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Rendered from {{PDB|1PE6}} | Pfam= PF00112 | Pfam_clan = CL0125 | InterPro = IPR000668 | SMART = SM00645 | PROSITE = PDOC00126 | MEROPS = C1 | SCOP = 1aec | TCDB = | OPM family = 355 | OPM protein = 1m6d | PDB = }} '''Cysteine proteases''', also known as '''thiol proteases''', are [[hydrolase]] [[enzyme]]s that degrade [[protein]]s. These [[protease]]s share a common [[catalysis|catalytic mechanism]] that involves a [[nucleophile|nucleophilic]] [[cysteine]] [[thiol]] in a [[catalytic triad]] or dyad.<ref name=":0">{{Cite journal|last1=Rawat|first1=Aadish|last2=Roy|first2=Mrinalini|last3=Jyoti|first3=Anupam|last4=Kaushik|first4=Sanket|last5=Verma|first5=Kuldeep|last6=Srivastava|first6=Vijay Kumar|date=August 2021|title=Cysteine proteases: Battling pathogenic parasitic protozoans with omnipresent enzymes|journal=Microbiological Research|volume=249|pages=126784|doi=10.1016/j.micres.2021.126784|issn=1618-0623|pmid=33989978|s2cid=234597200|doi-access=free}}</ref> Discovered by Gopal Chunder Roy in 1873, the first cysteine protease to be isolated and characterized was [[papain]], obtained from [[Papaya|''Carica papaya'']].<ref name=":0" /> Cysteine proteases are commonly encountered in [[fruits]] including the [[papaya]], [[pineapple]], [[Common fig|fig]] and [[kiwifruit]]. The proportion of protease tends to be higher when the fruit is unripe. In fact, the [[latex]] of dozens of different plant [[Family (biology)|families]] are known to contain cysteine proteases.<ref name="pmid18496785">{{cite journal | vauthors = Domsalla A, Melzig MF | title = Occurrence and properties of proteases in plant latices | journal = Planta Medica | volume = 74 | issue = 7 | pages = 699–711 | date = June 2008 | pmid = 18496785 | doi = 10.1055/s-2008-1074530 | doi-access = free }}</ref> Cysteine proteases are used as an ingredient in meat tenderizers. ==Classification== The [[MEROPS]] protease classification system counts 14 [[protein superfamily|superfamilies]] plus several currently unassigned families (as of 2013) each containing many [[protein family|families]]. Each superfamily uses the [[catalytic triad]] or dyad in a different [[protein fold]] and so represent [[convergent evolution]] of the [[catalytic mechanism]]. For [[protein superfamily|superfamilies]], P indicates a superfamily containing a mixture of [[nucleophile]] class families, and C indicates purely cysteine proteases. superfamily. Within each superfamily, [[protein family|families]] are designated by their catalytic nucleophile (C denoting cysteine proteases). :{| class="wikitable" |+Families of cysteine proteases ! [[protein superfamily|Superfamily]] !! [[protein family|Families]] !! Examples |- | [[clan CA|CA]] || C1, C2, C6, C10, C12, C16, C19, C28, C31, C32, C33, C39, C47, C51, C54, C58, C64, C65, C66, C67, C70, C71, C76, C78, C83, C85, C86, C87, C93, C96, C98, C101 |[[Papain]] (''[[Carica papaya]]''),<ref>{{cite journal | vauthors = Mitchel RE, Chaiken IM, Smith EL | title = The complete amino acid sequence of papain. Additions and corrections | journal = The Journal of Biological Chemistry | volume = 245 | issue = 14 | pages = 3485–92 | date = July 1970 | doi = 10.1016/S0021-9258(18)62954-0 | pmid = 5470818 | doi-access = free }}</ref> [[bromelain]] (''[[Ananas comosus]]''), [[cathepsin K]] (''[[liverwort]]'')<ref>{{cite journal | vauthors = Sierocka I, Kozlowski LP, Bujnicki JM, Jarmolowski A, Szweykowska-Kulinska Z | title = Female-specific gene expression in dioecious liverwort Pellia endiviifolia is developmentally regulated and