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48  structures 1630  species 0  interactions 13863  sequences 368  architectures

Family: Peptidase_C2 (PF00648)

Summary: Calpain family cysteine protease

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Calpain". More...

Calpain Edit Wikipedia article

PDB 1mdw EBI.jpg
Crystal structure of the peptidase core of Calpain II.
Pfam clanCL0125
EC number3.4.22.52
CAS number689772-75-6
IntEnzIntEnz view
ExPASyNiceZyme view
MetaCycmetabolic pathway
PDB structuresRCSB PDB PDBe PDBsum
EC number3.4.22.53
CAS number702693-80-9
IntEnzIntEnz view
ExPASyNiceZyme view
MetaCycmetabolic pathway
PDB structuresRCSB PDB PDBe PDBsum

A calpain (/ˈkælpeɪn/;[1] EC, EC is a protein belonging to the family of calcium-dependent, non-lysosomal cysteine proteases (proteolytic enzymes) expressed ubiquitously in mammals and many other organisms. Calpains constitute the C2 family of protease clan CA in the MEROPS database. The calpain proteolytic system includes the calpain proteases, the small regulatory subunit CAPNS1, also known as CAPN4, and the endogenous calpain-specific inhibitor, calpastatin.


The history of calpain originates in 1964, when calcium-dependent proteolytic activities caused by a “calcium-activated neutral protease” (CANP) were detected in brain, lens of the eye and other tissues. In the late 1960s the enzymes were isolated and characterised independently in both rat brain and skeletal muscle. These activities were caused by an intracellular cysteine protease not associated with the lysosome and having an optimum activity at neutral pH, which clearly distinguished it from the cathepsin family of proteases. The calcium-dependent activity, intracellular localization, and the limited, specific proteolysis on its substrates, highlighted calpain’s role as a regulatory, rather than a digestive, protease. When the sequence of this enzyme became known,[2] it was given the name “calpain”, to recognize it as a hybrid of two well-known proteins at the time, the calcium-regulated signalling protein, calmodulin, and the cysteine protease of papaya, papain. Shortly thereafter, the activity was found to be attributable to two main isoforms, dubbed μ ("mu")-calpain and m-calpain (or calpain I and II), that differed primarily in their calcium requirements in vitro. Their names reflect the fact that they are activated by micro- and nearly millimolar concentrations of Ca2+ within the cell, respectively.[3]

To date, these two isoforms remain the best characterised members of the calpain family. Structurally, these two heterodimeric isoforms share an identical small (28 k) subunit (CAPNS1 (formerly CAPN4)), but have distinct large (80 k) subunits, known as calpain 1 and calpain 2 (each encoded by the CAPN1 and CAPN2 genes, respectively).

Cleavage specificity

No specific amino acid sequence is uniquely recognized by calpains. Amongst protein substrates, tertiary structure elements rather than primary amino acid sequences are likely responsible for directing cleavage to a specific substrate. Amongst peptide and small-molecule substrates, the most consistently reported specificity is for small, hydrophobic amino acids (e.g. leucine, valine and isoleucine) at the P2 position, and large hydrophobic amino acids (e.g. phenylalanine and tyrosine) at the P1 position.[4] Arguably, the best currently available fluorogenic calpain substrate is (EDANS)-Glu-Pro-Leu-Phe=Ala-Glu-Arg-Lys-(DABCYL), with cleavage occurring at the Phe=Ala bond.

Extended family

The Human Genome Project has revealed that more than a dozen other calpain isoforms exist, some with multiple splice variants.[5][6][7] As the first calpain whose three-dimensional structure was determined, m-calpain is the type-protease for the C2 (calpain) family in the MEROPS database.

