View source for Ubiquitin

{{Short description|Regulatory protein found in most eukaryotic tissues}}
{{cs1 config|name-list-style=vanc|display-authors=6}}
{{Distinguish|Ubiquinol}}
{{Infobox protein family
| Symbol = ubiquitin
| Name = Ubiquitin family
| image = Ubiquitin cartoon-2-.png
| width =
| caption = '''A diagram of ubiquitin'''. The seven lysine sidechains are shown in yellow/orange.
| Pfam= PF00240
| InterPro= IPR000626
| SMART=
| Prosite = PDOC00271
| SCOP = 1aar
| TCDB =
| OPM family=
| OPM protein=
}}
'''Ubiquitin''' is a small ({{val|8.6|ul=kDa}}) [[regulatory protein]] found in most tissues of [[eukaryotes|eukaryotic]] organisms, i.e., it is found [[:wiktionary:ubiquitous|''ubiquitously'']]. It was discovered in 1975<ref name="pmid1078892"/> by [[Gideon Goldstein]] and further characterized throughout the late 1970s and 1980s.<ref name="pmid16230621">{{cite journal | vauthors = Wilkinson KD | title = The discovery of ubiquitin-dependent proteolysis | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 102 | issue = 43 | pages = 15280–2 | date = October 2005 | pmid = 16230621 | pmc = 1266097 | doi = 10.1073/pnas.0504842102 | bibcode = 2005PNAS..10215280W | doi-access = free }}</ref> Four genes in the [[human genome]] code for ubiquitin: [[Ubiquitin B|UBB]], [[Ubiquitin C|UBC]], [[Ubiquitin A-52 residue ribosomal protein fusion product 1|UBA52]] and [[RPS27A]].<ref name="pmid20418328"/>

The addition of ubiquitin to a substrate protein is called '''ubiquitylation''' (or '''ubiquitination''' or '''ubiquitinylation'''). Ubiquitylation affects proteins in many ways: it can mark them for [[protein degradation|degradation]] via the 26S [[proteasome]], alter their [[Subcellular localization|cellular location]], affect their activity, and promote or prevent [[protein–protein interaction|protein interactions]].<ref name="pmid11917093"/><ref name="pmid17218518"/><ref name="pmid12860974"/> Ubiquitylation involves three main steps: activation, conjugation, and ligation, performed by [[ubiquitin-activating enzyme]]s (E1s), [[ubiquitin-conjugating enzyme]]s (E2s), and [[ubiquitin ligase]]s (E3s), respectively. The result of this sequential cascade is to bind ubiquitin to [[lysine]] residues on the protein substrate via an [[isopeptide bond]], [[cysteine]] residues through a [[Thioester|thioester bond]]; [[serine]], [[threonine]], and tyrosine residues through an [[Ester|ester bond]]; or the amino group of the protein's [[N-terminus]] via a [[peptide bond]].<ref name="pmid15571809"/><ref name="pmid22524316"/><ref name="McDowell_2013" /><ref>{{cite journal | vauthors = Shen S, Yin H | title = E2-Ub-R74G strategy reveals E2-specific ubiquitin conjugation profiles in live cells | journal = Nature Chemical Biology | date = January 2025 | pmid = 39762535 | doi = 10.1038/s41589-024-01809-9 }}</ref>

The protein modifications can be either a single ubiquitin protein (monoubiquitylation) or a chain of ubiquitin (polyubiquitylation). Secondary ubiquitin molecules are always linked to one of the seven [[lysine]] residues or the N-terminal [[methionine]] of the previous ubiquitin molecule. These 'linking' residues are represented by a "K" or "M" (the [[one-letter amino acid notation]] of lysine and methionine, respectively) and a number, referring to its position in the ubiquitin molecule as in K48, K29 or M1. The first ubiquitin molecule is covalently bound through its [[C-terminal]] carboxylate group to a particular lysine, cysteine, serine, threonine or N-terminus of the target protein. Polyubiquitylation occurs when the C-terminus of another ubiquitin is linked to one of the seven lysine residues or the first methionine on the previously added ubiquitin molecule, creating a chain. This process repeats several times, leading to the addition of several ubiquitins. Only polyubiquitylation on defined lysines, mostly on K48 and K29, is related to degradation by the [[proteasome]] (referred to as the "molecular kiss of death"), while other polyubiquitylations (e.g. on K63, K11, K6 and M1) and monoubiquitylations may regulate processes such as [[endocytosis|endocytic trafficking]], [[inflammation]], [[translation (biology)|translation]] and [[DNA repair]].<ref name="pmid17609522"/>

The discovery that ubiquitin chains target proteins to the proteasome, which degrades and recycles proteins, was honored with the [[Nobel Prize in Chemistry]] in 2004.<ref name="pmid22524316"/><ref name="urlThe Nobel Prize in Chemistry 2004">{{cite web | url = http://nobelprize.org/nobel_prizes/chemistry/laureates/2004/ | title = The Nobel Prize in Chemistry 2004 | publisher = Nobelprize.org | access-date = 2010-10-16 }}</ref><ref name="urlPopular Information">{{
cite web | url = https://www.nobelprize.org/nobel_prizes/chemistry/laureates/2004/popular.html | title = The Nobel Prize in Chemistry 2004: Popular Information | publisher =  Nobelprize.org | access-date = 2013-12-14 }}</ref>

== Identification ==
[[Image:Ubiquitin 1UBQ surface.png|thumb|220px|Surface representation of ubiquitin]]
Ubiquitin (originally, '''ubiquitous immunopoietic polypeptide''') was first identified in 1975<ref name="pmid1078892">{{cite journal | vauthors = Goldstein G, Scheid M, Hammerling U, Schlesinger DH, Niall HD, Boyse EA | title = Isolation of a polypeptide that has lymphocyte-differentiating properties and is probably represented universally in living cells | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 72 | issue = 1 | pages = 11–5 | date = January 1975 | pmid = 1078892 | pmc = 432229 | doi = 10.1073/pnas.72.1.11 | bibcode = 1975PNAS...72...11G | doi-access = free }}</ref> as an {{val|8.6|ul=kDa}} protein expressed in all [[eukaryote|eukaryotic]] cells. The basic functions of ubiquitin and the components of the ubiquitylation pathway were elucidated in the early 1980s at the [[Technion]] by [[Aaron Ciechanover]], [[Avram Hershko]], and [[Irwin Rose]] for which the [[Nobel Prize in Chemistry]] was awarded in 2004.<ref name="urlThe Nobel Prize in Chemistry 2004"/>

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 [[lysozyme]] in an [[Adenosine triphosphate|ATP]]- and [[Magnesium|Mg]]<sup>2+</sup>-dependent process.<ref name="pmid22925675">{{cite journal | vauthors = Ciechanover A, Hod Y, Hershko A | title = A heat-stable polypeptide component of an ATP-dependent proteolytic system from reticulocytes. 1978 | journal = Biochemical and Biophysical Research Communications | volume = 425 | issue = 3 | pages = 565–70 | date = August 2012 | pmid = 22925675 | doi = 10.1016/j.bbrc.2012.08.025 }}</ref> 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 [[lysine]] residues.

== The protein ==
{| class=wikitable align=right style=clear:right
|+ Ubiquitin properties (human)
|-
! scope=row | Number of residues
| 76
|-
! scope=row | [[Molecular mass]]
| 8564.8448 [[dalton (unit)|Da]]
|-
! scope=row | [[Isoelectric point]] (pI)
| 6.79
|-
! scope=row |Gene names
| [[RPS27A]] (UBA80, UBCEP1), [[UBA52]] (UBCEP2), [[Ubiquitin B|UBB]], [[Ubiquitin C|UBC]]
|-
! scope=row |Sequence ([[Amino acid#Table of standard amino acid abbreviations and properties|single-letter]])
| {{monodiv|MQIFV'''K'''TLTG'''K'''TITLEVEPSDTIENV'''K'''A'''K'''IQD'''K'''EGIPPD
QQRLIFAG'''K'''QLEDGRTLSDYNIQ'''K'''ESTLHLVLRLRGG}}
|}

Ubiquitin is a small [[protein]] that exists in all [[eukaryote|eukaryotic]] [[cell (biology)|cell]]s. It performs its myriad functions through conjugation to a large range of target proteins. A variety of [[#Function|different modifications]] can occur. The ubiquitin protein itself consists of 76 [[amino acid]]s and has a [[molecular mass]] of about 8.6&nbsp;kDa. Key features include its C-terminal tail and the 7 [[lysine]] residues. It is highly conserved throughout eukaryote evolution; human and yeast ubiquitin share 96% [[sequence identity]].<ref>{{cite journal | vauthors = Sharp PM, Li WH | title = Molecular evolution of ubiquitin genes | journal = Trends in Ecology & Evolution | volume = 2 | issue = 11 | pages = 328–332 | date = November 1987 | pmid = 21227875 | doi = 10.1016/0169-5347(87)90108-X | bibcode = 1987TEcoE...2..328S }}</ref>

== Genes ==

Ubiquitin is encoded in mammals by four different genes. [[Ubiquitin A-52 residue ribosomal protein fusion product 1|UBA52]] and [[RPS27A]] genes code for a single copy of ubiquitin fused to the [[Ubiquitin A-52 residue ribosomal protein fusion product 1|ribosomal proteins L40]] and [[40S ribosomal protein S27a|S27a]], respectively. The [[Ubiquitin B|UBB]] and [[Ubiquitin C|UBC]] genes code for polyubiquitin precursor proteins.<ref name="pmid20418328">{{cite journal | vauthors = Kimura Y, Tanaka K | title = Regulatory mechanisms involved in the control of ubiquitin homeostasis | journal = Journal of Biochemistry | volume = 147 | issue = 6 | pages = 793–8 | date = June 2010 | pmid = 20418328 | doi = 10.1093/jb/mvq044 | doi-access = free }}</ref>

== Ubiquitylation ==

[[Image:Ubiquitylation.svg|thumb|right|300px|The ubiquitylation system (showing a RING E3 ligase)]]

