Zinc Finger

Information about 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.

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.

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.

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-X_2-4-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.

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.

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

• • [ e] 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

citation, footnoting or external linking.

A structural domain is an element of overall structure within a protein that is self-stabilizing and often folds independently of the rest of the protein chain.
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alpha helix (α-helix) is a right-handed coiled conformation, resembling a spring, in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier ( hydrogen bonding). (See also helix.
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Zinc (IPA: /ˈzɪŋk/, from German: Zink) is a chemical element in the periodic table that has the symbol Zn and atomic number 30.
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Cysteine (abbreviated as Cys or C)^[1] is an α-amino acid with the chemical formula HO₂CCH(NH₂)CH₂SH. It is not an essential amino acid, which means that humans can synthesize it. Its codons are UGU and UGC.
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Histidine (abbreviated as His or H)^[1] is one of the 20 most common natural amino acids present in proteins. In the nutritional sense, in humans, histidine is considered an essential amino acid, but mostly only in children.
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Zinc (IPA: /ˈzɪŋk/, from German: Zink) is a chemical element in the periodic table that has the symbol Zn and atomic number 30.
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This article or section may be confusing or unclear for some readers.
Please [improve the article] or discuss this issue on the talk page. This article has been tagged since December 2006.
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Zif268 is a mammalian transcription factor that is now officially known as Egr1 (Early Growth Response Protein 1). It was also named Krox-24, NGFI-A, TIS8, and ZENK. It was originally discovered in mouse.
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A helix (pl: helices), from the Greek word έλικας/έλιξ
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Zinc finger inhibition is the process by which the synthesis of zinc fingers is blocked. Zinc finger inhibitors have been tested for their efficacy in treating AIDS and HIV.
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Steroid hormone receptors are intracellular receptors (typically cytoplasmic) that perform signal transduction for steroid hormones. Steroid hormone receptors are part of the nuclear receptor family that include a group of homologous structured receptors (type II receptors) that
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citation, footnoting or external linking.

Basic Leucine Zipper Domain (bZIP domain) is found in many DNA binding eukaryotic proteins. One part of the domain contains a region that mediates sequence specific DNA binding properties and the Leucine zipper that is required for the dimerization of two DNA binding regions.
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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).
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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
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Src homology 2 domain (or SH2 domain) is a protein domain of about 100 amino acid residues first identified as a conserved sequence region among the oncoproteins Src and Fps.
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Src homology 3 domain (or SH3 domain) is a small protein domain of about 60 amino acid residues first identified as a conserved sequence in the non-catalytic part of several cytoplasmic tyrosine kinases such as Abl and Src and it has been then identified in several other
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coiled coil is a structural motif in proteins, in which 2-7^[1] alpha-helices are coiled together like the strands of a rope (Dimers and trimers are the most common types).
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A helix bundle is a small protein fold composed of three or four alpha helices and held together by nonlocal hydrophobic interactions.

Three-helix bundles

Three-helix bundles are among the smallest and fastest known cooperatively folding structural domains.
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globin fold is a common three-dimensional fold in proteins. This fold typically consists of eight alpha helices, although some proteins have additional helix extensions at their termini.
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TIM barrel is a conserved protein fold consisting of eight α-helices and eight parallel β-strands that alternate along the peptide backbone. The structure is named after triosephosphateisomerase, a conserved glycolytic enzyme.
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Greek key refers to a kind of supersecondary structure or motif of a protein (amino-acid) sequence. It is named for its resemblance to the Greek key meander pattern in art.
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leucine-rich repeat (LRR) is a protein structural motif that forms an α/β horseshoe fold. It is composed of repeating 20-30 amino acid stretches that are unusually rich in the hydrophobic amino acid leucine.
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beta-propeller domain is an all-β protein fold characterized by 4-8 blade-shaped beta sheets arranged toroidally around a central axis. Each sheet typically has four antiparallel β-strands twisted so that the first and fourth sheets are almost perpendicular to each other.
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'LIM domains' are protein structural domains, comprised of two contiguous zinc finger domains, separated by a two-amino acid residue hydrophobic linker. They are named after their initial discovery in the proteins Lin11, Isl-1 & Mec-3 ^[1].
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C2 domain is a protein structural domain involved in targeting proteins to cell membranes. It is composed of 8 β-sheets, forming a beta-sandwich motif, and co-ordinates 2 or 3 calcium ions, which bind in an indentation formed by the first and final loops of the domain, on the
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