Ubiquitin 32167 216627391 2008-06-02T14:20:26Z Rabbitvalley 7002315 /* Ubiquitin derivatives */ Changed "proteins" to "enzymes" [[Image:Ubiquitin cartoon.png|thumb|280px|Ribbon representation of ubiquitin.]] [[Image:Ubiquitin surface.png|thumb|280px|Molecular surface of ubiquitin.]] '''Ubiquitin''' is a highly-conserved regulatory [[protein]] that is [[:wiktionary:ubiquitous|''ubiquitously'']] expressed in [[eukaryotes]]. '''Ubiquitination''' (or '''ubiquitylation''') refers to the [[post-translational modification]] of a protein by the [[covalent]] attachment (via an [[isopeptide bond]]) of one or more ubiquitin [[monomers]]. The most prominent function of ubiquitin is labeling proteins for [[proteasome|proteasomal]] degradation. Besides this function, ubiquitination also controls the stability, function, and intracellular localization of a wide variety of proteins. ==Identification== Ubiquitin (originally, '''Ubiquitous Immunopoietic Polypeptide''') was first identified in 1975 as an 8.5-[[Atomic mass unit|kDa]] protein of unknown function expressed universally in living cells. The basic functions of ubiquitin and the components of the ubiquitination pathway were elucidated in the early 1980s in groundbreaking work performed by [[Aaron Ciechanover]], [[Avram Hershko]], and [[Irwin Rose]] for which the [[Nobel Prize in Chemistry]] was awarded in [[2004]].<ref>{{ cite web | title = Official website of Nobel Prize Commitee, list of 2004 winners| url = http://nobelprize.org/nobel_prizes/lists/2004.html| accessdate = 04/30/2008}}</ref> The ubiquitylation system was initially characterised as an [[Adenosine triphosphate|ATP]]-dependent [[proteolytic]] system present in cellular extracts. A heat-stable [[Peptide|polypeptide]] present in these extracts, ATP-dependent proteolysis factor 1 (APF-1), was found to become covalently attached to the model protein [[Substrate (biochemistry)|substrate]] [[lysozyme]] in an [[Adenosine triphosphate|ATP]]- and [[Magnesium|Mg]]<sup>2+</sup>-dependent process. Multiple APF-1 molecules were linked to a single [[Substrate (biochemistry)|substrate]] molecule by an [[isopeptide]] linkage, and conjugates were found to be rapidly degraded with the release of free APF-1. Soon after APF-1-protein conjugation was characterised, APF-1 was identified as ubiquitin. The carboxyl group of the C-terminal glycine residue of ubiquitin (Gly76) was identified as the moiety conjugated to [[Substrate (biochemistry)|substrate]] [[lysine]] residues. == The protein == {| cellpadding=10 align=right |- | {| border="1" cellpadding="5" cellspacing="0" |+ '''Ubiquitin properties (human)''' |- | style="background:#6699CC" | Number of residues || style="background:#99CCFF" | 76 |- | style="background:#6699CC" | [[Molecular mass]] || style="background:#99CCFF" | 8564.47 [[dalton (unit)|Da]] |- | style="background:#6699CC" | [[Isoelectric point]] (pI) || style="background:#99CCFF" | 6.79 |- | style="background:#6699CC" | Gene names || style="background:#99CCFF" | RPS27A (UBA80, UBCEP1), UBA52 (UBCEP2), [[Ubiquitin B|UBB]], UBC |} |} '''Ubiquitin''' is a small [[protein]] that occurs in all [[eukaryote|eukaryotic]] [[cell (biology)|cell]]s. Its main known function is to mark other proteins for destruction, known as [[proteolysis]]. At least four ubiquitin molecules attach to a lysine residue on the condemned protein, in a process called [[polyubiquitination]], and the protein then moves to a [[proteasome]], a barrel-shaped structure where the proteolysis occurs. It is observed that at least four ubiquitins are required on a substrate protein in order for the proteasome to bind and therefore degrade the substrate, though there are examples of non-ubiquitinated proteins being targeted to the proteasome. Ubiquitin can also mark [[transmembrane protein]]s (for example, [[Receptor (biochemistry)|receptors]]) for removal from [[Biological membrane|membranes]] and fulfill several signaling roles within the cell. Monoubiquitination has been associated with targeting of membrane proteins to the lysosome, for example. Ubiquitin consists of 76 [[amino acid]]s and has a [[molecular mass]] of about 8.5 kDa. Key features include its C-terminal tail and the [[lysine|Lys]] residues. It is highly conserved among eukaryotic species: Human and yeast ubiquitin share 96% [[sequence identity]]. The human ubiquitin sequence is: MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG [[Image:Ubiquitylation.png|thumb|280px|The ubiquitylation system.]] == Ubiquitination (Ubiquitylation) == [[Image:1NBF-KGramatikoff.jpg|right|thumb|200px|Crystal structure of ubiquitin aldehyde (top right) and deubiquitinating enzyme in complex at resolution 2.3{{e|-10}}m (2.3Å)<ref>Hu, M., Li, P., Li, M., Li, W., Yao, T., Wu, J.