Ubiquitylation (also known as ubiquitination or ubiquitinylation) is an enzymatic [[post-translational modification]] in which an ubiquitin protein is attached to a [[Enzyme substrate (biology)|substrate protein]]. This process most commonly binds the last [[amino acid]] of ubiquitin ([[glycine]] 76) to a [[lysine]] residue on the substrate. An [[isopeptide bond]] is formed between the [[carboxylic acid|carboxyl]] group (COO<sup>−</sup>) of the ubiquitin's glycine and the epsilon-[[amine|amino group]] (ε-{{chem|NH|3|+}}) of the substrate's lysine.<ref name="pmid11395416">{{cite journal | vauthors = Pickart CM | title = Mechanisms underlying ubiquitylation | journal = Annual Review of Biochemistry | volume = 70 | pages = 503–33 | year = 2001 | pmid = 11395416 | doi = 10.1146/annurev.biochem.70.1.503 }}</ref> Trypsin cleavage of a ubiquitin-conjugated substrate leaves a di-glycine "remnant" that is used to identify the site of ubiquitylation.<ref name="pmid 11955054">{{cite journal | vauthors = Marotti LA, Newitt R, Wang Y, Aebersold R, Dohlman HG | title = Direct identification of a G protein ubiquitylation site by mass spectrometry | journal = Biochemistry | volume = 41 | issue = 16 | pages = 5067–74 | date = April 2002 | pmid = 11955054 | doi = 10.1021/bi015940q }}</ref><ref name="pmid12872131">{{cite journal | vauthors = Peng J, Schwartz D, Elias JE, Thoreen CC, Cheng D, Marsischky G, Roelofs J, Finley D, Gygi SP | title = A proteomics approach to understanding protein ubiquitylation | journal = Nature Biotechnology | volume = 21 | issue = 8 | pages = 921–6 | date = August 2003 | pmid = 12872131 | doi = 10.1038/nbt849 | s2cid = 11992443 }}</ref> Ubiquitin can also be bound to other sites in a protein which are electron-rich [[nucleophile]]s, termed "non-canonical ubiquitylation".<ref name="McDowell_2013">{{cite journal | vauthors = McDowell GS, Philpott A | title = Non-canonical ubiquitylation: mechanisms and consequences | journal = The International Journal of Biochemistry & Cell Biology | volume = 45 | issue = 8 | pages = 1833–42 | date = August 2013 | pmid = 23732108 | doi = 10.1016/j.biocel.2013.05.026 | doi-access = free }}</ref> This was first observed with the [[amine group]] of a protein's [[N-terminus]] being used for ubiquitylation, rather than a lysine residue, in the protein [[MyoD]]<ref name="pmid9774340">{{cite journal | vauthors = Breitschopf K, Bengal E, Ziv T, Admon A, Ciechanover A | title = A novel site for ubiquitylation: the N-terminal residue, and not internal lysines of MyoD, is essential for conjugation and degradation of the protein | journal = The EMBO Journal | volume = 17 | issue = 20 | pages = 5964–73 | date = October 1998 | pmid = 9774340 | pmc = 1170923 | doi = 10.1093/emboj/17.20.5964 }}</ref> and has been observed since in 22 other proteins in multiple species,<ref name="pmid14532004">{{cite journal | vauthors = Bloom J, Amador V, Bartolini F, DeMartino G, Pagano M | title = Proteasome-mediated degradation of p21 via N-terminal ubiquitinylation | journal = Cell | volume = 115 | issue = 1 | pages = 71–82 | date = October 2003 | pmid = 14532004 | doi = 10.1016/S0092-8674(03)00755-4 | s2cid = 15114828 | doi-access = free }}</ref><ref name="pmid23696636">{{cite journal | vauthors = Scaglione KM, Basrur V, Ashraf NS, Konen JR, Elenitoba-Johnson KS, Todi SV, Paulson HL | title = The ubiquitin-conjugating enzyme (E2) Ube2w ubiquitinates the N terminus of substrates | journal = The Journal of Biological Chemistry | volume = 288 | issue = 26 | pages = 18784–8 | date = June 2013 | pmid = 23696636 | pmc = 3696654 | doi = 10.1074/jbc.C113.477596 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Sadeh R, Breitschopf K, Bercovich B, Zoabi M, Kravtsova-Ivantsiv Y, Kornitzer D, Schwartz A, Ciechanover A | title = The N-terminal domain of MyoD is necessary and sufficient for its nuclear localization-dependent degradation by the ubiquitin system | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 105 | issue = 41 | pages = 15690–5 | date = October 2008 | pmid = 18836078 | pmc = 2560994 | doi = 10.1073/pnas.0808373105 | bibcode = 2008PNAS..10515690S | doi-access = free }}</ref><ref>{{cite journal | vauthors = Coulombe P, Rodier G, Bonneil E, Thibault P, Meloche S | title = N-Terminal ubiquitylation of extracellular signal-regulated kinase 3 and p21 directs their degradation by the proteasome | journal = Molecular and Cellular Biology | volume = 24 | issue = 14 | pages = 6140–50 | date = July 2004 | pmid = 15226418 | pmc = 434260 | doi = 10.1128/MCB.24.14.6140-6150.2004 }}</ref><ref>{{cite journal | vauthors = Kuo ML, den Besten W, Bertwistle D, Roussel MF, Sherr CJ | title = N-terminal polyubiquitylation and degradation of the Arf tumor suppressor | journal = Genes & Development | volume = 18 | issue = 15 | pages = 1862–74 | date = August 2004 | pmid = 15289458 | pmc = 517406 | doi = 10.1101/gad.1213904 }}</ref><ref>{{cite journal | vauthors = Ben-Saadon R, Fajerman I, Ziv T, Hellman U, Schwartz AL, Ciechanover A | title = The tumor suppressor protein p16(INK4a) and the human papillomavirus oncoprotein-58 E7 are naturally occurring lysine-less proteins that are degraded by the ubiquitin system. Direct evidence for ubiquitylation at the N-terminal residue | journal = The Journal of Biological Chemistry | volume = 279 | issue = 40 | pages = 41414–21 | date = October 2004 | pmid = 15254040 | doi = 10.1074/jbc.M407201200 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Li H, Okamoto K, Peart MJ, Prives C | title = Lysine-independent turnover of cyclin G1 can be stabilized by B'alpha subunits of protein phosphatase 2A | journal = Molecular and Cellular Biology | volume = 29 | issue = 3 | pages = 919–28 | date = February 2009 | pmid = 18981217 | pmc = 2630686 | doi = 10.1128/MCB.00907-08 }}</ref><ref>{{cite journal | vauthors = Reinstein E, Scheffner M, Oren M, Ciechanover A, Schwartz A | title = Degradation of the E7 human papillomavirus oncoprotein by the ubiquitin-proteasome system: targeting via ubiquitylation of the N-terminal residue | journal = Oncogene | volume = 19 | issue = 51 | pages = 5944–50 | date = November 2000 | pmid = 11127826 | doi = 10.1038/sj.onc.1203989 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Aviel S, Winberg G, Massucci M, Ciechanover A | title = Degradation of the epstein-barr virus latent membrane protein 1 (LMP1) by the ubiquitin-proteasome pathway. Targeting via ubiquitylation of the N-terminal residue | journal = The Journal of Biological Chemistry | volume = 275 | issue = 31 | pages = 23491–9 | date = August 2000 | pmid = 10807912 | doi = 10.1074/jbc.M002052200 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Ikeda M, Ikeda A, Longnecker R | title = Lysine-independent ubiquitylation of Epstein-Barr virus LMP2A | journal = Virology | volume = 300 | issue = 1 | pages = 153–9 | date = August 2002 | pmid = 12202215 | doi = 10.1006/viro.2002.1562 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Yang J, Hong Y, Wang W, Wu W, Chi Y, Zong H, Kong X, Wei Y, Yun X, Cheng C, Chen K, Gu J | title = HSP70 protects BCL2L12 and BCL2L12A from N-terminal ubiquitylation-mediated proteasomal degradation | journal = FEBS Letters | volume = 583 | issue = 9 | pages = 1409–14 | date = May 2009 | pmid = 19376117 | doi = 10.1016/j.febslet.2009.04.011 | s2cid = 32330510 | doi-access = free | bibcode = 2009FEBSL.583.1409Y }}</ref><ref>{{cite journal | vauthors = Wang Y, Shao Q, Yu X, Kong W, Hildreth JE, Liu B | title = N-terminal hemagglutinin tag renders lysine-deficient APOBEC3G resistant to HIV-1 Vif-induced degradation by reduced polyubiquitylation | journal = Journal of Virology | volume = 85 | issue = 9 | pages = 4510–9 | date = May 2011 | pmid = 21345952 | pmc = 3126286 | doi = 10.1128/JVI.01925-10 }}</ref><ref>{{cite journal | vauthors = Trausch-Azar JS, Lingbeck J, Ciechanover A, Schwartz AL | title = Ubiquitin-Proteasome-mediated degradation of Id1 is modulated by MyoD | journal = The Journal of Biological Chemistry | volume = 279 | issue = 31 | pages = 32614–9 | date = July 2004 | pmid = 15163661 | doi = 10.1074/jbc.M403794200 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Trausch-Azar J, Leone TC, Kelly DP, Schwartz AL | title = Ubiquitin proteasome-dependent degradation of the transcriptional coactivator PGC-1{alpha} via the N-terminal pathway | journal = The Journal of Biological Chemistry | volume = 285 | issue = 51 | pages = 40192–200 | date = December 2010 | pmid = 20713359 | pmc = 3001001 | doi = 10.1074/jbc.M110.131615 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Fajerman I, Schwartz AL, Ciechanover A | title = Degradation of the Id2 developmental regulator: targeting via N-terminal ubiquitylation | journal = Biochemical and Biophysical Research Communications | volume = 314 | issue = 2 | pages = 505–12 | date = February 2004 | pmid = 14733935 | doi = 10.1016/j.bbrc.2003.12.116 }}</ref><ref name="Vosper_2009">{{cite journal | vauthors = Vosper JM, McDowell GS, Hindley CJ, Fiore-Heriche CS, Kucerova R, Horan I, Philpott A | title = Ubiquitylation on canonical and non-canonical sites targets the transcription factor neurogenin for ubiquitin-mediated proteolysis | journal = The Journal of Biological Chemistry | volume = 284 | issue = 23 | pages = 15458–68 | date = June 2009 | pmid = 19336407 | pmc = 2708843 | doi = 10.1074/jbc.M809366200 | doi-access = free }}</ref><ref name="McDowell_2010">{{cite journal | vauthors = McDowell GS, Kucerova R, Philpott A | title = Non-canonical ubiquitylation of the proneural protein Ngn2 occurs in both Xenopus embryos and mammalian cells | journal = Biochemical and Biophysical Research Communications | volume = 400 | issue = 4 | pages = 655–60 | date = October 2010 | pmid = 20807509 | doi = 10.1016/j.bbrc.2010.08.122 }}</ref><ref>{{cite journal | vauthors = Tatham MH, Plechanovová A, Jaffray EG, Salmen H, Hay RT | title = Ube2W conjugates ubiquitin to α-amino groups of protein N-termini | journal = The Biochemical Journal | volume = 453 | issue = 1 | pages = 137–45 | date = July 2013 | pmid = 23560854 | pmc = 3778709 | doi = 10.1042/BJ20130244 }}</ref><ref>{{cite journal | vauthors = Vittal V, Shi L, Wenzel DM, Scaglione KM, Duncan ED, Basrur V, Elenitoba-Johnson KS, Baker D, Paulson HL, Brzovic PS, Klevit RE | title = Intrinsic disorder drives N-terminal ubiquitylation by Ube2w | journal = Nature Chemical Biology | volume = 11 | issue = 1 | pages = 83–9 | date = January 2015 | pmid = 25436519 | pmc = 4270946 | doi = 10.1038/nchembio.1700 }}</ref>{{Excessive citations inline|date=April 2025}} including ubiquitin itself.<ref>{{cite journal | vauthors = Johnson ES, Ma PC, Ota IM, Varshavsky A | title = A proteolytic pathway that recognizes ubiquitin as a degradation signal | journal = The Journal of Biological Chemistry | volume = 270 | issue = 29 | pages = 17442–56 | date = July 1995 | pmid = 7615550 | doi = 10.1074/jbc.270.29.17442 | doi-access = free }}</ref><ref name="pmid17006537"/> There is also increasing evidence for nonlysine residues as ubiquitylation targets using non-amine groups, such as the [[thiol|sulfhydryl group]] on cysteine,<ref name="Vosper_2009" /><ref name="McDowell_2010" /><ref name="pmid17502423">{{cite journal | vauthors = Wang X, Herr RA, Chua WJ, Lybarger L, Wiertz EJ, Hansen TH | title = Ubiquitination of serine, threonine, or lysine residues on the cytoplasmic tail can induce ERAD of MHC-I by viral E3 ligase mK3 | journal = The Journal of Cell Biology | volume = 177 | issue = 4 | pages = 613–24 | date = May 2007 | pmid = 17502423 | pmc = 2064207 | doi = 10.1083/jcb.200611063 }}</ref><ref name="pmid15994556">{{cite journal | vauthors = Cadwell K, Coscoy L | title = Ubiquitination on nonlysine residues by a viral E3 ubiquitin ligase | journal = Science | volume = 309 | issue = 5731 | pages = 127–30 | date = July 2005 | pmid = 15994556 | doi = 10.1126/science.1110340 | bibcode = 2005Sci...309..127C | doi-access = free }}</ref><ref>{{cite journal | vauthors = Cadwell K, Coscoy L | title = The specificities of Kaposi's sarcoma-associated herpesvirus-encoded E3 ubiquitin ligases are determined by the positions of lysine or cysteine residues within the intracytoplasmic domains of their targets | journal = Journal of Virology | volume = 82 | issue = 8 | pages = 4184–9 | date = April 2008 | pmid = 18272573 | pmc = 2293015 | doi = 10.1128/JVI.02264-07 }}</ref><ref>{{cite journal | vauthors = Williams C, van den Berg M, Sprenger RR, Distel B | title = A conserved cysteine is essential for Pex4p-dependent ubiquitination of the peroxisomal import receptor Pex5p | journal = The Journal of Biological Chemistry | volume = 282 | issue = 31 | pages = 22534–43 | date = August 2007 | pmid = 17550898 | doi = 10.1074/jbc.M702038200 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Carvalho AF, Pinto MP, Grou CP, Alencastre IS, Fransen M, Sá-Miranda C, Azevedo JE | title = Ubiquitination of mammalian Pex5p, the peroxisomal import receptor | journal = The Journal of Biological Chemistry | volume = 282 | issue = 43 | pages = 31267–72 | date = October 2007 | pmid = 17726030 | doi = 10.1074/jbc.M706325200 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Léon S, Subramani S | title = A conserved cysteine residue of Pichia pastoris Pex20p is essential for its recycling from the peroxisome to the cytosol | journal = The Journal of Biological Chemistry | volume = 282 | issue = 10 | pages = 7424–30 | date = March 2007 | pmid = 17209040 | pmc = 3682499 | doi = 10.1074/jbc.M611627200 | doi-access = free }}</ref><ref name="ReferenceA">{{cite journal | vauthors = Tait SW, de Vries E, Maas C, Keller AM, D'Santos CS, Borst J | title = Apoptosis induction by Bid requires unconventional ubiquitination and degradation of its N-terminal fragment | journal = The Journal of Cell Biology | volume = 179 | issue = 7 | pages = 1453–66 | date = December 2007 | pmid = 18166654 | pmc = 2373500 | doi = 10.1083/jcb.200707063 }}</ref><ref name="Roark_2012">{{cite journal | vauthors = Roark R, Itzhaki L, Philpott A | title = Complex regulation controls Neurogenin3 proteolysis | journal = Biology Open | volume = 1 | issue = 12 | pages = 1264–72 | date = December 2012 | pmid = 23259061 | pmc = 3522888 | doi = 10.1242/bio.20121750 }}</ref> and the [[hydroxyl]] group on threonine and serine.<ref name="Vosper_2009" /><ref name="McDowell_2010" /><ref name="pmid17502423"/><ref name="ReferenceA"/><ref name="Roark_2012" /><ref>{{cite journal | vauthors = Magadán JG, Pérez-Victoria FJ, Sougrat R, Ye Y, Strebel K, Bonifacino JS | title = Multilayered mechanism of CD4 downregulation by HIV-1 Vpu involving distinct ER retention and ERAD targeting steps | journal = PLOS Pathogens | volume = 6 | issue = 4 | article-number = e1000869 | date = April 2010 | pmid = 20442859 | pmc = 2861688 | doi = 10.1371/journal.ppat.1000869 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Tokarev AA, Munguia J, Guatelli JC | title = Serine-threonine ubiquitination mediates downregulation of BST-2/tetherin and relief of restricted virion release by HIV-1 Vpu | journal = Journal of Virology | volume = 85 | issue = 1 | pages = 51–63 | date = January 2011 | pmid = 20980512 | pmc = 3014196 | doi = 10.1128/JVI.01795-10 }}</ref><ref>{{cite journal | vauthors = Ishikura S, Weissman AM, Bonifacino JS | title = Serine residues in the cytosolic tail of the T-cell antigen receptor alpha-chain mediate ubiquitination and endoplasmic reticulum-associated degradation of the unassembled protein | journal = The Journal of Biological Chemistry | volume = 285 | issue = 31 | pages = 23916–24 | date = July 2010 | pmid = 20519503 | pmc = 2911338 | doi = 10.1074/jbc.M110.127936 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Shimizu Y, Okuda-Shimizu Y, Hendershot LM | title = Ubiquitylation of an ERAD substrate occurs on multiple types of amino acids | journal = Molecular Cell | volume = 40 | issue = 6 | pages = 917–26 | date = December 2010 | pmid = 21172657 | pmc = 3031134 | doi = 10.1016/j.molcel.2010.11.033 }}</ref> The end result of this process is the addition of one ubiquitin molecule (monoubiquitylation) or a chain of ubiquitin molecules (polyubiquitination) to the substrate protein.<ref name="pmid22420755">{{cite journal | vauthors = Dikic I, Robertson M | title = Ubiquitin ligases and beyond | journal = BMC Biology | volume = 10 | page = 22 | date = March 2012 | pmid = 22420755 | pmc = 3305657 | doi = 10.1186/1741-7007-10-22 | doi-access = free }}</ref>