Gene Protein Aliases Tissue expression Disease linkage
CAPN1 Calpain 1 Calpain-1 large subunit, Calpain mu-type ubiquitous
CAPN2 Calpain 2 Calpain-2 large subunit ubiquitous
CAPN3 Calpain 3 skeletal muscle retina and lens specific Limb Girdle muscular dystrophy 2A
CAPN5 Calpain 5 ubiquitous (high in colon, small intestine and testis) might be linked to necrosis,
as it is an ortholog of the C. elegans necrosis gene tra-3
CAPN6 Calpain 6 CAPNX, Calpamodulin
CAPN7 Calpain 7 palBH ubiquitous
CAPN8 Calpain 8 exclusive to stomach mucosa and the GI track might be linked to colon polyp formation
CAPN9 Calpain 9 exclusive to stomach mucosa and the GI track might be linked to colon polyp formation
CAPN10 Calpain 10 susceptibility gene for type II diabetes
CAPN11 Calpain 11 testis
CAPN12 Calpain 12 ubiquitous but high in hair follicle
CAPN13 Calpain 13 testis and lung
CAPN14 Calpain 14 ubiquitous
CAPN17 Calpain 17 Fish and amphibian-only
SOLH Calpain 15 Sol H (homolog of the drosophila gene sol)
CAPNS1 Calpain small subunit 1 Calpain 4
CAPNS2 Calpain small subunit 2


Although the physiological role of calpains is still poorly understood, they have been shown to be active participants in processes such as cell mobility and cell cycle progression, as well as cell-type specific functions such as long-term potentiation in neurons and cell fusion in myoblasts. Under these physiological conditions, a transient and localized influx of calcium into the cell activates a small local population of calpains (for example, those close to Ca2+ channels), which then advance the signal transduction pathway by catalyzing the controlled proteolysis of its target proteins.[8] Additionally, phosphorylation by protein kinase A and dephosphorylation by alkaline phosphatase have been found to positively regulate the activity of μ-calpains by increasing random coils and decreasing β-sheets in its structure. Phosphorylation improves proteolytic activity and stimulates auto-activation of μ-calpains. However, increased calcium concentration overruns the effects of phosphorylation and dephosphorylation on calpain activity, and thus calpain activity ultimately depends on the presence of calcium.[9] Other reported roles of calpains are in cell function, helping to regulate clotting and the diameter of blood vessels, and playing a role in memory. Calpains have been implicated in apoptotic cell death, and appear to be an essential component of necrosis. Detergent fractionation revealed the cytosolic localization of calpain.[8]

Enhanced calpain activity, regulated by CAPNS1, significantly contributes to platelet hyperreactivity under hypoxic environment.[10]

In the brain, while μ-calpain is mainly located in the cell body and dendrites of neurons and to a lesser extent in axons and glial cells, m-calpain is found in glia and a small number in axons.[11] Calpain is also involved in skeletal muscle protein breakdown due to exercise and altered nutritional states.[12]

Clinical significance


The structural and functional diversity of calpains in the cell is reflected in their involvement in the pathogenesis of a wide range of disorders. At least two well known genetic disorders and one form of cancer have been linked to tissue-specific calpains. When defective, the mammalian calpain 3 (also known as p94) is the gene product responsible for limb-girdle muscular dystrophy type 2A,[13][14] calpain 10 has been identified as a susceptibility gene for type II diabetes mellitus, and calpain 9 has been identified as a tumour suppressor for gastric cancer. Moreover, the hyperactivation of calpains is implicated in a number of pathologies associated with altered calcium homeostasis such as Alzheimer's disease,[15] and cataract formation, as well as secondary degeneration resulting from acute cellular stress following myocardial ischemia, cerebral (neuronal) ischemia, traumatic brain injury and spinal cord injury. Excessive amounts of calpain can be activated due to Ca2+ influx after cerebrovascular accident (during the ischemic cascade) or some types of traumatic brain injury such as diffuse axonal injury. Increase in concentration of calcium in the cell results in calpain activation, which leads to unregulated proteolysis of both target and non-target proteins and consequent irreversible tissue damage. Excessively active calpain breaks down molecules in the cytoskeleton such as spectrin, microtubule subunits, microtubule-associated proteins, and neurofilaments.[16][17] It may also damage ion channels, other enzymes, cell adhesion molecules, and cell surface receptors.[11] This can lead to degradation of the cytoskeleton and plasma membrane. Calpain may also break down sodium channels that have been damaged due to axonal stretch injury,[18] leading to an influx of sodium into the cell. This, in turn, leads to the neuron's depolarization and the influx of more Ca2+. A significant consequence of calpain activation is the development of cardiac contractile dysfunction that follows ischemic insult to the heart. Upon reperfusion of the ischemic myocardium, there is development of calcium overload or excess in the heart cell (cardiomyocytes). This increase in calcium leads to activation of calpain.[19][irrelevant citation] Recently calpain has been implicated in promoting high altitude induced venous thrombosis by mediating platelet hyperactivation.[10]

