containing amino acid that is found in most proteins, although only in small quantities. ... Histidine is one of the 20 most common natural amino acids present in proteins. ... General Name, Symbol, Number zinc, Zn, 30 Chemical series transition metals Group, Period, Block 12, 4, d Appearance bluish pale gray Standard atomic weight 65. ...


Structure

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.


The consensus sequence of a single finger is: Cys-X2-4-Cys-X3-Phe-X5-Leu-X2-His-X3-His


Proteins with Zinc finger

Many transcription factors (such as Zif268), regulatory proteins, and other proteins that interact with DNA contain zinc fingers. These proteins typically interact with the major groove along the double helix of DNA in which case the zinc fingers are arranged around the DNA strand in such a way that the α-helix of each finger contacts the DNA, forming an almost continuous stretch of α-helices around the DNA molecule. In molecular biology, a transcription factor is a protein that binds DNA at a specific promoter or enhancer region or site, where it regulates transcription. ... Zif268 is a mouse transcription factor that was also named Krox-24, NGFI-A and EGr1. ... A helix (pl: helices), from the Greek word έλικας/έλιξ, is a twisted shape like a spring, screw or a spiral (correctly termed helical) staircase. ...


Some primary neuron-specific transcriptional regulator that may be involved in mediating early neural development are also zinc finger-based.


Binding specificity

The binding specificity for 3–4 base pairs are conferred by a short stretch of amino acid residues in the α-helix. The primary position of the amino acid residues within the α-helix interacting with the DNA are at positions -1, 3 and 6 relative to the first amino acid residue of the α-helix. Other amino acid positions can also influence binding specificity by assisting amino acid residues to bind a specific base or by contacting a fourth base in the opposite strand, causing target-site overlap.


See also

Zinc finger inhibition is the process by which the synthesis of zinc fingers is blocked. ... Steroid hormone receptors are generally intracellular (specifically cytoplasmatic) receptors that perform signal transduction for steroid hormones. ...

References

Luscombe, Nicholas, et al (9 June 2000). "An overview of the structures of protein-DNA complexes". Genome Biology Review 1 (1): 4-5. 


External links

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Protein domains

BZIP - DED - Kringle - PH - SH2 - SH3 - zinc finger - coiled coil - helix bundle - globin fold - twisted open sheet - alpha/beta barrels - up and down barrel - greek key barrel - jelly roll barrel - greek key - leucine-rich repeat - beta propeller - LIM domain - C2 domain Within a protein, a structural domain (domain) is an element of overall structure that is self-stabilizing and often folds independently of the rest of the protein chain. ... Basic Leucine zipper domain (bZIP domain) CREB (top) is a transcription factor capable of binding DNAvia the bZIP domain (bottom) and regulating gene expression. ... The death-effector domain (DED) is a protein interaction domain found in inactive procaspases (cysteine proteases) and proteins that regulate caspase activation in the apoptosis cascade such as FAS-associating death domain-containing protein (FADD). ... Kringle Domains are conserved sequences that fold into large loops stabilized by 3 disulfide linkages. ... Pleckstrin homology domain (PH domain) is a protein region of approximately 120 amino acids that can bind Phosphatidylinositol lipids within biological membranes (such as Phosphatidylinositol (3,4,5)-trisphosphate and phosphatidylinositol (4,5)-bisphosphate), and proteins such as the βγ-subunits of heterotrimeric G proteins and protein kinase C. Through these... Ribbon diagram of the SH2 domain of human P56-Lck tyrosine kinase (PDB accession code 1LKK, chain A), colored from blue (N-terminus) to red (C-terminus). ... An SH3 domain is a protein module, a characteristic peptide sequence. ... A coiled coil is a structural motif found in many proteins. ... A helix bundle is a small protein fold composed of three or four alpha helices and held together by nonlocal hydrophobic interactions. ... An example of the globin fold, the oxygen-carrying protein myoglobin (PDB ID 1MBA) from the mollusc Aplysia limacina. ... Top view of a triosephosphateisomerase (TIM) barrel (PDB accession code 8TIM), colored from blue (N-terminus) to red (C-terminus). ... A simple Greek key design A Greek Key is a repeating design element used in architecture, jewelry and fabrics. ... An example of a leucine-rich repeat protein, a porcine ribonuclease inhibitor (PDB ID 2BNH). ... Ribbon diagram of the C-terminal WD40 domain of Tup1 (a transcriptional co-repressor in yeast), which adopts a 7-bladed beta-propeller fold. ... Structure of the 4th LIM of PINCH. Zinc atoms are shown in grey. ... The C2-domain of α-toxin (PDB 1OLP). ...


  Results from FactBites:
 
Zinc finger - Wikipedia, the free encyclopedia (401 words)
The zinc ion is crucial for the stability of this domain type - in absence of the metal ion the domain unfolds as it is too small to have a hydrophobic core.
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.
These proteins typically interact with the major groove along the double helix of DNA in which case the zinc fingers are arranged around the DNA strand in such a way that the α-helix of each finger contacts the DNA, forming an almost continuous stretch of α-helices around the DNA molecule.
Linus Pauling Institute at Oregon State University (3645 words)
Zinc finger proteins have been found to regulate gene expression by acting as transcription factors (binding to DNA and influencing the transcription of specific genes).
Since a sensitive indicator of zinc nutritional status is not readily available, the RDA for zinc was based on a number of different indicators of zinc nutritional status and represents the daily intake likely to prevent deficiency in nearly all individuals in a specific age and gender group (4).
Zinc bioavailability (the fraction of zinc retained and used by the body) is relatively high in meat, eggs, and seafood because of the relative absence of compounds that inhibit zinc absorption and the presence of certain amino acids (cysteine and methionine) that improve zinc absorption.
  More results at FactBites »


 

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