Ubiquitination requires three types of enzyme: [[ubiquitin-activating enzyme]]s, [[ubiquitin-conjugating enzyme]]s, and [[ubiquitin ligase]]s, known as E1s, E2s, and E3s, respectively. The process consists of three main steps:
# '''Activation''': Ubiquitin is activated in a two-step reaction by an E1 [[ubiquitin-activating enzyme]], which is dependent on [[Adenosine triphosphate|ATP]]. The initial step involves production of a ubiquitin-adenylate intermediate. The E1 binds both ATP and ubiquitin and catalyses the acyl-adenylation of the [[C-terminus]] of the ubiquitin molecule. The second step transfers ubiquitin to an [[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]].<ref name="pmid11395416"/><ref name="pmid19352404">{{cite journal | vauthors = Schulman BA, Harper JW | title = Ubiquitin-like protein activation by E1 enzymes: the apex for downstream signalling pathways | journal = Nature Reviews Molecular Cell Biology | volume = 10 | issue = 5 | pages = 319–31 | date = May 2009 | pmid = 19352404 | pmc = 2712597 | doi = 10.1038/nrm2673 }}</ref> The human genome contains two genes that produce enzymes capable of activating ubiquitin: [[UBA1]] and [[UBE1L2|UBA6]].<ref name="pmid18353650">{{cite journal | vauthors = Groettrup M, Pelzer C, Schmidtke G, Hofmann K | title = Activating the ubiquitin family: UBA6 challenges the field | journal = Trends in Biochemical Sciences | volume = 33 | issue = 5 | pages = 230–7 | date = May 2008 | pmid = 18353650 | doi = 10.1016/j.tibs.2008.01.005 | url = http://nbn-resolving.de/urn:nbn:de:bsz:352-opus-85098 }}</ref>
# '''Conjugation''': E2 [[ubiquitin-conjugating enzyme]]s catalyse the transfer of ubiquitin from E1 to the [[active site]] cysteine of the E2 via a trans(thio)esterification reaction. In order to perform this reaction, the E2 binds to both activated ubiquitin and the E1 enzyme. Humans possess 35 different E2 enzymes, whereas other [[eukaryotic]] organisms have between 16 and 35. They are characterised by their highly conserved structure, known as the ubiquitin-conjugating catalytic (UBC) fold.<ref name="pmid19940261">{{cite journal | vauthors = van Wijk SJ, Timmers HT | title = The family of ubiquitin-conjugating enzymes (E2s): deciding between life and death of proteins | journal = FASEB Journal | volume = 24 | issue = 4 | pages = 981–93 | date = April 2010 | pmid = 19940261 | doi = 10.1096/fj.09-136259 | s2cid = 21280193 | doi-access = free }}</ref>[[File:Glycine lysine isopeptide v2.svg|thumb|300px|Glycine and lysine linked by an isopeptide bond. The isopeptide bond is highlighted yellow.]]
# '''Ligation''': E3 [[ubiquitin ligase]]s catalyse the final step of the ubiquitylation cascade. Most commonly, they create an isopeptide bond between a lysine of the target protein and the C-terminal glycine of ubiquitin. In general, this step requires the activity of one of the hundreds of E3s. E3 enzymes function as the [[Substrate (biochemistry)|substrate]] recognition modules of the system and are capable of interaction with both E2 and substrate. Some E3 enzymes also activate the E2 enzymes. E3 enzymes possess one of two [[Protein domain|domains]]: the homologous to the E6-AP carboxyl terminus ([[HECT domain|HECT]]) domain and the really interesting new gene ([[RING finger domain|RING]]) domain (or the closely related U-box domain). HECT domain E3s transiently bind ubiquitin in this process (an obligate thioester intermediate is formed with the active-site cysteine of the E3), whereas RING domain E3s catalyse the direct transfer from the E2 enzyme to the substrate.<ref name="pmid22389392">{{cite journal | vauthors = Metzger MB, Hristova VA, Weissman AM | title = HECT and RING finger families of E3 ubiquitin ligases at a glance | journal = Journal of Cell Science | volume = 125 | issue = Pt 3 | pages = 531–7 | date = February 2012 | pmid = 22389392 | pmc = 3381717 | doi = 10.1242/jcs.091777 }}</ref> 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 ubiquitylation of specific target proteins for degradation by the [[proteasome]].<ref name="pmid19775879">{{cite journal | vauthors = Skaar JR, Pagano M | title = Control of cell growth by the SCF and APC/C ubiquitin ligases | journal = Current Opinion in Cell Biology | volume = 21 | issue = 6 | pages = 816–24 | date = December 2009 | pmid = 19775879 | pmc = 2805079 | doi = 10.1016/j.ceb.2009.08.004 }}</ref>

In the ubiquitylation cascade, E1 can bind with many E2s, which can bind with hundreds of E3s in a hierarchical way. Having levels within the cascade allows tight regulation of the ubiquitylation machinery.<ref name="pmid15571809">{{cite journal | vauthors = Pickart CM, Eddins MJ | title = Ubiquitin: structures, functions, mechanisms | journal = Biochimica et Biophysica Acta (BBA) - Molecular Cell Research | volume = 1695 | issue = 1–3 | pages = 55–72 | date = November 2004 | pmid = 15571809 | doi = 10.1016/j.bbamcr.2004.09.019 | doi-access = free }}</ref> Other ubiquitin-like proteins (UBLs) are also modified via the E1–E2–E3 cascade, although variations in these systems do exist.<ref name="pmid16753028">{{cite journal | vauthors = Kerscher O, Felberbaum R, Hochstrasser M | title = Modification of proteins by ubiquitin and ubiquitin-like proteins | journal = Annual Review of Cell and Developmental Biology | volume = 22 | pages = 159–80 | year = 2006 | pmid = 16753028 | doi = 10.1146/annurev.cellbio.22.010605.093503 }}</ref>

E4 enzymes, or ubiquitin-chain elongation factors, are capable of adding pre-formed polyubiquitin chains to substrate proteins.<ref>{{cite journal | vauthors = Koegl M, Hoppe T, Schlenker S, Ulrich HD, Mayer TU, Jentsch S | title = A novel ubiquitination factor, E4, is involved in multiubiquitin chain assembly | journal = Cell | volume = 96 | issue = 5 | pages = 635–44 | date = March 1999 | pmid = 10089879 | doi = 10.1016/S0092-8674(00)80574-7 | doi-access = free }}</ref> For example, multiple monoubiquitylation of the tumor suppressor [[p53]] by [[Mdm2]]<ref>{{cite journal | vauthors = Lai Z, Ferry KV, Diamond MA, Wee KE, Kim YB, Ma J, Yang T, Benfield PA, Copeland RA, Auger KR | title = Human mdm2 mediates multiple mono-ubiquitination of p53 by a mechanism requiring enzyme isomerization | journal = The Journal of Biological Chemistry | volume = 276 | issue = 33 | pages = 31357–67 | date = August 2001 | pmid = 11397792 | doi = 10.1074/jbc.M011517200 | doi-access = free }}</ref> can be followed by addition of a polyubiquitin chain using [[P300-CBP coactivator family|p300 and CBP]].<ref>{{cite journal | vauthors = Grossman SR, Deato ME, Brignone C, Chan HM, Kung AL, Tagami H, Nakatani Y, Livingston DM | title = Polyubiquitination of p53 by a ubiquitin ligase activity of p300 | journal = Science | volume = 300 | issue = 5617 | pages = 342–4 | date = April 2003 | pmid = 12690203 | doi = 10.1126/science.1080386 | bibcode = 2003Sci...300..342G | s2cid = 11526100 }}</ref><ref>{{cite journal | vauthors = Shi D, Pop MS, Kulikov R, Love IM, Kung AL, Kung A, Grossman SR | title = CBP and p300 are cytoplasmic E4 polyubiquitin ligases for p53 | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 106 | issue = 38 | pages = 16275–80 | date = September 2009 | pmid = 19805293 | pmc = 2752525 | doi = 10.1073/pnas.0904305106 | bibcode = 2009PNAS..10616275S | doi-access = free }}</ref>

=== Types ===
{{see also|Ubiquitin ligase#Mono- and poly-ubiquitylation}}

Ubiquitylation affects cellular process by regulating the degradation of proteins (via the [[proteasome]] and [[lysosome]]), coordinating the [[Subcellular localization|cellular localization]] of proteins, activating and inactivating proteins, and modulating [[protein–protein interaction]]s.<ref name="pmid11917093">{{cite journal | vauthors = Glickman MH, Ciechanover A | title = The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction | journal = Physiological Reviews | volume = 82 | issue = 2 | pages = 373–428 | date = April 2002 | pmid = 11917093 | doi = 10.1152/physrev.00027.2001 }}</ref><ref name="pmid17218518">{{cite journal | vauthors = Mukhopadhyay D, Riezman H | title = Proteasome-independent functions of ubiquitin in endocytosis and signaling | journal = Science | volume = 315 | issue = 5809 | pages = 201–5 | date = January 2007 | pmid = 17218518 | doi = 10.1126/science.1127085 | bibcode = 2007Sci...315..201M | s2cid = 35434448 }}</ref><ref name="pmid12860974">{{cite journal | vauthors = Schnell JD, Hicke L | title = Non-traditional functions of ubiquitin and ubiquitin-binding proteins | journal = The Journal of Biological Chemistry | volume = 278 | issue = 38 | pages = 35857–60 | date = September 2003 | pmid = 12860974 | doi = 10.1074/jbc.R300018200 | doi-access = free }}</ref> These effects are mediated by different types of substrate ubiquitylation, for example the addition of a single ubiquitin molecule (monoubiquitylation) or different types of ubiquitin chains (polyubiquitylation).<ref name="pmid19754430"/>

==== Monoubiquitylation ====

Monoubiquitylation is the addition of one ubiquitin molecule to one substrate protein residue. Multi-monoubiquitylation is the addition of one ubiquitin molecule to multiple substrate residues. The monoubiquitylation of a protein can have different effects to the polyubiquitylation of the same protein. The addition of a single ubiquitin molecule is thought to be required prior to the formation of polyubiquitin chains.<ref name="pmid19754430">{{cite journal | vauthors = Komander D | title = The emerging complexity of protein ubiquitination | journal = Biochemical Society Transactions | volume = 37 | issue = Pt 5 | pages = 937–53 | date = October 2009 | pmid = 19754430 | doi = 10.1042/BST0370937 }}</ref> Monoubiquitylation affects cellular processes such as [[membrane trafficking]], [[endocytosis]] and [[viral budding]].<ref name="pmid17609522"/><ref name="pmid18516089">{{cite journal | vauthors = Ikeda F, Dikic I | title = Atypical ubiquitin chains: new molecular signals. 'Protein Modifications: Beyond the Usual Suspects' review series | journal = EMBO Reports | volume = 9 | issue = 6 | pages = 536–42 | date = June 2008 | pmid = 18516089 | pmc = 2427391 | doi = 10.1038/embor.2008.93 }}</ref>

==== Polyubiquitin chains ====

[[File:diubiquitin-lysine-48.png|thumb|'''Diagram of lysine 48-linked diubiquitin'''. The linkage between the two ubiquitin chains is shown in orange.]]
[[File:diubiquitin-lysine-63.png|thumb|'''Diagram of lysine 63-linked diubiquitin'''. The linkage between the two ubiquitin chains is shown in orange.]]
Polyubiquitylation is the formation of a ubiquitin chain on a single lysine residue on the substrate protein. Following addition of a single ubiquitin moiety to a protein substrate, further ubiquitin molecules can be added to the first, yielding a polyubiquitin chain.<ref name="pmid19754430"/> These chains are made by linking the glycine residue of a ubiquitin molecule to a lysine of ubiquitin bound to a substrate. Ubiquitin has seven [[lysine]] residues and an [[N-terminus]] that serves as points of ubiquitination; they are K6, K11, K27, K29, K33, K48, K63 and M1, respectively.<ref name="pmid22524316" /> Lysine 48-linked chains were the first identified and are the best-characterised type of ubiquitin chain. K63 chains have also been well-characterised, whereas the function of other lysine chains, mixed chains, branched chains, M1-linked linear chains, and heterologous chains (mixtures of ubiquitin and other ubiquitin-like proteins) remains more unclear.<ref name="pmid12872131"/><ref name="pmid17006537">{{cite journal | vauthors = Kirisako T, Kamei K, Murata S, Kato M, Fukumoto H, Kanie M, Sano S, Tokunaga F, Tanaka K, Iwai K | title = A ubiquitin ligase complex assembles linear polyubiquitin chains | journal = The EMBO Journal | volume = 25 | issue = 20 | pages = 4877–87 | date = October 2006 | pmid = 17006537 | pmc = 1618115 | doi = 10.1038/sj.emboj.7601360 }}</ref><ref name="pmid19754430"/><ref name="pmid18516089"/><ref name="pmid18351785">{{cite journal | vauthors = Xu P, Peng J | title = Characterization of polyubiquitin chain structure by middle-down mass spectrometry | journal = Analytical Chemistry | volume = 80 | issue = 9 | pages = 3438–44 | date = May 2008 | pmid = 18351785 | pmc = 2663523 | doi = 10.1021/ac800016w }}</ref>