Therapeutic inhibitors

The exogenous regulation of calpain activity is therefore of interest for the development of therapeutics in a wide array of pathological states. As a few of the many examples supporting the therapeutic potential of calpain inhibition in ischemia, calpain inhibitor AK275 protected against focal ischemic brain damage in rats when administered after ischemia, and MDL28170 significantly reduced the size of damaged infarct tissue in a rat focal ischemia model. Also, calpain inhibitors are known to have neuroprotective effects: PD150606,[20] SJA6017,[21] ABT-705253,[22][23] and SNJ-1945.[24]

Calpain may be released in the brain for up to a month after a head injury, and may be responsible for a shrinkage of the brain sometimes found after such injuries.[25] However, calpain may also be involved in a "resculpting" process that helps repair damage after injury.[25]

See also


  1. ^ "the definition of calpain". Retrieved 23 April 2018.
  2. ^ Ohno S, Emori Y, Imajoh S, Kawasaki H, Kisaragi M, Suzuki K (1984). "Evolutionary origin of a calcium-dependent protease by fusion of genes for a thiol protease and a calcium-binding protein?". Nature. 312 (5994): 566–70. doi:10.1038/312566a0. PMID 6095110.
  3. ^ Glass JD, Culver DG, Levey AI, Nash NR (April 2002). "Very early activation of m-calpain in peripheral nerve during Wallerian degeneration". J. Neurol. Sci. 196 (1–2): 9–20. doi:10.1016/S0022-510X(02)00013-8. PMID 11959150.
  4. ^ Cuerrier D, Moldoveanu T, Davies PL (December 2005). "Determination of peptide substrate specificity for mu-calpain by a peptide library-based approach: the importance of primed side interactions". J. Biol. Chem. 280 (49): 40632–41. doi:10.1074/jbc.M506870200. PMID 16216885.
  5. ^ Thompson V (2002-02-12). "Calpain Nomenclature". College of Agriculture and Life Sciences at the University of Arizona. Retrieved 2010-08-06.
  6. ^ Huang Y, Wang KK (August 2001). "The calpain family and human disease". Trends Mol Med. 7 (8): 355–62. doi:10.1016/S1471-4914(01)02049-4. PMID 11516996.
  7. ^ Suzuki K, Hata S, Kawabata Y, Sorimachi H (February 2004). "Structure, activation, and biology of calpain". Diabetes. 53. Suppl 1: S12–8. doi:10.2337/diabetes.53.2007.s12. PMID 14749260.
  8. ^ a b Jaguva Vasudevan, AA; Perkovic, M; Bulliard, Y; Cichutek, K; Trono, D; Häussinger, D; Münk, C (August 2013). "Prototype foamy virus Bet impairs the dimerization and cytosolic solubility of human APOBEC3G". Journal of Virology. 87 (16): 9030–40. doi:10.1128/JVI.03385-12. PMC 3754047. PMID 23760237.
  9. ^ Du, Manting; Li, Xin; Li, Zheng; Shen, Qingwu; Wang, Ying; Li, Guixia; Zhang, Dequan (2018-06-30). "Phosphorylation regulated by protein kinase A and alkaline phosphatase play positive roles in μ-calpain activity". Food Chemistry. 252: 33–39. doi:10.1016/j.foodchem.2018.01.103. ISSN 0308-8146. PMID 29478550.
  10. ^ a b Tyagi, T.; Ahmad, S.; Gupta, N.; Sahu, A.; Ahmad, Y.; Nair, V.; Chatterjee, T.; Bajaj, N.; Sengupta, S.; Ganju, L.; Singh, S. B.; Ashraf, M. Z. (Feb 2014). "Altered expression of platelet proteins and calpain activity mediate hypoxia-induced prothrombotic phenotype". Blood. 123 (8): 1250–60. doi:10.1182/blood-2013-05-501924. PMID 24297866.
  11. ^ a b Lenzlinger PM, Saatman KE, Raghupathi R, Mcintosh TK (2000). "Chapter 1: Overview of basic mechanisms underlying neuropathological consequences of head trauma". In Newcomb JK, Miller LS, Hayes RL (eds.). Head trauma: basic, preclinical, and clinical directions. New York: Wiley-Liss. ISBN 978-0-471-36015-5.
  12. ^ Belcastro AN, Albisser TA, Littlejohn B (October 1996). "Role of calcium-activated neutral protease (calpain) with diet and exercise". Can J Appl Physiol. 21 (5): 328–46. doi:10.1139/h96-029. PMID 8905185.