-W., Gu, W., Cohen, R.E., Shi, Y. Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde. Cell (2002) 111, pp.1041-1054</ref>.]] The process of marking a protein with ubiquitin (ubiquitylation or ubiquitination) consists of a series of steps: # Activation of ubiquitin: Ubiquitin is activated in a two-step reaction by an E1 ubiquitin-activating enzyme in a process requiring [[Adenosine triphosphate|ATP]] as an energy source. The initial step involves production of a ubiquitin-adenylate intermediate. The second step transfers ubiquitin to the E1 [[active site]] [[cysteine]] residue, with release of [[Adenosine monophosphate|AMP]]. This step results in a thioester linkage between the C-terminal carboxyl group of ubiquitin and the E1 cysteine [[thiol|sulfhydryl group]]. # Transfer of ubiquitin from E1 to the [[active site]] cysteine of a [[ubiquitin-conjugating enzyme]] E2 via a trans(thio)esterification reaction. Mammalian genomes contain 20-30 UBCs. # The final step of the ubiquitylation cascade, in general, requires the activity of one of the hundreds of E3 ubiquitin-protein ligases (often termed simply [[ubiquitin ligase]]). E3 enzymes function as the [[Substrate (biochemistry)|substrate]] recognition modules of the system and are capable of interaction with both E2 and [[Substrate (biochemistry)|substrate]]. E3 enzymes possess one of two [[Protein domain|domains]]: #*The '''HECT''' (Homologous to the E6-AP Carboxyl Terminus) domain #*The '''[[RING finger domain|RING]]''' (Really Interesting New Gene) domain (or the closely-related '''U-box''' domain) : Transfer can occur in two ways: ::*Directly from E2, catalysed by RING domain E3s. ::*Via an E3 enzyme, catalysed by HECT domain E3s. In this case, a covalent E3-ubiquitin intermediate is formed before transfer of ubiquitin to the substrate protein. In many cases, ubiquitin molecules are further added on to previously-conjugated ubiquitin molecules to form a polyubiquitin chain. If the chain is longer than 3 ubiquitin molecules, the tagged protein is rapidly degraded by the 26S-[[proteasome]] into small [[peptide]]s (usually 3-24 [[amino acid]] residues in length). Ubiquitin moieties are cleaved off the protein by [[deubiquitinating enzyme]]s and are recycled for further use. Cell-surface transmembrane molecules that are tagged with ubiquitin are often monoubiquitinated, and this modification alters the subcellular localization of the protein, often targeting the protein for destruction in lysosomes. The [[Anaphase-promoting complex]] (APC) and the [[SCF complex]] (for Skp1-Cullin-F-box protein complex) are two examples of multi-[[Protein subunit|subunit]] E3s involved in recognition and ubiquitination of specific target proteins for degradation by the [[proteasome]]. == Disease association == Protein modification by ubiquitin also has unconventional (non-degradative) functions such as the regulation of DNA repair and endocytosis. These non-traditional functions are dictated by the number of ubiquitin units attached to proteins (mono- versus poly-ubiquitination) and also by the type of ubiquitin chain linkage that is present. As such, the Ubiquitin Proteasome Pathway has been linked to diseases involving all types of cellular activity including: * Antigen processing * Apoptosis * Biogenesis of organelles * Cell cycle and division * DNA transcription and repair * Differentiation and development * Immune response and inflammation * Neural and muscular degeneration * Morphogenesis of neural networks * Modulation of cell surface receptors, ion channels and the secretory pathway * Response to stress and extracellular modulators * Ribosome biogenesis * Viral infection <ref>{{ cite web | title = Ubiquitin Proteasome Pathway Overview| url = http://www.bostonbiochem.com/upp.php| accessdate = 04/30/2008}}</ref> === Genetic disorders === Some [[genetic