Lysine 48-linked polyubiquitin chains target proteins for destruction, by a process known as [[proteolysis]]. Multi-ubiquitin chains at least four ubiquitin molecules long must be attached to a lysine residue on the condemned protein in order for it to be recognised by the [[proteasome|26S proteasome]].<ref name="pmid11265249">{{cite journal | vauthors = Hicke L | title = Protein regulation by monoubiquitin | journal = Nature Reviews Molecular Cell Biology | volume = 2 | issue = 3 | pages = 195–201 | date = March 2001 | pmid = 11265249 | doi = 10.1038/35056583 | s2cid = 205013847 }}</ref> This is a barrel-shape structure comprising a central proteolytic core made of four ring structures, flanked by two cylinders that selectively allow entry of ubiquitylated proteins. Once inside, the proteins are rapidly degraded into small [[peptide]]s (usually 3–25 amino acid residues in length). Ubiquitin molecules are cleaved off the protein immediately prior to destruction and are recycled for further use.<ref name="pmid16738015">{{cite journal | vauthors = Lecker SH, Goldberg AL, Mitch WE | title = Protein degradation by the ubiquitin-proteasome pathway in normal and disease states | journal = Journal of the American Society of Nephrology | volume = 17 | issue = 7 | pages = 1807–19 | date = July 2006 | pmid = 16738015 | doi = 10.1681/ASN.2006010083 | doi-access = free }}</ref> Although the majority of protein substrates are ubiquitylated, there are examples of non-ubiquitylated proteins targeted to the proteasome.<ref name="pmid22389393"/> The polyubiquitin chains are recognised by a subunit of the proteasome: S5a/Rpn10. This is achieved by a [[ubiquitin-interacting motif]] (UIM) found in a hydrophobic patch in the [[C-terminus|C-terminal]] region of the S5a/Rpn10 unit.<ref name="pmid11917093"/>

Lysine 63-linked chains are not associated with proteasomal degradation of the substrate protein. Instead, they allow the coordination of other processes such as [[endocytosis|endocytic trafficking]], [[inflammation]], [[translation (biology)|translation]], and [[DNA repair]].<ref name="pmid17609522">{{cite journal | vauthors = Miranda M, Sorkin A | title = Regulation of receptors and transporters by ubiquitination: new insights into surprisingly similar mechanisms | journal = Molecular Interventions | volume = 7 | issue = 3 | pages = 157–67 | date = June 2007 | pmid = 17609522 | doi = 10.1124/mi.7.3.7 }}</ref> In cells, lysine 63-linked chains are bound by the [[ESCRT|ESCRT-0]] complex, which prevents their binding to the proteasome. This complex contains two proteins, Hrs and STAM1, that contain a UIM, which allows it to bind to lysine 63-linked chains.<ref name="pmid23314748">{{cite journal | vauthors = Nathan JA, Kim HT, Ting L, Gygi SP, Goldberg AL | title = Why do cellular proteins linked to K63-polyubiquitin chains not associate with proteasomes? | journal = The EMBO Journal | volume = 32 | issue = 4 | pages = 552–65 | date = February 2013 | pmid = 23314748 | pmc = 3579138 | doi = 10.1038/emboj.2012.354 }}</ref><ref name="pmid12551915">{{cite journal | vauthors = Bache KG, Raiborg C, Mehlum A, Stenmark H | title = STAM and Hrs are subunits of a multivalent ubiquitin-binding complex on early endosomes | journal = The Journal of Biological Chemistry | volume = 278 | issue = 14 | pages = 12513–21 | date = April 2003 | pmid = 12551915 | doi = 10.1074/jbc.M210843200 | doi-access = free }}</ref>

Methionine 1-linked (or linear) polyubiquitin chains are another type of non-degradative ubiquitin chains. In this case, ubiquitin is linked in a head-to-tail manner, meaning that the C-terminus of the last ubiquitin molecule binds directly to the N-terminus of the next one. Although initially believed to target proteins for proteasomal degradation,<ref>{{cite journal | vauthors = Nakamura M, Tokunaga F, Sakata S, Iwai K | title = Mutual regulation of conventional protein kinase C and a ubiquitin ligase complex | journal = Biochemical and Biophysical Research Communications | volume = 351 | issue = 2 | pages = 340–347 | date = December 2006 | pmid = 17069764 | doi = 10.1016/j.bbrc.2006.09.163 }}</ref> linear ubiquitin later proved to be indispensable for NF-kB signaling.<ref>{{cite journal | vauthors = Tokunaga F, Sakata S, Saeki Y, Satomi Y, Kirisako T, Kamei K, Nakagawa T, Kato M, Murata S, Yamaoka S, Yamamoto M, Akira S, Takao T, Tanaka K, Iwai K | title = Involvement of linear polyubiquitylation of NEMO in NF-kappaB activation | journal = Nature Cell Biology | volume = 11 | issue = 2 | pages = 123–132 | date = February 2009 | pmid = 19136968 | doi = 10.1038/ncb1821 | s2cid = 23733705 }}</ref> Currently, there is only one known E3 ubiquitin ligase generating M1-linked polyubiquitin chains - [[LUBAC|linear ubiquitin chain assembly complex]] (LUBAC).<ref name="pmid17006537" /><ref>{{cite journal | vauthors = Gerlach B, Cordier SM, Schmukle AC, Emmerich CH, Rieser E, Haas TL, Webb AI, Rickard JA, Anderton H, Wong WW, Nachbur U, Gangoda L, Warnken U, Purcell AW, Silke J, Walczak H | title = Linear ubiquitination prevents inflammation and regulates immune signalling | journal = Nature | volume = 471 | issue = 7340 | pages = 591–596 | date = March 2011 | pmid = 21455173 | doi = 10.1038/nature09816 | s2cid = 4384869 | bibcode = 2011Natur.471..591G }}</ref>

Less is understood about atypical (non-lysine 48-linked) ubiquitin chains but research is starting to suggest roles for these chains.<ref name="pmid18516089" /> There is evidence that atypical chains linked by lysine 6, 11, 27, 29 and methionine 1 can induce proteasomal degradation.<ref name="pmid22389393">{{cite journal | vauthors = Kravtsova-Ivantsiv Y, Ciechanover A | title = Non-canonical ubiquitin-based signals for proteasomal degradation | journal = Journal of Cell Science | volume = 125 | issue = Pt 3 | pages = 539–48 | date = February 2012 | pmid = 22389393 | doi = 10.1242/jcs.093567 | doi-access = free }}</ref><ref name="pmid20385835" />

Branched ubiquitin chains containing multiple linkage types can be formed.<ref name="pmid17426036">{{cite journal | vauthors = Kim HT, Kim KP, Lledias F, Kisselev AF, Scaglione KM, Skowyra D, Gygi SP, Goldberg AL | title = Certain pairs of ubiquitin-conjugating enzymes (E2s) and ubiquitin-protein ligases (E3s) synthesize nondegradable forked ubiquitin chains containing all possible isopeptide linkages | journal = The Journal of Biological Chemistry | volume = 282 | issue = 24 | pages = 17375–86 | date = June 2007 | pmid = 17426036 | doi = 10.1074/jbc.M609659200 | doi-access = free }}</ref> The function of these chains is unknown.<ref name="pmid22524316"/>

==== Structure ====

Differently linked chains have specific effects on the protein to which they are attached, caused by differences in the conformations of the protein chains. K29-, K33-,<ref name="pmid25752577">{{cite journal | vauthors = Michel MA, Elliott PR, Swatek KN, Simicek M, Pruneda JN, Wagstaff JL, Freund SM, Komander D | title = Assembly and specific recognition of k29- and k33-linked polyubiquitin | journal = Molecular Cell | volume = 58 | issue = 1 | pages = 95–109 | date = April 2015 | pmid = 25752577 | pmc =  4386031| doi = 10.1016/j.molcel.2015.01.042 }}</ref> K63- and M1-linked chains have a fairly linear conformation; they are known as open-conformation chains. K6-, K11-, and K48-linked chains form closed conformations. The ubiquitin molecules in open-conformation chains do not interact with each other, except for the covalent [[isopeptide bond]]s linking them together. In contrast, the closed conformation chains have interfaces with interacting residues. Altering the chain conformations exposes and conceals different parts of the ubiquitin protein, and the different linkages are recognized by proteins that are specific for the unique [[topology|topologies]] that are intrinsic to the linkage. Proteins can specifically bind to ubiquitin via [[ubiquitin-binding domain]]s (UBDs). The distances between individual ubiquitin units in chains differ between lysine 63- and 48-linked chains. The UBDs exploit this by having small spacers between [[ubiquitin-interacting motif]]s that bind lysine 48-linked chains (compact ubiquitin chains) and larger spacers for lysine 63-linked chains. The machinery involved in recognising polyubiquitin chains can also differentiate between K63-linked chains and M1-linked chains, demonstrated by the fact that the latter can induce proteasomal degradation of the substrate.<ref name="pmid22524316">{{cite journal | vauthors = Komander D, Rape M | title = The ubiquitin code | journal = Annual Review of Biochemistry | volume = 81 | pages = 203–29 | year = 2012 | pmid = 22524316 | doi = 10.1146/annurev-biochem-060310-170328 | s2cid = 30693177 }}</ref><ref name="pmid17609522"/><ref name="pmid20385835">{{cite journal | vauthors = Zhao S, Ulrich HD | title = Distinct consequences of posttranslational modification by linear versus K63-linked polyubiquitin chains | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 107 | issue = 17 | pages = 7704–9 | date = April 2010 | pmid = 20385835 | pmc = 2867854 | doi = 10.1073/pnas.0908764107 | bibcode = 2010PNAS..107.7704Z | doi-access = free }}</ref>

== Function ==

The ubiquitylation system functions in a wide variety of cellular processes, including:<ref name="bostonbiochem.com">{{cite web | title = Ubiquitin Proteasome Pathway Overview| url = http://www.bostonbiochem.com/upp.php| access-date = 2008-04-30 |archive-url =https://web.archive.org/web/20080330210016/http://www.bostonbiochem.com/upp.php <!-- Bot retrieved archive -->|archive-date = 2008-03-30}}</ref>
* [[Antigen processing]]
* [[Apoptosis]]
* [[Biogenesis]] of organelles
* Cell cycle and division
* [[Transcription (genetics)|DNA transcription]] and repair
* Differentiation and development
* Immune response and inflammation
* Neural and muscular degeneration
* Maintenance of [[pluripotency]]<ref>{{cite journal | vauthors = Bax M, McKenna J, Do-Ha D, Stevens CH, Higginbottom S, Balez R, Cabral-da-Silva ME, Farrawell NE, Engel M, Poronnik P, Yerbury JJ, Saunders DN, Ooi L | title = The Ubiquitin Proteasome System Is a Key Regulator of Pluripotent Stem Cell Survival and Motor Neuron Differentiation | journal = Cells | volume = 8 | issue = 6 | page = 581 | date = June 2019 | pmid = 31200561 | pmc = 6627164 | doi = 10.3390/cells8060581 | doi-access = free }}</ref>
* 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
* Phage defense

=== Membrane proteins ===
Multi-monoubiquitylation can mark [[transmembrane protein]]s (for example, [[Receptor (biochemistry)|receptors]]) for removal from [[Biological membrane|membranes]] (internalisation) and fulfil several signalling roles within the cell. When cell-surface transmembrane molecules are tagged with ubiquitin, the subcellular localization of the protein is altered, often targeting the protein for destruction in lysosomes. This serves as a negative feedback mechanism, because often the stimulation of receptors by ligands increases their rate of ubiquitylation and internalisation. Like monoubiquitylation, lysine 63-linked polyubiquitin chains also has a role in the trafficking some membrane proteins.<ref name="pmid17609522"/><ref name="pmid19754430"/><ref name="pmid11265249" /><ref name="Soni_2018">{{cite journal | vauthors = Soni D, Wang DM, Regmi SC, Mittal M, Vogel SM, Schlüter D, Tiruppathi C | title = Deubiquitinase function of A20 maintains and repairs endothelial barrier after lung vascular injury | journal = Cell Death Discovery | volume = 4 | issue = 60 | date = May 2018 | page = 60 | pmid = 29796309| pmc =5955943 | doi = 10.1038/s41420-018-0056-3}}</ref>