  13. ^ Richard I, Broux O, Allamand V, et al. (April 1995). "Mutations in the proteolytic enzyme calpain 3 cause limb-girdle muscular dystrophy type 2A". Cell. 81 (1): 27–40. doi:10.1016/0092-8674(95)90368-2. PMID 7720071.
  14. ^ Ono Y, Shimada H, Sorimachi H, et al. (July 1998). "Functional defects of a muscle-specific calpain, p94, caused by mutations associated with limb-girdle muscular dystrophy type 2A". J. Biol. Chem. 273 (27): 17073–8. doi:10.1074/jbc.273.27.17073. PMID 9642272.
  15. ^ Yamashima T (2013). "Reconsider Alzheimer's disease by the 'calpain-cathepsin hypothesis'--a perspective review". Progress in Neurology. 105: 1–23. doi:10.1016/j.pneurobio.2013.02.004. PMID 23499711.
  16. ^ Liu J, Liu MC, Wang KK (April 2008). "Calpain in the CNS: from synaptic function to neurotoxicity". Sci. Signal. 1 (14): re 1. doi:10.1126/stke.114re1. PMID 18398107.
  17. ^ Castillo MR, Babson JR (October 1998). "Ca2+-dependent mechanisms of cell injury in cultured cortical neurons". Neuroscience. 86 (4): 1133–44. doi:10.1016/S0306-4522(98)00070-0. PMID 9697120.
  18. ^ Iwata A, Stys PK, Wolf JA, et al. (May 2004). "Traumatic axonal injury induces proteolytic cleavage of the voltage-gated sodium channels modulated by tetrodotoxin and protease inhibitors". J. Neurosci. 24 (19): 4605–13. doi:10.1523/JNEUROSCI.0515-03.2004. PMID 15140932.
  19. ^ Wang KK, Larner SF, Robinson G, Hayes RL (December 2006). "Neuroprotection targets after traumatic brain injury". Curr. Opin. Neurol. 19 (6): 514–9. doi:10.1097/WCO.0b013e3280102b10. PMID 17102687.
  20. ^ Wang KK, Nath R, Posner A, Raser KJ, Buroker-Kilgore M, Hajimohammadreza I, Probert AW, Marcoux FW, Ye Q, Takano E, Hatanaka M, Maki M, Caner H, Collins JL, Fergus A, Lee KS, Lunney EA, Hays SJ, Yuen P (June 1996). "An alpha-mercaptoacrylic acid derivative is a selective nonpeptide cell-permeable calpain inhibitor and is neuroprotective". Proc. Natl. Acad. Sci. U.S.A. 93 (13): 6687–92. doi:10.1073/pnas.93.13.6687. PMC 39087. PMID 8692879.
  21. ^ Kupina NC, Nath R, Bernath EE, Inoue J, Mitsuyoshi A, Yuen PW, Wang KK, Hall ED (November 2001). "The novel calpain inhibitor SJA6017 improves functional outcome after delayed administration in a mouse model of diffuse brain injury" (PDF). J. Neurotrauma. 18 (11): 1229–40. doi:10.1089/089771501317095269. PMID 11721741.
  22. ^ Lubisch W, Beckenbach E, Bopp S, Hofmann HP, Kartal A, Kästel C, Lindner T, Metz-Garrecht M, Reeb J, Regner F, Vierling M, Möller A (June 2003). "Benzoylalanine-derived ketoamides carrying vinylbenzyl amino residues: discovery of potent water-soluble calpain inhibitors with oral bioavailability". J. Med. Chem. 46 (12): 2404–12. doi:10.1021/jm0210717. PMID 12773044.
  23. ^ Nimmrich V, Reymann KG, Strassburger M, Schöder UH, Gross G, Hahn A, Schoemaker H, Wicke K, Möller A (April 2010). "Inhibition of calpain prevents NMDA-induced cell death and beta-amyloid-induced synaptic dysfunction in hippocampal slice cultures". Br. J. Pharmacol. 159 (7): 1523–31. doi:10.1111/j.1476-5381.2010.00652.x. PMC 2850408. PMID 20233208.
  24. ^ Koumura A, Nonaka Y, Hyakkoku K, Oka T, Shimazawa M, Hozumi I, Inuzuka T, Hara H (November 2008). "A novel calpain inhibitor, ((1S)-1((((1S)-1-benzyl-3-cyclopropylamino-2,3-di-oxopropyl)amino)carbonyl)-3-methylbutyl) carbamic acid 5-methoxy-3-oxapentyl ester, protects neuronal cells from cerebral ischemia-induced damage in mice". Neuroscience. 157 (2): 309–18. doi:10.1016/j.neuroscience.2008.09.007. PMID 18835333.
  25. ^ a b White V (1999-10-21). "– 'Biochemical Storm' Following Brain Trauma An Important Factor In Treatment, University of Florida Researcher Finds". University of Florida News. Archived from the original on 2011-06-23. Retrieved 2010-08-07.