connected to archegonia production | journal = BMC Plant Biology | volume = 14 | pages = 168 | date = June 2014 | pmid = 24939387 | pmc = 4074843 | doi = 10.1186/1471-2229-14-168 | doi-access = free }}</ref> and [[calpain]] (''[[Homo sapiens]]'')<ref>{{cite journal | vauthors = Sorimachi H, Ohmi S, Emori Y, Kawasaki H, Saido TC, Ohno S, Minami Y, Suzuki K | display-authors = 6 | title = A novel member of the calcium-dependent cysteine protease family | journal = Biological Chemistry Hoppe-Seyler | volume = 371 Suppl | pages = 171–6 | date = May 1990 | pmid = 2400579 }}</ref> |- | CD||C11, C13, C14, C25, C50, C80, C84||[[Caspase 1]] (''[[Rattus norvegicus]]'') and [[separase]] (''[[Saccharomyces cerevisiae]]'') |- | CE||C5, C48, C55, C57, C63, C79||[[Adenain]] (human [[adenovirus]] type 2) |- | CF||C15||[[Pyroglutamyl-peptidase I]] (''[[Bacillus amyloliquefaciens]]'') |- | CL||C60, C82||[[Sortase A]] (''[[Staphylococcus aureus]]'') |- | CM||C18||[[NS2-3 protease|Hepatitis C virus peptidase 2]] ([[hepatitis C virus]]) |- | CN||C9||[[Sindbis virus protease|Sindbis virus-type nsP2 peptidase]] ([[sindbis virus]]) |- | CO||C40||[[Dipeptidyl-peptidase VI]] (''[http://microbewiki.kenyon.edu/index.php/Lysinibacillus_sphaericus_C3-41 Lysinibacillus sphaericus]'') |- | CP||C97||[[DeSI-1 peptidase]] (''[[Mus musculus]]'') |- | [[PA clan|PA]]||[[Picornain 3C|C3]], [[TEV protease|C4]], C24, [[3C-like protease|C30]], C37, C62, C74, C99||[[TEV protease]] ([[tobacco etch virus]]) |- | PB||C44, C45, C59, C69, C89, C95||[[Amidophosphoribosyltransferase]] precursor (''[[Homo sapiens]]'') |- | PC||C26, C56||[[Gamma-glutamyl hydrolase]] (''[[Rattus norvegicus]]'') |- | PD||C46||[[Hedgehog protein]] (''[[Drosophila melanogaster]]'') |- | PE||P1||[[Beta-peptidyl aminopeptidase|DmpA aminopeptidase]] (''[[Brucella anthropi]]'') |- | unassigned||C7, C8, C21, C23, C27, C36, C42, C53, C75|| |} == Catalytic mechanism == [[Image:Cysteinprotease Reaktionsmechanismus.svg|thumb|300px|Reaction mechanism of the cysteine protease mediated cleavage of a peptide bond.]] {{See also|catalytic triad}} The first step in the reaction mechanism by which cysteine proteases catalyze the hydrolysis of peptide bonds is de[[protonation]] of a [[thiol]] in the [[enzyme]]'s active site by an adjacent [[amino acid]] with a basic [[side chain]], usually a [[histidine]] residue. The next step is nucleophilic attack by the [[deprotonated]] cysteine's [[anion]]ic [[sulfur]] on the [[Substrate (biochemistry)|substrate]] [[carbonyl]] [[carbon]]. In this step, a fragment of the substrate is released with an [[amine]] terminus, the [[histidine]] residue in the [[protease]] is restored to its deprotonated form, and a [[thioester]] intermediate linking the new [[carboxy-terminus]] of the substrate to the cysteine [[thiol]] is formed. Therefore, they are also sometimes referred to as thiol proteases. The [[thioester]] bond is subsequently [[hydrolysis|hydrolyzed]] to generate a [[carboxylic acid]] moiety on the remaining substrate fragment, while regenerating the free enzyme.<ref name=":1" /> == Biological importance == Cysteine proteases play multifaceted roles, virtually in every aspect of physiology and development. In plants they are important in growth and development and in accumulation and mobilization of storage proteins such as in seeds. In addition, they are involved in [[signalling pathway]]s and in the response to [[Biotic component|biotic]] and [[abiotic]] stresses.