Structural domain: Difference between revisions
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Within a [[protein]], a '''structural domain''' ("domain") is an element of [[tertiary structure|overall structure]] that is self-stabilizing and often [[protein folding|folds]] independently of the rest of the protein chain. Many domains are not unique to the protein products of one [[gene]] or one [[gene family]] but instead appear in a variety of proteins. Domains often are named and singled out because they figure prominently in the biological function of the protein they belong to; for example, the "calcium-binding" domain of [[calmodulin]]. Because they are self-stabilizing, domains can be "swapped" by [[genetic engineering]] between one protein and another to make [[chimera (protein)|chimera]]s. A domain may be composed of one, more than one or not any [[structural motif]]s. |
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An important tool in the determination of ''domains'' is [[structural alignment]] and [[sequence alignment]]. |
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==Examples of protein structural domains== |
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*'''[[Arginine Finger]]''' |
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* '''[[Armadillo repeats]].''' Named after the β-catenin-like Armadillo protein of the fruit fly ''[[Drosophila melanogaster|Drosophila]]''. These domains are about 40 amino acids long and proteins that contain them often have many tandemly repeated domains. β-catenin is a protein involved in linking cadherin cell adhesion proteins to the [[cytoskeleton]]. This type of protein domain is important in transducing WNT signals during [[Developmental biology|embryonic development]]. |
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*'''Basic Leucine zipper domain (bZIP domain)''' The [[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. The DNA binding region comprises a number of basic aminoacids such as [[arginine]] and [[lysine]] |
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* '''[[Cadherin repeats]]'''. Cadherins function as Ca<sup>2+</sup>-dependent cell-cell [[cell adhesion|adhesion]] proteins. Cadherin domains are extracellular regions which mediate cell-to-cell homophilic binding between cadherins on the surface of adjacent cells. |
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* '''[[Death effector domain]]''' (DED). DED allows protein-protein binding by homotypic interactions (DED-DED). [[Caspase]] [[protease]]s trigger [[apoptosis]] via proteolytic cascades. Pro-Caspase-8 and pro-caspase-9 bind to specific adaptor molecules via DED domains and this leads to autoactivation of caspases. |
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* '''[[Phosphotyrosine-binding domain]]''' (PTB). PTB domains usually bind to phosphorylated tyrosine residues. They are often found in signal transduction proteins. PTB-domain binding specificity is determined by residues to the amino-terminal side of the phosphotyrosine. Examples: the PTB domains of both SHC and IRS-1 bind to a NPXpY sequence. PTB-containing proteins such as SHC and IRS-1 are important for [[insulin]] responses of human cells. |
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* '''[[Pleckstrin homology domain]]''' (PH). PH domains bind phosphoinositides with high affinity. Specificity for PtdIns(3)P, PtdIns(4)P, PtdIns(3,4)P2, PtdIns(4,5)P2, and PtdIns(3,4,5)P3 have all been observed. Given the fact that phosphoinositides are sequestered to various cell membranes (due to their long lipophilic tail) the PH domains usually cause localization of the protein in question to one or another cell membrane, which is useful for expediting activation of the protein and continuation of a signaling pathway. A large number of PH domains have poor affinity for phosphoinositides and are hypothesized to function as protein binding domains. |
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* '''[[Src homology 2 domain]]''' (SH2). SH2 domains are often found in signal transduction proteins. SH2 domains confer binding to phosphorylated tyrosine (pTyr). Named after the phosphotyrosine binding domain of the src viral [[oncogene]], which is itself a [[tyrosine kinase]]. ''See also'': [[SH3 domain]]. |
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* '''[[Zinc finger|Zinc finger DNA binding domain]]''' (ZnF_GATA). ZnF_GATA domain-containing proteins are typically [[transcription factor]]s that usually bind to the DNA sequence [AT]GATA[AG] of [[promoter]]s. |
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==See also== |
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*[[structural biology]] |
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==External links== |
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*The Protein Families (Pfam) database [http://www.sanger.ac.uk//Software/Pfam/browse/clans.shtml#159 clan browser] provides easy access to information about protein structural domains. A clan contains two or more '''Pfam''' families that have arisen from a single evolutionary origin. |
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=== Domain databases === |
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* [http://www.ncbi.nlm.nih.gov:80/Structure/cdd/cdd.shtml NCBI Conserved Domain Database] |
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* [http://www.sanger.ac.uk/Software/Pfam/ Pfam Domain Database] |
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* [http://smart.embl-heidelberg.de/ SMART Domain Database] |
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{{Protein domains}} |
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{{Template:Protein topics}} |
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[[Category:Protein structure]] |
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[[Category:Protein domains]] |
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[[pl:Domena białka]] |
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[[zh:结构域]] |
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Latest revision as of 18:31, 3 April 2008
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