Further reading

  • Liu J, Liu MC, Wang KK (2008). "Calpain in the CNS: from synaptic function to neurotoxicity". Sci Signal. 1 (14): re1. doi:10.1126/stke.114re1. PMID 18398107.
  • Suzuki K, Hata S, Kawabata Y, Sorimachi H (February 2004). "Structure, activation, and biology of calpain". Diabetes. 53. Suppl 1: S12–8. doi:10.2337/diabetes.53.2007.s12. PMID 14749260.
  • Yuen PW, Wang KW (1999). Calpains : Pharmacology and Toxicology of a Cellular Protease. Boca Raton: CRC Press. ISBN 978-1-56032-713-4.

External links

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Calpain family cysteine protease Provide feedback

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Internal database links

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This tab holds annotation information from the InterPro database.

InterPro entry IPR001300

This group of cysteine peptidases belong to the MEROPS peptidase family C2 (calpain family, clan CA). A type example is calpain, which is an intracellular protease involved in many important cellular functions that are regulated by calcium [ PUBMED:2539381 , PUBMED:11517928 ]. The protein is a complex of 2 polypeptide chains (light and heavy), with eleven known active peptidases in humans and two non-peptidase homologues known as calpamodulin and androglobin [ PUBMED:21864727 ]. These include a highly calcium-sensitive (i.e., micro-molar range) form known as mu-calpain, mu-CANP or calpain I; a form sensitive to calcium in the milli-molar range, known as m-calpain, m-CANP or calpain II; and a third form, known as p94, which is found in skeletal muscle only [ PUBMED:2555341 ].

All forms have identical light but different heavy chains. Both mu- and m-calpain are heterodimers containing an identical 28kDa subunit and an 80kDa subunit that shares 55-65% sequence homology between the two proteases [ PUBMED:7845226 , PUBMED:2539381 ]. The crystallographic structure of m-calpain reveals six "domains" in the 80kDa subunit [ PUBMED:9396712 , PUBMED:11328585 ]:

  1. A 19-amino acid NH2-terminal sequence;
  2. Active site domain IIa;
  3. Active site domain IIb. Domain 2 shows low levels of sequence similarity to papain; although the catalytic His has not been located by biochemical means, it is likely that calpain and papain are related [ PUBMED:7845226 ].
  4. Domain III;
  5. An 18-amino acid extended sequence linking domain III to domain IV;
  6. Domain IV, which resembles the penta EF-hand family of polypeptides, binds calcium and regulates activity [ PUBMED:7845226 ]. Ca 2+ -binding causes a rearrangement of the protein backbone, the net effect of which is that a Trp side chain, which acts as a wedge between catalytic domains IIa and IIb in the apo state, moves away from the active site cleft allowing for the proper formation of the catalytic triad [ PUBMED:11914728 ].