=== Genomic maintenance ===
[[Proliferating cell nuclear antigen]] (PCNA) is a protein involved in [[DNA synthesis]]. Under normal physiological conditions PCNA is [[sumoylation|sumoylated]] (a similar post-translational modification to ubiquitylation). When [[DNA]] is damaged by [[ultra-violet radiation]] or chemicals, the [[SUMO protein|SUMO]] molecule that is attached to a lysine residue is replaced by ubiquitin. Monoubiquitylated PCNA recruits [[polymerase]]s that can carry out DNA synthesis with damaged DNA; but this is very error-prone, possibly resulting in the synthesis of mutated DNA. Lysine 63-linked polyubiquitylation of PCNA allows it to perform a less error-prone mutation bypass known by the template switching pathway.<ref name="pmid12860974" /><ref name="pmid20847899">{{cite journal | vauthors = Shaheen M, Shanmugam I, Hromas R | title = The Role of PCNA Posttranslational Modifications in Translesion Synthesis | journal = Journal of Nucleic Acids | volume = 2010 | pages = 1–8 | date = August 2010 | pmid = 20847899 | pmc = 2935186 | doi = 10.4061/2010/761217 | doi-access = free }}</ref><ref name="pmid23416108">{{cite journal | vauthors = Jackson SP, Durocher D | title = Regulation of DNA damage responses by ubiquitin and SUMO | journal = Molecular Cell | volume = 49 | issue = 5 | pages = 795–807 | date = March 2013 | pmid = 23416108 | doi = 10.1016/j.molcel.2013.01.017 | doi-access = free }}</ref>

Ubiquitylation of [[H2AFX|histone H2AX]] is involved in [[DNA repair|DNA damage recognition]] of DNA double-strand breaks. Lysine 63-linked polyubiquitin chains are formed on H2AX histone by the [[Ubiquitin ligase|E2/E3 ligase pair]], Ubc13-Mms2/RNF168.<ref name="pmid22589545">{{cite journal | vauthors = Campbell SJ, Edwards RA, Leung CC, Neculai D, Hodge CD, Dhe-Paganon S, Glover JN | title = Molecular insights into the function of RING finger (RNF)-containing proteins hRNF8 and hRNF168 in Ubc13/Mms2-dependent ubiquitylation | journal = The Journal of Biological Chemistry | volume = 287 | issue = 28 | pages = 23900–10 | date = July 2012 | pmid = 22589545 | pmc = 3390666 | doi = 10.1074/jbc.M112.359653 | doi-access = free }}</ref><ref name="pmid17709392">{{cite journal | vauthors = Ikura T, Tashiro S, Kakino A, Shima H, Jacob N, Amunugama R, Yoder K, Izumi S, Kuraoka I, Tanaka K, Kimura H, Ikura M, Nishikubo S, Ito T, Muto A, Miyagawa K, Takeda S, Fishel R, Igarashi K, Kamiya K | title = DNA damage-dependent acetylation and ubiquitination of H2AX enhances chromatin dynamics | journal = Molecular and Cellular Biology | volume = 27 | issue = 20 | pages = 7028–40 | date = October 2007 | pmid = 17709392 | pmc = 2168918 | doi = 10.1128/MCB.00579-07 }}</ref> This K63 chain appears to recruit RAP80, which contains a UIM, and [[UIMC1|RAP80]] then helps localize [[BRCA1]]. This pathway will eventually recruit the necessary proteins for [[DNA repair#Double-strand breaks|homologous recombination repair]].<ref name="pmid17525342">{{cite journal | vauthors = Kim H, Chen J, Yu X | title = Ubiquitin-binding protein RAP80 mediates BRCA1-dependent DNA damage response | journal = Science | volume = 316 | issue = 5828 | pages = 1202–5 | date = May 2007 | pmid = 17525342 | doi = 10.1126/science.1139621 | bibcode = 2007Sci...316.1202K | s2cid = 31636419 }}</ref>

=== Transcriptional regulation ===
[[Histones]] can be ubiquitinated, usually in the form of monoubiquitylation, although polyubiquitylated forms do occur. Histone ubiquitylation alters chromatin structure and allows the access of enzymes involved in transcription. Ubiquitin on histones also acts as a binding site for proteins that either activate or inhibit transcription and also can induce further post-translational modifications of the protein. These effects can all modulate the transcription of genes.<ref name="pmid19213613">{{cite journal | vauthors = Hofmann K | title = Ubiquitin-binding domains and their role in the DNA damage response | journal = DNA Repair | volume = 8 | issue = 4 | pages = 544–56 | date = April 2009 | pmid = 19213613 | doi = 10.1016/j.dnarep.2009.01.003 }}</ref><ref name="pmid22033037">{{cite journal | vauthors = Hammond-Martel I, Yu H, Affar el B | title = Roles of ubiquitin signaling in transcription regulation | journal = Cellular Signalling | volume = 24 | issue = 2 | pages = 410–21 | date = February 2012 | pmid = 22033037 | doi = 10.1016/j.cellsig.2011.10.009 }}</ref>

== Deubiquitination ==

[[Deubiquitinating enzyme]]s (deubiquitinases; DUBs) oppose the role of ubiquitylation by removing ubiquitin from substrate proteins. They are [[cysteine protease]]s that cleave the [[amide bond]] between the two proteins. They are highly specific, as are the E3 ligases that attach the ubiquitin, with only a few substrates per enzyme. They can cleave both [[isopeptide bond|isopeptide]] (between ubiquitin and lysine) and [[peptide bond]]s (between ubiquitin and the [[N-terminus]]). 
In addition to removing ubiquitin from substrate proteins, DUBs have many other roles within the cell. Ubiquitin is either expressed as multiple copies joined in a chain (polyubiquitin) or attached to ribosomal subunits. DUBs cleave these proteins to produce active ubiquitin. They also recycle ubiquitin that has been bound to small [[nucleophilic]] molecules during the ubiquitylation process. Monoubiquitin is formed by DUBs that cleave ubiquitin from free polyubiquitin chains that have been previously removed from proteins.<ref name="pmid19489724">{{cite journal | vauthors = Reyes-Turcu FE, Ventii KH, Wilkinson KD | title = Regulation and cellular roles of ubiquitin-specific deubiquitinating enzymes | journal = Annual Review of Biochemistry | volume = 78 | pages = 363–97 | year = 2009 | pmid = 19489724 | pmc = 2734102 | doi = 10.1146/annurev.biochem.78.082307.091526 }}</ref><ref name="pmid16325574">{{cite journal | vauthors = Nijman SM, Luna-Vargas MP, Velds A, Brummelkamp TR, Dirac AM, Sixma TK, Bernards R | title = A genomic and functional inventory of deubiquitinating enzymes | journal = Cell | volume = 123 | issue = 5 | pages = 773–86 | date = December 2005 | pmid = 16325574 | doi = 10.1016/j.cell.2005.11.007 | hdl = 1874/20959 | s2cid = 15575576 | hdl-access = free }}</ref>

== Ubiquitin-binding domains ==
<!-- redirect [[Ubiquitin Binding Domains]] -->

{| border="1" class="wikitable" align="right"
|+ Table of characterized Ubiquitin-binding domains<ref name="Hicke 2005 610-621"/>
! Domain
! Number of proteins
in proteome 
! Length
(amino acids)
! Ubiquitin binding
Affinity
|-
! CUE
|''S. cerevisiae'': 7
''H. sapiens'': 21
| 42–43
| ~2–160 μM
|-
! GATII
|''S. cerevisiae'': 2
''H. sapiens'': 14
| 135
| ~180 μM
|-
! GLUE
|''S. cerevisiae'': ?
''H. sapiens'': ?
| ~135
| ~460 μM
|-
! NZF
|''S. cerevisiae'': 1
''H. sapiens'': 25
| ~35
| ~100–400 μM
|-
! PAZ
|''S. cerevisiae'': 5
''H. sapiens'': 16
| ~58
| Not known
|-
! UBA
|''S. cerevisiae'': 10
''H. sapiens'': 98
| 45–55
| ~0.03–500 μM
|-
! UEV
|''S. cerevisiae'': 2
''H. sapiens'': ?
| ~145
| ~100–500 μM
|-
! UIM
|''S. cerevisiae'': 8
''H. sapiens'': 71
| ~20
| ~100–400 μM
|-
! VHS
|''S. cerevisiae'': 4
''H. sapiens'': 28
| 150
| Not known
|}

[[Ubiquitin-binding domain]]s (UBDs) are modular protein domains that non-covalently bind to ubiquitin, these motifs control various cellular events. Detailed molecular structures are known for a number of UBDs, binding specificity determines their mechanism of action and regulation, and how it regulates cellular proteins and processes.<ref name="Hicke 2005 610-621">{{cite journal | vauthors = Hicke L, Schubert HL, Hill CP | title = Ubiquitin-binding domains | journal = Nature Reviews Molecular Cell Biology | volume = 6 | issue = 8 | pages = 610–21 | date = August 2005 | pmid = 16064137 | doi = 10.1038/nrm1701 | s2cid = 3056635 }}</ref><ref>{{cite journal | vauthors = Husnjak K, Dikic I | title = Ubiquitin-binding proteins: decoders of ubiquitin-mediated cellular functions | journal = Annual Review of Biochemistry | volume = 81 | pages = 291–322 | date = 2012-01-01 | pmid = 22482907 | doi = 10.1146/annurev-biochem-051810-094654 }}</ref>

== Disease associations ==

=== Pathogenesis ===

The ubiquitin pathway has been implicated in the pathogenesis of a wide range of diseases and disorders, including:<ref name="nature.com">{{cite journal | vauthors = Popovic D, Vucic D, Dikic I | title = Ubiquitination in disease pathogenesis and treatment | journal = Nature Medicine | volume = 20 | issue = 11 | pages = 1242–1253 | date = November 2014 | pmid = 25375928 | doi = 10.1038/nm.3739 | s2cid = 205394130 }}</ref>
* [[Neurodegeneration]]
* Infection and immunity
* [[Genetic disorders]]
* [[Cancer]]

=== Neurodegeneration ===
Ubiquitin is implicated in neurodegenerative diseases associated with proteostasis dysfunction, including [[Alzheimer's disease]], [[motor neuron disease]],<ref>{{cite journal | vauthors = Yerbury JJ, Farrawell NE, McAlary L | title = Proteome Homeostasis Dysfunction: A Unifying Principle in ALS Pathogenesis | journal = Trends in Neurosciences | volume = 43 | issue = 5 | pages = 274–284 | date = May 2020 | pmid = 32353332 | doi = 10.1016/j.tins.2020.03.002 | s2cid = 216095994 }}</ref> [[Huntington's disease]] and [[Parkinson's disease]].<ref name="nature.com"/> Transcript variants encoding different isoforms of [[UBQLN1|ubiquilin-1]] are found in lesions associated with Alzheimer's and Parkinson's disease.<ref>{{cite web|title=UBQLN1 ubiquilin 1 [ Homo sapiens ]|url=https://www.ncbi.nlm.nih.gov/gene?Db=gene&Cmd=DetailsSearch&Term=29979%5Buid%5D|work=Gene|publisher=National Center for Biotechnology Information|access-date=9 May 2012}}</ref> Higher levels of ubiquilin in the brain have been shown to decrease malformation of [[amyloid precursor protein|amyloid precursor protein (APP)]], which plays a key role in triggering Alzheimer's disease.<ref name="pmid21852239">{{cite journal | vauthors = Stieren ES, El Ayadi A, Xiao Y, Siller E, Landsverk ML, Oberhauser AF, Barral JM, Boehning D | title = Ubiquilin-1 is a molecular chaperone for the amyloid precursor protein | journal = The Journal of Biological Chemistry | volume = 286 | issue = 41 | pages = 35689–35698 | date = October 2011 | pmid = 21852239 | pmc = 3195644 | doi = 10.1074/jbc.M111.243147 | doi-access = free }}
*{{cite press release |date=September 1, 2011 |title=Alzheimer's brains found to have lower levels of key protein |website=ScienceDaily |url=https://www.sciencedaily.com/releases/2011/09/110901112537.htm}}</ref> Conversely, lower levels of ubiquilin-1 in the brain have been associated with increased malformation of APP.<ref name="pmid21852239"/> A frameshift mutation in [[ubiquitin B]] can result in a truncated peptide missing the [[C-terminus|C-terminal]] [[glycine]]. This abnormal peptide, known as [[UBB+1]], has been shown to accumulate selectively in Alzheimer's disease and other [[tauopathy|tauopathies]].

=== Infection and immunity ===
Ubiquitin and ubiquitin-like molecules extensively regulate immune [[Signal transduction|signal transduction pathways]] at virtually all stages, including steady-state repression, activation during infection, and attenuation upon clearance. Without this regulation, immune activation against [[pathogen]]s may be defective, resulting in chronic disease or death. Alternatively, the immune system may become hyperactivated and organs and tissues may be subjected to [[Autoimmunity|autoimmune damage]].

