)
Structure of the 4th LIM of PINCH. Zinc atoms are shown in grey.
LIM domains have highly divergent sequences, apart from certain key residues. The sequence divergence allow a great many different binding sites to be grafted onto the same basic domain. The conserved residues are those involved in zinc binding or the hydrophobic core of the protein. The sequence signature of LIM domains are as follows:
[C]-[X]2-4-[C]-[X]13-19-[W]-[H]-[X]2-4-[C]-[F]-[LVI]-[C]-[X]2-4-[C]-[X]13-20-C-[X]2-4-[C]
)
Lim domain organsiation
LIM domains frequently occur in multiples, as seen in proteins such as TES, LMO4, and can also be attached to other domains in order to confer a binding or targeting function upon them, such as LIM-kinase.
References
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 |
Proteins are large organic compounds made of amino acids arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues.
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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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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
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amino acid is a molecule that contains both amine and carboxyl functional groups. In biochemistry, this term refers to alpha-amino acids with the general formula H2NCHRCOOH, where R is an organic substituent.
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hydrophobicity (from the combining form of water in Attic Greek hydro- and for fear phobos) refers to the physical property of a molecule (known as a hydrophobe) that is repelled from a mass of water [1].
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cytoskeleton is a cellular "scaffolding" or "skeleton" contained, as all other organelles, within the cytoplasm. It is contained in all eukaryotic cells and recent research has shown it can be present in prokaryotic cells too.
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An oncogenic process is any tumor-forming process. Oncovirinae, retroviruses which contain an onc gene, are categorized as such because they trigger the growth of tumorous tissues in the host. Oncogenesis is the process of malignant tumor growth.
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Protein-protein interactions refer to the association of protein molecules and the study of these associations from the perspective of biochemistry, signal transduction and networks.
The interactions between proteins are important for many biological functions.
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The interactions between proteins are important for many biological functions.
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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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hydrophobicity (from the combining form of water in Attic Greek hydro- and for fear phobos) refers to the physical property of a molecule (known as a hydrophobe) that is repelled from a mass of water [1].
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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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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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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
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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.
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Three-helix bundles
Three-helix bundles are among the smallest and fastest known cooperatively folding structural domains...... Click the link for more information.
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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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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