Calpain-like mRNAs have been identified in other organisms including bacteria, but the molecules encoded by these mRNAs have not been isolated, so little is known about their properties. How calpain activity is regulated in these organisms cells is still unclear In metazoans, the activity of calpain is controlled by a single proteinase inhibitor, calpastatin ( INTERPRO ). The calpastatin gene can produce eight or more calpastatin polypeptides ranging from 17 to 85kDa by use of different promoters and alternative splicing events. The physiological significance of these different calpastatins is unclear, although all bind to three different places on the calpain molecule; binding to at least two of the sites is Ca2+ dependent. The calpains ostensibly participate in a variety of cellular processes including remodelling of cytoskeletal/membrane attachments, different signal transduction pathways, and apoptosis. Deregulated calpain activity following loss of Ca2+ homeostasis results in tissue damage in response to events such as myocardial infarcts, stroke, and brain trauma [ PUBMED:12843408 ].

Calpains are a family of cytosolic cysteine proteinases (see PROSITEDOC ). Members of the calpain family are believed to function in various biological processes, including integrin-mediated cell migration, cytoskeletal remodeling, cell differentiation and apoptosis [ PUBMED:11854009 , PUBMED:11950589 ].

The calpain family includes numerous members from C. elegans to mammals and with homologues in yeast and bacteria. The best characterised members are the m- and mu-calpains, both proteins are heterodimer composed of a large catalytic subunit and a small regulatory subunit. The large subunit comprises four domains (dI-dIV) while the small subunit has two domains (dV-dVI). Domain dI is a short region cleaved by autolysis, dII is the catalytic core, dIII is a C2-like domain, dIV consists of five calcium binding EF-hand motifs [ PUBMED:11950589 ].

The crystal structure of calpain has been solved [ PUBMED:10601010 , PUBMED:11893336 ]. The catalytic region consists of two distinct structural domains (dIIa and dIIb). dIIa contains a central helix flanked on three faces by a cluster of alpha-helices and is entirely unrelated to the corresponding domain in the typical thiol proteinases. The fold of dIIb is similar to the corresponding domain in other cysteine proteinases and contains two three-stranded anti-parallel beta-sheets. The catalytic triad residues (C,H,N) are located in dIIa and dIIb. The activation of the domain is dependent on the binding of two calcium atoms in two non EF-hand calcium binding sites located in the catalytic core, one close to the Cys active site in dIIa and one at the end of dIIb. Calcium-binding induced conformational changes in the catalytic domain which align the active site [ PUBMED:11893336 ][ PUBMED:11914728 ].

The profile covers the whole catalytic domain.

Cysteine peptidases with a chymotrypsin-like fold are included in clan PA, which also includes serine peptidases. Cysteine peptidases that are N-terminal nucleophile hydrolases are included in clan PB. Cysteine peptidases with a tertiary structure similar to that of the serine-type aspartyl dipeptidase are included in clan PC. Cysteine peptidases with an intein-like fold are included in clan PD, which also includes asparagine lyases.

A cysteine peptidase is a proteolytic enzyme that hydrolyses a peptide bond using the thiol group of a cysteine residue as a nucleophile. Hydrolysis involves usually a catalytic triad consisting of the thiol group of the cysteine, the imidazolium ring of a histidine, and a third residue, usually asparagine or aspartic acid, to orientate and activate the imidazolium ring. In only one family of cysteine peptidases, is the role of the general base assigned to a residue other than a histidine: in peptidases from family C89 (acid ceramidase) an arginine is the general base. Cysteine peptidases can be grouped into fourteen different clans, with members of each clan possessing a tertiary fold unique to the clan. Four clans of cysteine peptidases share structural similarities with serine and threonine peptidases and asparagine lyases. From sequence similarities, cysteine peptidases can be clustered into over 80 different families [ PUBMED:11517925 ]. Clans CF, CM, CN, CO, CP and PD contain only one family.

Cysteine peptidases are often active at acidic pH and are therefore confined to acidic environments, such as the animal lysosome or plant vacuole. Cysteine peptidases can be endopeptidases, aminopeptidases, carboxypeptidases, dipeptidyl-peptidases or omega-peptidases. They are inhibited by thiol chelators such as iodoacetate, iodoacetic acid, N -ethylmaleimide or p -chloromercuribenzoate.