On the other hand, [[virus]]es must block or redirect host cell processes including [[Immune system|immunity]] to effectively replicate, yet many viruses relevant to disease have informationally limited [[genome]]s. Because of its very large number of roles in the cell, manipulating the ubiquitin system represents an efficient way for such viruses to block, subvert or redirect critical host cell processes to support their own replication.<ref>{{cite journal | vauthors = Heaton SM, Borg NA, Dixit VM | title = Ubiquitin in the activation and attenuation of innate antiviral immunity | journal = The Journal of Experimental Medicine | volume = 213 | issue = 1 | pages = 1–13 | date = January 2016 | pmid = 26712804 | pmc = 4710203 | doi = 10.1084/jem.20151531 }}</ref>

The retinoic acid-inducible gene I ([[RIG-I]]) protein is a primary immune system sensor for viral and other invasive RNA in human cells.<ref>{{cite journal | vauthors = Takeuchi O, Akira S | title = Pattern recognition receptors and inflammation | language = en | journal = Cell | volume = 140 | issue = 6 | pages = 805–20 | date = March 2010 | pmid = 20303872 | doi = 10.1016/j.cell.2010.01.022 | s2cid = 223338 | doi-access = free }}</ref> The RIG-I-like receptor ([[RIG-I-like receptor|RLR]]) immune signaling pathway is one of the most extensively studied in terms of the role of ubiquitin in immune regulation.<ref>{{cite journal | vauthors = Okamoto M, Kouwaki T, Fukushima Y, Oshiumi H | title = Regulation of RIG-I Activation by K63-Linked Polyubiquitination | language = en | journal = Frontiers in Immunology | volume = 8 | page = 1942 | date = 2018 | pmid = 29354136 | pmc = 5760545 | doi = 10.3389/fimmu.2017.01942 | doi-access = free }}</ref>

=== Genetic disorders ===
* [[Angelman syndrome]] is caused by a disruption of ''[[UBE3A]]'', which encodes a ubiquitin ligase (E3) enzyme termed E6-AP.
* [[Von Hippel–Lindau syndrome]] involves disruption of a ubiquitin E3 ligase termed the VHL tumor suppressor, or ''[[Von Hippel–Lindau tumor suppressor|VHL]]'' gene.
* [[Fanconi anemia]]: Eight of the thirteen identified genes whose disruption can cause this disease encode proteins that form a large ubiquitin ligase (E3) complex.
* [[3-M syndrome]] is an autosomal-recessive growth retardation disorder associated with mutations of the [[CUL7|Cullin7]] E3 ubiquitin ligase.<ref name="pmid16142236">{{cite journal | vauthors = 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 | title = Identification of mutations in CUL7 in 3-M syndrome | journal = Nature Genetics | volume = 37 | issue = 10 | pages = 1119–24 | date = October 2005 | pmid = 16142236 | doi = 10.1038/ng1628 | s2cid = 44003147 }}</ref>

=== Diagnostic use ===
[[Immunohistochemistry]] using [[antibody|antibodies]] to ubiquitin can identify abnormal accumulations of this protein inside cells, indicating a disease process. These protein accumulations are referred to as [[Inclusion body|inclusion bodies]] (which is a general term for any microscopically visible collection of abnormal material in a cell). Examples include:
* [[Neurofibrillary tangle]]s in [[Alzheimer's disease]]
* [[Lewy body]] in [[Parkinson's disease]]
* [[Pick bodies]] in [[Pick's disease]]
* Inclusions in [[motor neuron disease]] and [[Huntington's disease]]
* [[Mallory body|Mallory bodies]] in [[alcoholic liver disease]]
* [[Rosenthal fiber]]s in [[astrocyte]]s

=== Link to cancer ===
[[Post-translational modification]] of proteins is a generally used mechanism in [[Eukaryote|eukaryotic]] cell signaling.<ref name="Nguyen_2013">{{cite journal | vauthors = Nguyen LK, Kolch W, Kholodenko BN | title = When ubiquitination meets phosphorylation: a systems biology perspective of EGFR/MAPK signalling | journal = Cell Communication and Signaling | volume = 11 | page = 52 | date = July 2013 | pmid = 23902637 | pmc = 3734146 | doi = 10.1186/1478-811X-11-52 | doi-access = free }}</ref> Ubiquitylation, ubiquitin conjugation to [[protein]]s, is a crucial process for [[cell cycle]] progression and [[cell proliferation]] and development. Although ubiquitylation usually serves as a signal for protein degradation through the [[26S proteasome]], it could also serve for other fundamental cellular processes,<ref name="Nguyen_2013" /> in [[endocytosis]],<ref>{{cite journal | vauthors = Sorkin A, Goh LK | title = Endocytosis and intracellular trafficking of ErbBs | journal = Experimental Cell Research | volume = 314 | issue = 17 | pages = 3093–106 | date = October 2008 | pmid = 18793634 | pmc = 2605728 | doi = 10.1016/j.yexcr.2008.07.029  }}</ref> enzymatic activation<ref>{{cite journal | vauthors = Nguyen LK, Muñoz-García J, Maccario H, Ciechanover A, Kolch W, Kholodenko BN | title = Switches, excitable responses and oscillations in the Ring1B/Bmi1 ubiquitination system | journal = PLOS Computational Biology | volume = 7 | issue = 12 | article-number = e1002317 | date = December 2011 | pmid = 22194680 | pmc = 3240587 | doi = 10.1371/journal.pcbi.1002317 | bibcode = 2011PLSCB...7E2317N | doi-access = free }}</ref> and DNA repair.<ref>{{cite journal | vauthors = Zhou W, Wang X, Rosenfeld MG | title = Histone H2A ubiquitination in transcriptional regulation and DNA damage repair | journal = The International Journal of Biochemistry & Cell Biology | volume = 41 | issue = 1 | pages = 12–5 | date = January 2009 | pmid = 18929679 | doi = 10.1016/j.biocel.2008.09.016  }}</ref> Moreover, since ubiquitylation functions to tightly regulate the cellular level of [[cyclin]]s, its misregulation is expected to have severe impacts. First evidence of the importance of the ubiquitin/proteasome pathway in [[oncogenic]] processes was observed due to the high antitumor activity of proteasome inhibitors.<ref>{{cite journal | vauthors = Dou QP, Li B | title = Proteasome inhibitors as potential novel anticancer agents | journal = Drug Resistance Updates | volume = 2 | issue = 4 | pages = 215–223 | date = August 1999 | pmid = 11504494 | doi = 10.1054/drup.1999.0095  | doi-access = free }}</ref><ref name="Vries_2000">{{cite journal | vauthors = Vries EG, Verweij J | title = Clinical Cancer Research 2000: New Agents and Therapies | journal = Drug Resistance Updates | volume = 3 | issue = 4 | pages = 197–201 | year = 2000 | pmid = 11498385 | doi = 10.1054/drup.2000.0153 }}</ref><ref name="Pray_2002">{{cite journal | vauthors = Pray TR, Parlati F, Huang J, Wong BR, Payan DG, Bennett MK, Issakani SD, Molineaux S, Demo SD | title = Cell cycle regulatory E3 ubiquitin ligases as anticancer targets | journal = Drug Resistance Updates | volume = 5 | issue = 6 | pages = 249–58 | date = December 2002 | pmid = 12531181 | doi=10.1016/s1368-7646(02)00121-8}}</ref> Various studies have shown that defects or alterations in ubiquitylation processes are commonly associated with or present in human carcinoma.<ref name="Clifford_2001">{{cite journal | vauthors = Clifford SC, Cockman ME, Smallwood AC, Mole DR, Woodward ER, Maxwell PH, Ratcliffe PJ, Maher ER | title = Contrasting effects on HIF-1alpha regulation by disease-causing pVHL mutations correlate with patterns of tumourigenesis in von Hippel–Lindau disease | journal = Human Molecular Genetics | volume = 10 | issue = 10 | pages = 1029–38 | year = 2001 | pmid = 11331613 | doi = 10.1093/hmg/10.10.1029| doi-access = free }}</ref><ref name="Sparks_1998">{{cite journal | vauthors = Sparks AB, Morin PJ, Vogelstein B, Kinzler KW | title = Mutational analysis of the APC/beta-catenin/Tcf pathway in colorectal cancer | journal = Cancer Research | volume = 58 | issue = 6 | pages = 1130–4 | date = March 1998 | pmid = 9515795  }}</ref><ref name="Scheffner_1993">{{cite journal | vauthors = Scheffner M, Huibregtse JM, Vierstra RD, Howley PM | title = The HPV-16 E6 and E6-AP complex functions as a ubiquitin-protein ligase in the ubiquitination of p53 | journal = Cell | volume = 75 | issue = 3 | pages = 495–505 | date = November 1993 | pmid = 8221889 | doi=10.1016/0092-8674(93)90384-3| s2cid = 27437768 }}</ref><ref name="Momand_1998">{{cite journal | vauthors = Momand J, Jung D, Wilczynski S, Niland J | title = The MDM2 gene amplification database | journal = Nucleic Acids Research | volume = 26 | issue = 15 | pages = 3453–9 | date = August 1998 | pmid = 9671804 | pmc = 147746 | doi=10.1093/nar/26.15.3453}}</ref><ref name="Hashizume_2001">{{cite journal | vauthors = Hashizume R, Fukuda M, Maeda I, Nishikawa H, Oyake D, Yabuki Y, Ogata H, Ohta T | title = The RING heterodimer BRCA1-BARD1 is a ubiquitin ligase inactivated by a breast cancer-derived mutation | journal = The Journal of Biological Chemistry | volume = 276 | issue = 18 | pages = 14537–40 | date = May 2001 | pmid = 11278247 | doi = 10.1074/jbc.C000881200  | doi-access = free }}</ref><ref name="Zhu_2004">{{cite journal | vauthors = Zhu CQ, Blackhall FH, Pintilie M, Iyengar P, Liu N, Ho J, Chomiak T, Lau D, Winton T, Shepherd FA, Tsao MS | title = Skp2 gene copy number aberrations are common in non-small cell lung carcinoma, and its overexpression in tumors with ras mutation is a poor prognostic marker | journal = Clinical Cancer Research  | volume = 10 | issue = 6 | pages = 1984–91 | year = 2004 | pmid = 15041716 | doi = 10.1158/1078-0432.ccr-03-0470 | doi-access = free }}</ref><ref name="Schmidt_2003">{{cite journal | vauthors = Schmidt MH, Furnari FB, Cavenee WK, Bögler O | title = Epidermal growth factor receptor signaling intensity determines intracellular protein interactions, ubiquitination, and internalization | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 100 | issue = 11 | pages = 6505–10 | date = May 2003 | pmid = 12734385 | pmc = 164476 | doi = 10.1073/pnas.1031790100  | bibcode = 2003PNAS..100.6505S | doi-access = free }}</ref><ref name="Knuutila_1999">{{cite journal | vauthors = Knuutila S, Aalto Y, Autio K, Björkqvist AM, El-Rifai W, Hemmer S, Huhta T, Kettunen E, Kiuru-Kuhlefelt S, Larramendy ML, Lushnikova T, Monni O, Pere H, Tapper J, Tarkkanen M, Varis A, Wasenius VM, Wolf M, Zhu Y | title = DNA copy number losses in human neoplasms | journal = The American Journal of Pathology | volume = 155 | issue = 3 | pages = 683–94 | date = September 1999 | pmid = 10487825 | pmc = 1866903 | doi = 10.1016/S0002-9440(10)65166-8  }}</ref> Malignancies could be developed through [[Loss of function|loss of function mutation]] directly at the [[tumor suppressor gene]], increased activity of ubiquitylation, and/or indirect attenuation of ubiquitylation due to mutation in related proteins.<ref name="Mani_2005">{{cite journal | vauthors = Mani A, Gelmann EP | title = The ubiquitin-proteasome pathway and its role in cancer | journal = Journal of Clinical Oncology | volume = 23 | issue = 21 | pages = 4776–89 | date = July 2005 | pmid = 16034054 | doi = 10.1200/JCO.2005.05.081 }}</ref>

=== Direct loss of function mutation of E3 ubiquitin ligase ===

==== Renal cell carcinoma ====
The VHL ([[Von Hippel–Lindau tumor suppressor|Von Hippel–Lindau]]) gene encodes a component of an [[E3 ubiquitin ligase]]. VHL complex targets a member of the [[Hypoxia-inducible factor|hypoxia-inducible transcription factor family]] (HIF) for degradation by interacting with the oxygen-dependent destruction domain under normoxic conditions. HIF activates downstream targets such as the [[vascular endothelial growth factor]] (VEGF), promoting [[angiogenesis]]. Mutations in VHL prevent degradation of HIF and thus lead to the formation of [[Hypervascularity|hypervascular]] lesions and renal tumors.<ref name="Clifford_2001" /><ref name="Mani_2005" />

==== Breast cancer ====
The ''[[BRCA1]]'' gene is another tumor suppressor gene in humans which encodes the BRCA1 protein that is involved in response to DNA damage. The protein contains a [[RING finger domain|RING]] motif with E3 Ubiquitin Ligase activity. BRCA1 could form dimer with other molecules, such as [[BARD1]] and [[BAP1]], for its ubiquitylation activity. Mutations that affect the ligase function are often found and associated with various cancers.<ref name="Hashizume_2001" /><ref name="Mani_2005" />

==== Cyclin E ====
As processes in cell cycle progression are the most fundamental processes for cellular growth and differentiation, and are the most common to be altered in human carcinomas, it is expected for cell cycle-regulatory proteins to be under tight regulation. The level of cyclins, as the name suggests, is high only at certain a time point during the cell cycle. This is achieved by continuous control of cyclins or CDKs levels through ubiquitylation and degradation. When cyclin E is partnered with CDK2 and gets phosphorylated, an SCF-associated [[F-box protein]] Fbw7 recognizes the complex and thus targets it for degradation. Mutations in Fbw7 have been found in more than 30% of human tumors, characterizing it as a tumor suppressor protein.<ref name="Knuutila_1999" />

=== Increased ubiquitination activity ===

==== Cervical cancer ====
Oncogenic types of the [[Human papillomavirus infection|human papillomavirus (HPV)]] are known to hijack cellular ubiquitin-[[proteasome]] pathway for viral infection and replication. The E6 proteins of HPV will bind to the N-terminus of the cellular E6-AP E3 ubiquitin ligase, redirecting the complex to bind [[TP53|p53]], a well-known tumor suppressor gene whose inactivation is found in many types of cancer.<ref name="Scheffner_1993" /> Thus, p53 undergoes ubiquitylation and proteasome-mediated degradation. Meanwhile, E7, another one of the early-expressed HPV genes, will bind to [[Retinoblastoma protein|Rb]], also a tumor suppressor gene, mediating its degradation.<ref name="Mani_2005" /> The loss of p53 and Rb in cells allows limitless cell proliferation to occur.