<ref name="pmid15448724">{{cite journal | vauthors = Grudkowska M, Zagdańska B | title = Multifunctional role of plant cysteine proteinases | journal = Acta Biochimica Polonica | volume = 51 | issue = 3 | pages = 609–24 | year = 2004 | pmid = 15448724 | doi = 10.18388/abp.2004_3547 | doi-access = free }}</ref> In humans and other animals, they are responsible for [[senescence]] and [[apoptosis]] (programmed cell death), MHC class II [[immune response]]s, [[prohormone]] processing, and [[extracellular matrix]] remodeling important to bone development. The ability of [[macrophages]] and other cells to mobilize elastolytic cysteine proteases to their surfaces under specialized conditions may also lead to accelerated [[collagen]] and [[elastin]] degradation at sites of [[inflammation]] in [[diseases]] such as [[atherosclerosis]] and [[emphysema]].<ref name="pmid9074757">{{cite journal | vauthors = Chapman HA, Riese RJ, Shi GP | title = Emerging roles for cysteine proteases in human biology | journal = Annual Review of Physiology | volume = 59 | pages = 63–88 | year = 1997 | pmid = 9074757 | doi = 10.1146/annurev.physiol.59.1.63 }}</ref> Several viruses (such as [[polio]] and [[Hepatitis C virus|hepatitis C]]) express their entire [[genome]] as a single massive [[polyprotein]] and use a protease to cleave it into functional units (for example, [[tobacco etch virus protease]]). == Regulation == The activity of cysteine proteases is regulated by a few general mechanisms, which includes the production of [[Zymogenous|zymogens]], selective expression, pH modification, cellular compartmentalization, and regulation of their enzymatic activity by endogenous [[Enzyme inhibitor|inhibitors]], which seemingly is the most efficient mechanism associated with the regulation of the activity of cysteine proteases.<ref name=":1">{{Cite journal |last1=Roy |first1=Mrinalini |last2=Rawat |first2=Aadish |last3=Kaushik |first3=Sanket |last4=Jyoti |first4=Anupam |last5=Srivastava |first5=Vijay Kumar |date=May 2022 |title=Endogenous cysteine protease inhibitors in upmost pathogenic parasitic protozoa |journal=Microbiological Research |volume=261 |language=en |pages=127061 |doi=10.1016/j.micres.2022.127061|pmid=35605309 |s2cid=248741177 |doi-access=free }}</ref> Proteases are usually synthesized as large precursor proteins called [[zymogens]], such as the [[serine protease]] precursors [[trypsinogen]] and [[chymotrypsinogen]], and the [[aspartic protease]] precursor [[pepsinogen]]. The protease is activated by removal of an inhibitory segment or protein. Activation occurs once the protease is delivered to a specific intracellular compartment (for example the [[lysosome]]) or extracellular environment (for example the [[stomach]]). This system prevents the [[cell (biology)|cell]] that produces the protease from being damaged by it. Protease [[Enzyme inhibitor|inhibitor]]s are usually proteins with [[structural domain|domain]]s that enter or block a protease [[active site]] to prevent [[Substrate (biochemistry)|substrate]] access. In [[competitive inhibition]], the inhibitor binds to the active site, thus preventing enzyme-substrate interaction. In [[non-competitive inhibition]], the inhibitor binds to an [[allosteric site]], which alters the active site and makes it inaccessible to the substrate. Examples of protease inhibitors include: * [[Serpin]]s * [[Stefin]]s * [[Inhibitor of apoptosis|IAP]]s == Uses == {{see also|Papain#Uses|Bromelain#Uses|Ficain|Chymopapain#Medical applications}} === Potential pharmaceuticals === Currently there is no widespread use of cysteine proteases as approved and effective [[anthelmintic]]s but research into the subject is a promising field of study. Plant cysteine proteases isolated from these plants have been found to have high [[proteolysis|proteolytic activities]] that are known to digest [[nematode]] [[cuticle]]s, with very low toxicity.