Clan CA includes proteins with a papain-like fold. There is a catalytic triad which occurs in the order: Cys/His/Asn (or Asp). A fourth residue, usually Gln, is important for stabilising the acyl intermediate that forms during catalysis, and this precedes the active site Cys. The fold consists of two subdomains with the active site between them. One subdomain consists of a bundle of helices, with the catalytic Cys at the end of one of them, and the other subdomain is a beta-barrel with the active site His and Asn (or Asp). There are over thirty families in the clan, and tertiary structures have been solved for members of most of these. Peptidases in clan CA are usually sensitive to the small molecule inhibitor E64, which is ineffective against peptidases from other clans of cysteine peptidases [ PUBMED:7044372 ].

Clan CD includes proteins with a caspase-like fold. Proteins in the clan have an alpha/beta/alpha sandwich structure. There is a catalytic dyad which occurs in the order His/Cys. The active site His occurs in a His-Gly motif and the active site Cys occurs in an Ala-Cys motif; both motifs are preceded by a block of hydrophobic residues [ PUBMED:9891971 ]. Specificity is predominantly directed towards residues that occupy the S1 binding pocket, so that caspases cleave aspartyl bonds, legumains cleave asparaginyl bonds, and gingipains cleave lysyl or arginyl bonds.

Clan CE includes proteins with an adenain-like fold. The fold consists of two subdomains with the active site between them. One domain is a bundle of helices, and the other a beta barrell. The subdomains are in the opposite order to those found in peptidases from clan CA, and this is reflected in the order of active site residues: His/Asn/Gln/Cys. This has prompted speculation that proteins in clans CA and CE are related, and that members of one clan are derived from a circular permutation of the structure of the other.

Clan CL includes proteins with a sortase B-like fold. Peptidases in the clan hydrolyse and transfer bacterial cell wall peptides. The fold shows a closed beta barrel decorated with helices with the active site at one end of the barrel [ PUBMED:14725770 ]. The active site consists of a His/Cys catalytic dyad.

Gene Ontology

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Curation View help on the curation process

Seed source: Prosite
Previous IDs: Cys_protease_2;
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 149
Number in full: 13863
Average length of the domain: 262.80 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 35.38 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.8 23.8
Trusted cut-off 23.8 23.8
Noise cut-off 23.5 23.7
Model length: 299
Family (HMM) version: 24
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Peptidase_C2 domain has been found. There are 48 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0G2KAS0 View 3D Structure Click here
A0A0G2KGQ3 View 3D Structure Click here
A0A0R4IA57 View 3D Structure Click here
A0A0R4IFK0 View 3D Structure Click here
A0A0R4IG81 View 3D Structure Click here
A0A0R4IX46 View 3D Structure Click here
A0A131MD14 View 3D Structure Click here
A0A2R8Q964 View 3D Structure Click here
A0A2R8Q9Z9 View 3D Structure Click here
A0A2R8RNP1 View 3D Structure Click here
A0A2R8RVY7 View 3D Structure Click here
A0A5K1K8Q4 View 3D Structure Click here
A4HS39 View 3D Structure Click here
A4HXY0 View 3D Structure Click here
A4HYN0 View 3D Structure Click here
A4HYW1 View 3D Structure Click here
A4HYW2 View 3D Structure Click here
A4HYW3 View 3D Structure Click here
A4HYW4 View 3D Structure Click here
A4I1J4 View 3D Structure Click here
A4I5N1 View 3D Structure Click here
A4I6E4 View 3D Structure Click here
A4I6E6 View 3D Structure Click here
A4I6F0 View 3D Structure Click here
A4I6K4 View 3D Structure Click here
A4I6K5 View 3D Structure Click here
A4I6K6 View 3D Structure Click here
A4I7R3 View 3D Structure Click here
A4I963 View 3D Structure Click here
A4I9J8 View 3D Structure Click here
A4ICQ6 View 3D Structure Click here
A5PMP0 View 3D Structure Click here
A6NHC0 View 3D Structure Click here
A8MX76 View 3D Structure Click here
B8A6G0 View 3D Structure Click here
D3ZJZ8 View 3D Structure Click here
E7F0H3 View 3D Structure Click here
E7F7F1 View 3D Structure Click here
E9QE31 View 3D Structure Click here
E9QFN0 View 3D Structure Click here