==== p53 regulation ====
Gene amplification often occur in various tumor cases, including of [[Mdm2|''MDM2'']], a gene encodes for a RING E3 Ubiquitin ligase responsible for downregulation of p53 activity. MDM2 targets p53 for ubiquitylation and proteasomal degradation thus keeping its level appropriate for normal cell condition. Overexpression of MDM2 causes loss of p53 activity and therefore allowing cells to have a limitless replicative potential.<ref name="Momand_1998" /><ref name="Mani_2005" />

==== p27 ====
Another gene that is a target of gene amplification is ''[[SKP2]]''. SKP2 is an [[F-box protein]] with a role in substrate recognition for ubiquitylation and degradation. SKP2 targets [[CDKN1B|p27<sup>Kip-1</sup>]], an inhibitor of cyclin-dependent kinases ([[Cyclin-dependent kinase|CDKs]]). CDKs2/4 partner with the [[cyclin]]s E/D, respectively, forming a family of cell cycle regulators which control cell cycle progression through the G1 phase. Low level of p27<sup>Kip-1</sup> protein is often found in various cancers and is due to overactivation of ubiquitin-mediated proteolysis through overexpression of SKP2.<ref name="Zhu_2004" /><ref name="Mani_2005" />

==== Efp ====
[[TRIM25|Efp]], or estrogen-inducible RING-finger protein, is an E3 ubiquitin ligase whose overexpression has been shown to be the major cause of [[estrogen]]-independent [[breast cancer]].<ref name="Pray_2002" /><ref name="Nalepa_2003">{{cite journal | vauthors = Nalepa G, Wade Harper J | title = Therapeutic anti-cancer targets upstream of the proteasome | journal = Cancer Treatment Reviews | volume = 29 | pages = 49–57 | date = May 2003 | issue = Suppl 1 | pmid = 12738243 | doi=10.1016/s0305-7372(03)00083-5}}</ref> Efp's substrate is [[14-3-3 protein]] which negatively regulates cell cycle.

=== Evasion of ubiquitination ===

==== Colorectal cancer ====
The gene associated with [[colorectal cancer]] is the [[adenomatous polyposis coli]] (APC), which is a classic [[tumor suppressor gene]]. APC gene product targets [[beta-catenin]] for degradation via ubiquitylation at the [[N-terminus]], thus regulating its cellular level. Most colorectal cancer cases are found with mutations in the APC gene. However, in cases where APC gene is not mutated, mutations are found in the N-terminus of beta-catenin which renders it ubiquitination-free and thus increased activity.<ref name="Sparks_1998" /><ref name="Mani_2005" />

==== Glioblastoma ====
As the most aggressive cancer originated in the brain, mutations found in patients with [[glioblastoma]] are related to the deletion of a part of the extracellular domain of the [[epidermal growth factor receptor]] (EGFR). This deletion causes [[CBL (gene)|CBL]] E3 ligase unable to bind to the receptor for its recycling and degradation via a ubiquitin-lysosomal pathway. Thus, EGFR is constitutively active in the cell membrane and activates its downstream effectors that are involved in cell proliferation and migration.<ref name="Schmidt_2003" />

=== Phosphorylation-dependent ubiquitylation ===
The interplay between ubiquitylation and [[phosphorylation]] has been an ongoing research interest since phosphorylation often serves as a marker where ubiquitylation leads to degradation.<ref name="Nguyen_2013" /> Moreover, ubiquitylation can also act to turn on/off the [[kinase]] activity of a protein.<ref>{{cite journal | vauthors = Witowsky JA, Johnson GL | title = Ubiquitylation of MEKK1 inhibits its phosphorylation of MKK1 and MKK4 and activation of the ERK1/2 and JNK pathways | journal = The Journal of Biological Chemistry | volume = 278 | issue = 3 | pages = 1403–6 | date = January 2003 | pmid = 12456688 | doi = 10.1074/jbc.C200616200 | doi-access = free }}</ref> The critical role of phosphorylation is largely underscored in the activation and removal of autoinhibition in the [[CBL (gene)|Cbl]] protein.<ref name="Kobashigawa_2011">{{cite journal | vauthors = Kobashigawa Y, Tomitaka A, Kumeta H, Noda NN, Yamaguchi M, Inagaki F | title = Autoinhibition and phosphorylation-induced activation mechanisms of human cancer and autoimmune disease-related E3 protein Cbl-b | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 108 | issue = 51 | pages = 20579–84 | date = December 2011 | pmid = 22158902 | pmc = 3251137 | doi = 10.1073/pnas.1110712108 | bibcode = 2011PNAS..10820579K | doi-access = free }}</ref> Cbl is an E3 ubiquitin ligase with a RING finger domain that interacts with its [[Cbl TKB domain|tyrosine kinase binding (TKB) domain]], preventing interaction of the RING domain with an [[Ubiquitin-conjugating enzyme|E2 ubiquitin-conjugating enzyme]]. This intramolecular interaction is an autoinhibition regulation that prevents its role as a negative regulator of various growth factors and [[tyrosine kinase]] signaling and [[T cell|T-cell]] activation.<ref name="Kobashigawa_2011" /> Phosphorylation of [[Tyrosine|Y363]] relieves the autoinhibition and enhances binding to E2.<ref name="Kobashigawa_2011" /> Mutations that render the Cbl protein dysfunctional due to the loss of its ligase/tumor suppressor function and maintenance of its positive signaling/oncogenic function have been shown to cause the development of cancer.<ref>{{cite journal | vauthors = Niemeyer CM, Kang MW, Shin DH, Furlan I, Erlacher M, Bunin NJ, Bunda S, Finklestein JZ, Sakamoto KM, Gorr TA, Mehta P, Schmid I, Kropshofer G, Corbacioglu S, Lang PJ, Klein C, Schlegel PG, Heinzmann A, Schneider M, Starý J, van den Heuvel-Eibrink MM, Hasle H, Locatelli F, Sakai D, Archambeault S, Chen L, Russell RC, Sybingco SS, Ohh M, Braun BS, Flotho C, Loh ML | title = Germline CBL mutations cause developmental abnormalities and predispose to juvenile myelomonocytic leukemia | journal = Nature Genetics | volume = 42 | issue = 9 | pages = 794–800 | date = September 2010 | pmid = 20694012 | pmc = 4297285 | doi = 10.1038/ng.641  }}</ref><ref>{{cite journal | vauthors = Kales SC, Ryan PE, Nau MM, Lipkowitz S | title = Cbl and human myeloid neoplasms: the Cbl oncogene comes of age | journal = Cancer Research | volume = 70 | issue = 12 | pages = 4789–94 | date = June 2010 | pmid = 20501843 | pmc = 2888780 | doi = 10.1158/0008-5472.CAN-10-0610  }}</ref>

=== As a drug target ===

==== Screening for ubiquitin ligase substrates ====
Deregulation of E3-substrate interactions is a key cause of many human disorders, therefore identifying E3 ligase substrates is crucial. In 2008, 'Global Protein Stability (GPS) Profiling' was developed to discover E3 ubiquitin ligase substrates.<ref name="Yen_2008">{{cite journal | vauthors = Yen HC, Elledge SJ | title = Identification of SCF ubiquitin ligase substrates by global protein stability profiling | journal = Science | volume = 322 | issue = 5903 | pages = 923–9 | year = 2008 | pmid = 18988848 | doi = 10.1126/science.1160462 | bibcode = 2008Sci...322..923Y | s2cid = 23586705 }}</ref> This high-throughput system made use of reporter proteins fused with thousands of potential substrates independently. By inhibition of the ligase activity (through the making of Cul1 dominant negative thus renders ubiquitination not to occur), increased reporter activity shows that the identified substrates are being accumulated. This approach added a large number of new substrates to the list of E3 ligase substrates.

==== Possible therapeutic applications ====
Blocking of specific substrate recognition by the E3 ligases, e.g. [[bortezomib]].<ref name="Nalepa_2003" />

==== Challenge ====
Finding a specific molecule that selectively inhibits the activity of a certain E3 ligase and/or the protein–protein interactions implicated in the disease remains as one of the important and expanding research area. Moreover, as ubiquitination is a multi-step process with various players and intermediate forms, consideration of the much complex interactions between components needs to be taken heavily into account while designing the small molecule inhibitors.<ref name="Pray_2002" />

== Similar proteins ==
{{anchor|Ubiquitin-like modifiers}}
{{main|Ubiquitin-like protein}}
Ubiquitin is the most-understood post-translation modifier, however, several family of [[ubiquitin-like protein]]s (UBLs) can modify cellular targets in a parallel but distinct route. Known UBLs include: small ubiquitin-like modifier ([[SUMO protein|SUMO]]), ubiquitin cross-reactive protein (UCRP, also known as interferon-stimulated gene-15 [[ISG15]]), ubiquitin-related modifier-1 ([[URM1]]), neuronal-precursor-cell-expressed developmentally downregulated protein-8 ([[NEDD8]], also called Rub1 in ''[[Saccharomyces cerevisiae|S. cerevisiae]]''), human leukocyte antigen F-associated ([[Ubiquitin D|FAT10]]), autophagy-8 ([[ATG8]]) and -12 ([[ATG12]]), Few ubiquitin-like protein ([[FAU (gene)|FUB1]]), MUB (membrane-anchored UBL),<ref name="pmid16831869">{{cite journal | vauthors = Downes BP, Saracco SA, Lee SS, Crowell DN, Vierstra RD | title = MUBs, a family of ubiquitin-fold proteins that are plasma membrane-anchored by prenylation | journal = The Journal of Biological Chemistry | volume = 281 | issue = 37 | pages = 27145–57 | date = September 2006 | pmid = 16831869 | doi = 10.1074/jbc.M602283200 | doi-access = free }}</ref> ubiquitin fold-modifier-1 ([[UFM1]]) and ubiquitin-like protein-5 ([[UBL5]], which is but known as homologous to ubiquitin-1 [Hub1] in ''[[Schizosaccharomyces pombe|S. pombe]]'').<ref name="pmid16064136">{{cite journal | vauthors = Welchman RL, Gordon C, Mayer RJ | title = Ubiquitin and ubiquitin-like proteins as multifunctional signals | journal = Nature Reviews Molecular Cell Biology | volume = 6 | issue = 8 | pages = 599–609 | date = August 2005 | pmid = 16064136 | doi = 10.1038/nrm1700 | s2cid = 7373421 }}</ref><ref name="pmid19253967">{{cite journal | vauthors = Grabbe C, Dikic I | title = Functional roles of ubiquitin-like domain (ULD) and ubiquitin-binding domain (UBD) containing proteins | journal = Chemical Reviews | volume = 109 | issue = 4 | pages = 1481–94 | date = April 2009 | pmid = 19253967 | doi = 10.1021/cr800413p }}</ref> Although these proteins share only modest primary sequence identity with ubiquitin, they are closely related three-dimensionally. For example, SUMO shares only 18% sequence identity, but they contain the same structural fold. This fold is called "ubiquitin fold". FAT10 and UCRP contain two. This compact globular beta-grasp fold is found in ubiquitin, UBLs, and proteins that comprise a ubiquitin-like domain, e.g. the ''S. cerevisiae'' spindle pole body duplication protein, Dsk2, and NER protein, Rad23, both contain N-terminal ubiquitin domains.

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 name="bostonbiochem.com"/>

Within some species, the recognition and destruction of sperm mitochondria through a mechanism involving ubiquitin is responsible for sperm mitochondria's disposal after fertilization occurs.<ref name="pmid10906068">{{cite journal | vauthors = Sutovsky P, Moreno RD, Ramalho-Santos J, Dominko T, Simerly C, Schatten G | title = Ubiquitinated sperm mitochondria, selective proteolysis, and the regulation of mitochondrial inheritance in mammalian embryos | journal = Biology of Reproduction | volume = 63 | issue = 2 | pages = 582–90 | date = August 2000 | pmid = 10906068 | doi = 10.1095/biolreprod63.2.582 | doi-access = free }}</ref>

===Prokaryotic origins ===
Ubiquitin is believed to have descended from bacterial proteins similar to [[ThiS]] ({{UniProt|O32583}})<ref name="pmid11135670">{{cite journal | vauthors = Wang C, Xi J, Begley TP, Nicholson LK | title = Solution structure of ThiS and implications for the evolutionary roots of ubiquitin | journal = Nature Structural Biology | volume = 8 | issue = 1 | pages = 47–51 | date = January 2001 | pmid = 11135670 | doi = 10.1038/83041 | s2cid = 29632248 }}</ref> or [[MoaD]] ({{UniProt|P30748}}).<ref name="pmid11713534">{{cite journal | vauthors = Lake MW, Wuebbens MM, Rajagopalan KV, Schindelin H | title = Mechanism of ubiquitin activation revealed by the structure of a bacterial MoeB-MoaD complex | journal = Nature | volume = 414 | issue = 6861 | pages = 325–9 | date = November 2001 | pmid = 11713534 | doi = 10.1038/35104586 | bibcode = 2001Natur.414..325L | s2cid = 3224437 }}</ref> These prokaryotic proteins, despite having little sequence identity (ThiS has 14% identity to ubiquitin), share the same protein fold. These proteins also share sulfur chemistry with ubiquitin. MoaD, which is involved in [[molybdopterin]] biosynthesis, interacts with MoeB, which acts like an [[Ubiquitin-activating enzyme|E1 ubiquitin-activating enzyme]] for MoaD, strengthening the link between these prokaryotic proteins and the ubiquitin system. A similar system exists for ThiS, with its E1-like enzyme [[ThiF]]. It is also believed that the ''[[Saccharomyces cerevisiae]]'' protein [[Urm1]], a ubiquitin-related modifier, is a "[[molecular fossil]]" that connects the evolutionary relation with the prokaryotic ubiquitin-like molecules and ubiquitin.<ref name="pmid19325621">{{cite journal | vauthors = Hochstrasser M | title = Origin and function of ubiquitin-like proteins | journal = Nature | volume = 458 | issue = 7237 | pages = 422–9 | date = March 2009 | pmid = 19325621 | pmc = 2819001 | doi = 10.1038/nature07958 | bibcode = 2009Natur.458..422H }}</ref>