disorders]] associated with ubiquitin are: * The gene whose disruption causes [[Angelman syndrome]], ''UBE3A'', encodes a ubiquitin ligase (E3) enzyme termed E6-AP. * The gene disrupted in [[Von Hippel-Lindau syndrome]] encodes a ubiquitin E3 ligase termed the VHL tumor suppressor or VHL gene. * The gene disrupted in [[Liddle's Syndrome]] results in disregulation of an epithelial Na+ channel (ENaC) and causes hypertension. * Eight of the thirteen identified genes whose disruption causes [[Fanconi anemia]] encode proteins that form a large ubiquitin ligase (E3) complex. * mutations of the [[Cullin7]] E3 ubiquitin ligase gene are linked to [[3-M syndrome]], an autosomal-recessive growth retardation disorder <ref>Huber C, Dias-Santagata D, Glaser A, O'Sullivan J, Brauner R, Wu K, Xu X, Pearce K, Wang R, Uzielli ML, Dagoneau N, Chemaitilly W, Superti-Furga A, Dos Santos H, Mégarbané A, Morin G, Gillessen-Kaesbach G, Hennekam R, Van der Burgt I, Black GC, Clayton PE, Read A, Le Merrer M, Scambler PJ, Munnich A, Pan ZQ, Winter R, Cormier-Daire V.Identification of mutations in CUL7 in 3-M syndrome.Nat Genet. 2005 Oct;37(10):1119-24.</ref> === Immunohistochemistry === [[antibody|Antibodies]] to ubiquitin are used in [[histology]] to identify abnormal accumulations of protein inside cells that are markers of disease. These accumulations are called inclusion bodies. Examples of such abnormal inclusions in cells are * [[Neurofibrillary tangle]]s in [[Alzheimer's disease]] * [[Lewy body]] in [[Parkinson's disease]] * [[Pick bodies]] in [[Pick's disease]] * Inclusions in [[motor neuron disease]] * [[Mallory's Hyalin]] in [[alcoholic liver disease]] * [[Rosenthal fibre]]s in [[astrocyte]]s ==Ubiquitin hydrolase== Human [[ubiquitin hydrolase]] has the most complicated [[knot theory|knot]] structure yet discovered for a protein, with five knot crossings. It is speculated that a knot structure increases a protein's resistance to degradation in the [[proteasome]].<ref>[http://www.sciencenews.org/articles/20061014/mathtrek.asp Knots in proteins], Science News, 14 Oct 2006</ref> ==Ubiquitin derivatives== Chemical modification of ubiquitin protein results in several useful derivatives. Modifying the C-terminal glycine carboxyl of ubiquitin to an aldehyde thus results in a highly potent inhibitor of de-ubiquitinating enzymes(also known as DUBs for "DeUBiquitinating enzymes"). Alternatively, a fluorogenic substrate for DUBs is generated by synthetically conjugating AMC to the C-terminus of ubiquitin. In addition, reductive methylation of the amine groups prevents the formation of poly-ubiquitin chains via lysine linkages. Ubiquitin can also be coupled to agarose via its primary amines, leaving the C-terminus free and available to purify ubiquitin binding proteins.<ref>{{ cite web | title = Boston Biochem Ubiquitin and Ubiquitin Derivatives Overview| url = http://www.bostonbiochem.com/overview.php?prod=ubderiv| accessdate = 04/30/2008}}</ref> * Ubiquitin Aldehyde - A potent and specific inhibitor of all ubiquitin C-terminal hydrolases (UCHs), ubiquitin-specific proteases (USPs) and deubiquinating enzymes (DUBs). This protein blocks the hydrolysis of poly-ubiquitin chains on substrate proteins in vitro and thus enhances poly-ubiquitin chain accumulation.<ref>{{ cite web | title = Boston Biochem Material Data Sheet: Ubiqutin Aldehyde| url = http://www.bostonbiochem.com/datasheets/Ubiquitin%20and%20derivatives/201_UbH.pdf| accessdate = 04/30/2008}}</ref> * Methylated Ubiquitin - Reductive methylation of lysine residues renders ubiquitin unable to form poly-ubiquitin chains via lysine linkages with other Ub molecules. Methylated Ub can form an E1-catalyzed active thioester at the C-terminus allowing the molecule to be transferred to the lysines of substrate proteins (which can be mono-ubiquitinated). Ideal for the reduction in poly-ubiquitin chain length and rates of ubiquitin conjugation.<ref>{{ cite web | title = Boston Biochem Material Data Sheet: Methylated Ubiquitin| url = http://www.bostonbiochem.com/datasheets/Ubiquitin%20and%20derivatives/501_methUb.pdf| accessdate = 04/30/2008}}</ref> * Ubiquitin AMC - Fluorogenic substrate for ubiquitin hydrolases based on the C-terminus derivatization of ubiquitin with 7-amido-4-methylcoumarin (AMC). Ubiquitin-AMC is an exquisitely sensitive substrate for UCH-L3 (Km = 0.039 μM) and for the Isopeptidase-T (Km = 0.17 - 1.4 μM). Ub-AMC is useful for studying ubiquitin hydrolases when detection sensitivity or continuous monitoring of activity is essential.