<ref name="pmid15193563">{{cite journal | vauthors = Stepek G, Behnke JM, Buttle DJ, Duce IR | title = Natural plant cysteine proteinases as anthelmintics? | journal = Trends in Parasitology | volume = 20 | issue = 7 | pages = 322–7 | date = July 2004 | pmid = 15193563 | doi = 10.1016/j.pt.2004.05.003 }}</ref> Successful results have been reported against nematodes such as ''[[Heligmosomoides bakeri]]'', ''[[Trichinella spiralis]]'', ''[[Nippostrongylus brasiliensis]]'', ''[[Trichuris muris]]'', and ''[[Ancylostoma ceylanicum]]''; the [[tapeworm]] ''[[Rodentolepis microstoma]]'', and the [[porcine]] [[acanthocephala]]n parasite ''[[Macracanthorhynchus]] hirundinaceus''.<ref name="pmid18761736">{{cite journal | vauthors = Behnke JM, Buttle DJ, Stepek G, Lowe A, Duce IR | title = Developing novel anthelmintics from plant cysteine proteinases | journal = Parasites & Vectors | volume = 1 | issue = 1 | pages = 29 | date = September 2008 | pmid = 18761736 | pmc = 2559997 | doi = 10.1186/1756-3305-1-29 | doi-access = free }}</ref> A useful property of cysteine proteases is the resistance to acid digestion, allowing possible [[oral administration]]. They provide an alternative mechanism of action to current anthelmintics and the development of resistance is thought to be unlikely because it would require a complete change of structure of the helminth [[cuticle]]. In several [[traditional medicine]]s, the fruits or latex of the papaya, pineapple and fig are widely used for treatment of [[intestinal parasite|intestinal worm]] [[infections]] both in humans and [[livestock]]. === Other === Cysteine proteases are used as feed additives for livestock to improve the digestibility of proteins and amino acids.<ref>{{cite web|title=Protease enzymes improve amino acid digestibility|url=https://www.wattagnet.com/articles/12390-protease-enzymes-improve-amino-acid-digestibility|first1=Terrence|last1=O'Keefe|publisher=Wattagnet|date=6 April 2012|access-date=6 January 2018}}</ref> == See also == {{colbegin}} *[[Protease]] **[[Serine protease]] **[[Threonine protease]] **[[Aspartic protease]] **[[Metalloprotease]] *[[Enzyme]] *[[Proteolysis]] *[[Catalytic triad]] *[[Convergent evolution]] *[[PA clan]] *[[The Proteolysis Map]] *[[Protease inhibitor (pharmacology)]] *[[Protease inhibitor (biology)]] *[[TopFIND]] – database of protease specificity, substrates, products and inhibitors *[[MEROPS]] – database of protease evolutionary groups {{colend}} == References == {{Reflist}} == External links == * The [[MEROPS]] online database for peptidases and their inhibitors: [http://merops.sanger.ac.uk/cgi-bin/family_index?type=P#C Cysteine Peptidases] {{Webarchive|url=https://web.archive.org/web/20170404112415/http://merops.sanger.ac.uk/cgi-bin/family_index?type=P#C |date=2017-04-04 }} * {{MeshName|Cysteine+endopeptidases}} {{Proteases}} {{Cysteine proteases}} {{Enzymes}} {{Portal bar|Biology|border=no}} [[Category:EC 3.4.22|*]] [[Category:Proteases]] </textarea><div class="templatesUsed"><div class="mw-templatesUsedExplanation"><p><span id="templatesused">Pages transcluded onto the current version of this page<span class="posteditwindowhelplinks"> (<a href="/wiki/Help:Transclusion" title="Help:Transclusion">help</a>)</span>:</span> </p></div><ul> <li><a href="/wiki/Template:Cite_journal" title="Template:Cite journal">Template:Cite journal</a> (<a 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