[[Archaea]] have a functionally closer homolog of the ubiquitin modification system, where "sampylation" with SAMPs (small archaeal modifier proteins) is performed. The sampylation system only uses E1 to guide proteins to the [[proteosome]].<ref>{{cite book | vauthors = Maupin-Furlow JA | title = Regulated Proteolysis in Microorganisms | chapter = Archaeal Proteasomes and Sampylation | series = Subcellular Biochemistry | volume = 66 | pages = 297–327 | date = 2013 | pmid = 23479445 | pmc = 3936409 | doi = 10.1007/978-94-007-5940-4_11 | isbn = 978-94-007-5939-8 }}</ref> [[Proteoarchaeota]], which are related to the ancestor of eukaryotes, possess all of the E1, E2, and E3 enzymes plus a regulated Rpn11 system. Unlike SAMP which are more similar to ThiS or MoaD, Proteoarchaeota ubiquitin are most similar to eukaryotic homologs.<ref>{{cite journal | vauthors = Fuchs AC, Maldoner L, Wojtynek M, Hartmann MD, Martin J | title = Rpn11-mediated ubiquitin processing in an ancestral archaeal ubiquitination system | journal = Nature Communications | volume = 9 | issue = 1 | page = 2696 | date = July 2018 | pmid = 30002364 | pmc = 6043591 | doi = 10.1038/s41467-018-05198-1 | bibcode = 2018NatCo...9.2696F }}</ref>

== Prokaryotic ubiquitin-like protein (Pup) and ubiquitin bacterial (UBact) ==
{{main|Prokaryotic ubiquitin-like protein}}
[[Prokaryotic ubiquitin-like protein]] (Pup) is a [[Convergent evolution|functional analog]] of ubiquitin which has been found in the [[Gram-positive bacteria|gram-positive]] bacterial phylum [[Actinomycetota]]. It serves the same function (targeting proteins for degradations), although the enzymology of ubiquitylation and pupylation is different, and the two families share no homology. In contrast to the three-step reaction of ubiquitylation, pupylation requires two steps, therefore only two enzymes are involved in pupylation.

In 2017, homologs of Pup were reported in five phyla of [[gram-negative]] bacteria, in seven candidate bacterial phyla and in one archaeon<ref name="UBact paper">{{cite journal | vauthors = Lehmann G, Udasin RG, Livneh I, Ciechanover A | title = Identification of UBact, a ubiquitin-like protein, along with other homologous components of a conjugation system and the proteasome in different gram-negative bacteria | journal = Biochemical and Biophysical Research Communications | volume = 483 | issue = 3 | pages = 946–950 | date = February 2017 | pmid = 28087277 | doi = 10.1016/j.bbrc.2017.01.037 }}</ref> The sequences of the Pup homologs are very different from the sequences of Pup in gram-positive bacteria and were termed [[Ubiquitin bacterial]] (UBact), although the distinction has yet not been proven to be phylogenetically supported by a separate evolutionary origin and is without experimental evidence.<ref name="UBact paper" />

The finding of the Pup/UBact-proteasome system in both gram-positive and gram-negative bacteria suggests that either the Pup/UBact-proteasome system evolved in bacteria prior to the split into gram positive and negative clades over 3000 million years ago or,<ref name="evolution timeline">{{cite journal | vauthors = Marin J, Battistuzzi FU, Brown AC, Hedges SB | title = The Timetree of Prokaryotes: New Insights into Their Evolution and Speciation | journal = Molecular Biology and Evolution | volume = 34 | issue = 2 | pages = 437–446 | date = February 2017 | pmid = 27965376 | doi = 10.1093/molbev/msw245 | doi-access = free }}</ref> that these systems were acquired by different bacterial lineages through [[horizontal gene transfer]](s) from a third, yet unknown, organism. In support of the second possibility, two ''UBact'' loci were found in the genome of an uncultured anaerobic methanotrophic Archaeon (ANME-1;locus [https://www.ncbi.nlm.nih.gov/protein/268325220 CBH38808.1] and locus [https://www.ncbi.nlm.nih.gov/protein/268325670 CBH39258.1]).

== Antiphage defense in Bacteria ==

Bacterial ubiquitination is an evolutionarily conserved protein modification pathway that plays a role in bacterial antiviral defense. It exhibits structural and functional parallels to eukaryotic ubiquitination systems and contributes to bacterial defense against [[Bacteriophage]]. Recent reviews highlight the conservation and similarity of bacterial and eukaryotic innate immunity mechanisms.<ref name="Ledvina_2024">{{cite journal | vauthors = Ledvina HE, Whiteley AT | title = Conservation and similarity of bacterial and eukaryotic innate immunity | journal = Nat Rev Microbiol | volume = 22 | pages = 420–434 | date = 2024 | issue = 7 | doi = 10.1038/s41579-024-01017-1 | pmid = 38418927 | pmc = 11389603 }}</ref>

In one study, it was demonstrated that during phage infection, a bacterial system conjugates a Ubl protein to the phage's central tail fiber, a component essential for tail assembly and host recognition. This modification leads to the production of defective phage particles with impaired infectivity, thereby protecting the bacterial population from phage proliferation.<ref name="Hör_2024">{{cite journal | vauthors = Hör J, Wolf SG, Sorek R | title = Bacteria conjugate ubiquitin-like proteins to interfere with phage assembly | journal = Nature | volume = 631 | pages = 850–856 | date = 2024 | issue = 8022 | doi = 10.1038/s41586-024-07616-5 | pmid = 39020165 | bibcode = 2024Natur.631..850H }}</ref>

Another study revealed that a bacterial operon associated with phage defense encodes a complete ubiquitination pathway. Structural analyses of the bacterial E1–E2–Ubl complex showed significant similarities to canonical eukaryotic ubiquitination machinery, suggesting that the ubiquitination pathway may have originated in bacteria.<ref name="Chambers_2024">{{cite journal | vauthors = Chambers LR, Ye Q, Cai J | title = A eukaryotic-like ubiquitination system in bacterial antiviral defence | journal = Nature | volume = 631 | pages = 843–849 | date = 2024 | issue = 8022 | doi = 10.1038/s41586-024-07730-4 | pmid = 39020180 | pmc = 11476048 | bibcode = 2024Natur.631..843C }}</ref>

In all organisms, innate immune pathways sense infection and rapidly activate potent immune responses while avoiding inappropriate activation (autoimmunity). In humans, the innate immune receptor cyclic GMP–AMP synthase (cGAS) detects viral infection to produce the nucleotide second messenger cyclic GMP–AMP (cGAMP), which initiates stimulator of interferon genes (STING)-dependent antiviral signaling. Bacteria encode evolutionary predecessors of cGAS, called cGAS/DncV-like nucleotidyltransferases (CD-NTases), which detect bacteriophage infection and produce diverse nucleotide second messengers.<ref name="Ledvina_2023">{{cite journal | vauthors = Ledvina HE, Ye Q, Gu Y, et al. | title = An E1–E2 fusion protein primes antiviral immune signalling in bacteria | journal = Nature | volume = 616 | pages = 319–325 | date = 2023 | issue = 7956 | doi = 10.1038/s41586-022-05647-4 | pmid = 36755092 | pmc = 10292035 | bibcode = 2023Natur.616..319L }}</ref> 

The regulation of bacterial CD-NTase activation remains an open question. Recent research has shown that CD-NTase-associated protein 2 (Cap2) primes bacterial CD-NTases for activation through a ubiquitin transferase-like mechanism. A cryo-electron microscopy structure of the Cap2–CD-NTase complex reveals Cap2 as an all-in-one ubiquitin transferase-like protein, with distinct domains resembling eukaryotic E1 and E2 proteins. The structure captures a reactive-intermediate state with the CD-NTase C-terminus positioned in the Cap2 E1 active site and conjugated to AMP. Cap2 conjugates the CD-NTase C-terminus to a target molecule that primes the CD-NTase for increased cGAMP production. Additionally, a specific endopeptidase, Cap3, balances Cap2 activity by cleaving CD-NTase–target conjugates. This research demonstrates that bacteria control immune signaling using an ancient, minimized ubiquitin transferase-like system, providing insights into the evolution of E1 and E2 machinery across domains of life.<ref name="Ledvina_2023" />

== Human proteins containing ubiquitin domain ==
These include ubiquitin-like proteins.

[[ANUBL1]];    [[BAG1]];      [[BAT3|BAT3/BAG6]];       [[C1orf131]];       [[DDI1]];      [[DDI2]];      [[FAU (gene)|FAU]];       [[HERPUD1]];   [[HERPUD2]]; [[HOPS]];      [[IKBKB]];     [[ISG15]];     [[LOC391257]]; [[Midnolin|MIDN]];      [[NEDD8]];     [[OASL]];      [[PARK2]]; [[RAD23A]];    [[RAD23B]];    [[RPS27A]];    [[Sacsin|SACS]];     8U [[SF3A1]];     [[SUMO1]];     [[SUMO2]];     [[SUMO3]]; [[SUMO4]];     [[TMUB1]];     [[TMUB2]];     [[UBA52]];     [[Ubiquitin B|UBB]];       [[Ubiquitin C|UBC]];       [[Ubiquitin D|UBD]];       [[UBFD1]]; [[UBL4A]];     [[UBL4B]];     [[UBL7]];      [[UBLCP1]];    [[UBQLN1]];    [[UBQLN2]];    [[UBQLN3]]; [[UBQLN4]];    [[UBQLNL]];    [[UBTD1]];     [[UBTD2]];     [[UHRF1]];     [[UHRF2]];

== Related proteins ==
* [[UBA protein domain|Ubiquitin-associated protein domain]]

== Prediction of ubiquitination ==

Currently available prediction programs are:
* '''UbiPred''' is a [[Support Vector Machine|SVM]]-based prediction server using 31 physicochemical properties for predicting ubiquitylation sites.<ref name="UbiPred paper">{{cite journal | vauthors = Tung CW, Ho SY | title = Computational identification of ubiquitylation sites from protein sequences | journal = BMC Bioinformatics | volume = 9 | page = 310 | date = July 2008 | pmid = 18625080 | pmc = 2488362 | doi = 10.1186/1471-2105-9-310 | doi-access = free }}</ref>
* '''UbPred''' is a [[random forest]]-based predictor of potential ubiquitination sites in proteins. It was trained on a combined set of 266 non-redundant experimentally verified ubiquitination sites available from our experiments and from two large-scale proteomics studies.<ref name="UbPred paper">{{cite journal | vauthors = Radivojac P, Vacic V, Haynes C, Cocklin RR, Mohan A, Heyen JW, Goebl MG, Iakoucheva LM | title = Identification, analysis, and prediction of protein ubiquitination sites | journal = Proteins | volume = 78 | issue = 2 | pages = 365–80 | date = February 2010 | pmid = 19722269 | pmc = 3006176 | doi = 10.1002/prot.22555 }}</ref>
* '''CKSAAP_UbSite''' is SVM-based prediction that employs the composition of k-spaced amino acid pairs surrounding a query site (i.e. any lysine in a query sequence) as input, uses the same dataset as UbPred.<ref name="CKSAAP_UbSite paper">{{cite journal | vauthors = Chen Z, Chen YZ, Wang XF, Wang C, Yan RX, Zhang Z | title = Prediction of ubiquitination sites by using the composition of k-spaced amino acid pairs | journal = PLOS ONE | volume = 6 | issue = 7 | article-number = e22930 | year = 2011 | pmid = 21829559 | pmc = 3146527 | doi = 10.1371/journal.pone.0022930 | bibcode = 2011PLoSO...622930C | veditors = Fraternali F | doi-access = free }}</ref>

== See also ==
* [[Autophagy]]
* [[Autophagin]]
* [[Endoplasmic-reticulum-associated protein degradation]]
* [[JUNQ and IPOD]]
* [[Prokaryotic ubiquitin-like protein]]
* [[SUMO enzymes]]

== References ==
{{reflist|33em}}

== External links ==
* [https://www.ncbi.nlm.nih.gov/books/NBK1144/  GeneReviews/NCBI/NIH/UW entry on Angelman syndrome]
* [https://omim.org/search?index=entry&start=1&limit=10&search=omim/105830,601623,105830,601623&sort=score+desc&field=number OMIM entries on Angelman syndrome]
* [https://web.archive.org/web/20060324041127/http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinAc=P62988 UniProt entry for ubiquitin]
* {{cite web |title=7.340 Ubiquitination: The Proteasome and Human Disease |year=2004 |work=MIT OpenCourseWare |url=http://ocw.mit.edu/courses/biology/7-340-ubiquitination-the-proteasome-and-human-disease-fall-2004/ }} Notes from MIT course.
* {{MeshName|Ubiquitin}}

{{Protein posttranslational modification}}
{{Posttranslational modification}}
{{Chemokine receptor modulators}}
{{Authority control}}

[[Category:Proteins]]
[[Category:Post-translational modification]]
[[Category:Protein structure]]