<ref>{{ cite web | title = Boston Biochem Material Data Sheet: Ubiquitin AMC| url = http://www.bostonbiochem.com/datasheets/Ubiquitin%20and%20derivatives/550_UbAMC.pdf| accessdate = 04/30/2008}}</ref> * Ubiquitin Vinyl Sulfone - A potent, irreversible and specific inhibitor of all ubiquitin C-terminal hydrolases (UCHs), ubiquitin-specific proteases (USPs) and deubiquitinating enzymes (DUBs). Useful for inhibiting the hydrolysis of poly-ubiquitin chains on substrate proteins in vitro and thus enhances polyubiquitin chain accumulation.<ref>{{ cite web | title = Boston Biochem Material Data Sheet: Ubiqutin Vinyl Sulfone| url = http://www.bostonbiochem.com/datasheets/Ubiquitin%20and%20derivatives/U202_Ub%20VS.pdf| accessdate = 04/30/2008}}</ref> ==Ubiquitin-like Modifiers== Although ubiquitin is the most well understood post-translation modifier, there is a growing family of ubiquitin-like proteins (UBLs) that modify cellular targets in a pathway that is parallel to but distinct from that of ubiquitin. These alternative modifiers include: [[SUMO protein | SUMO]] (Sentrin, Smt3 in yeast), [[NEDD8]] (Rub1 in yeast), [[ISG15]] (UCRP), [[APG8]], [[APG12]], [[FAT10]], [[Ufm1]] URM1 & [[Hub1]]. These related molecules have novel functions and influence diverse biological processes. There is also cross-regulation between the various conjugation pathways since some proteins can become modified by more than one UBL, and sometimes even at the same lysine residue. For instance, SUMO modification often acts antagonistically to that of ubiquitination and serves to stabilize protein substrates. Proteins conjugated to UBLs are typically not targeted for degradation by the proteasome, but rather function in diverse regulatory activities. Attachment of UBLs might alter substrate conformation, affect the affinity for ligands or other interacting molecules, alter substrate localization and influence protein stability. UBLs are structurally similar to ubiquitin and are processed, activated, conjugated and released from conjugates by enzymatic steps that are similar to the corresponding mechanisms for ubiquitin. UBLs are also translated with C-terminal extensions that are processed to expose the invariant C-terminal LRGG. These modifiers have their own specific E1 (activating), E2 (conjugating) and E3 (ligating) enzymes that conjugate the UBLs to intracellular targets. These conjugates can be reversed by UBL-specific isopeptidases that have similar mechanisms to that of the deubiquitinating enzymes.<ref>{{ cite web | title = Ubiquitin Proteasome Pathway Overview| url = http://www.bostonbiochem.com/upp.php| accessdate = 04/30/2008}}</ref> ==References== {{Reflist}} ==See also== *[[Autophagy]] *[[Autophagin]] *[[ERAD]] *[[SUMO protein]] *[[SUMO enzymes]] *[[SUMO network]] *[[Autophagy network]] *[[Ubiquitin ligase]] Note: Ubiquitin is also used to mark paternal mitochondria for destruction during human fertilization. ==External links== *[http://www.BostonBiochem.com Boston Biochem] : Ubiquitin Proteasome System Research and Reagents *[http://www.bostonbiochem.com/upppub.php UPP Reference Lit] : Ubiquitin Proteasome Pathway research paper reference literature list *[http://www.invitrogen.com/ubiquitin Invitrogen] : Drug discovery assays * [http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinAc=P62988 UniProt entry for ubiquitin]. * {{MeshName|Ubiquitin}} *[http://www.progenra.com Progenra Inc.] : Ubiquitin-based Biotechnology Corporation *[http://stud.chem.uni.wroc.pl/users/lucek/JAREMKO/ubiquitin.htm Ubiquitin Web-page] ==Further reading== * Essays in Biochemistry, Volume 41 (2005): The Ubiquitin-Proteasome System (Portland Press) {{Protein posttranslational modification}} [[Category:Proteins]] [[Category:Posttranslational modification]] [[zh-min-nan:Ubiquitin]] [[bg:Убиквитин]] [[ca:Ubiquitina]] [[de:Ubiquitin]] [[el:Ουβικουιτίνη]] [[es:Ubiquitina]] [[eo:Ubikvitino]] [[fr:Ubiquitine]] [[ko:유비퀴틴]] [[it:Ubiquitina]] [[he:אוביקוויטין]] [[ja:ユビキチン]] [[pl:Ubikwityna]] [[pt:Ubiquitina]] [[sl:Ubikvitin]] [[sv:Ubiquitin]] [[uk:Убіквітин]] [[zh:泛素]]