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373  structures 1160  species 5  interactions 7017  sequences 153  architectures

Family: Peptidase_C1 (PF00112)

Summary: Papain 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 "Cysteine protease". More...

Cysteine protease Edit Wikipedia article

Cysteine Peptidase
Papain enzyme.png
Crystal structure of the cysteine peptidase papain in complex with its covalent inhibtor E-64. Rendered from PDB 1PE6
Symbol Peptidase_C1
Pfam PF00112
Pfam clan CL0125
InterPro IPR000668
SCOP 1aec
OPM superfamily 420
OPM protein 1m6d

Cysteine proteases, also known as thiol proteases, are enzymes that degrade proteins. These proteases share a common catalytic mechanism that involves a nucleophilic cysteine thiol in a catalytic triad or dyad.

Cysteine proteases are commonly encountered in fruits including the papaya, pineapple, fig and kiwifruit. The proportion of protease tends to be higher when the fruit is unripe. In fact, dozens of latices of different plant families are known to contain cysteine proteases.[1] Cysteine proteases are used as an ingredient in meat tenderizers.

Reaction mechanism of the cysteine protease mediated cleavage of a peptide bond.


The MEROPS protease classification system counts 14 superfamilies plus several currently unassigned families (as of 2013) each containing many families. Each superfamily uses the catalytic triad or dyad in a different protein fold and so represent convergent evolution of the catalytic mechanism.

For superfamilies, P = superfamily containing a mixture of nucleophile class families, C = purely cysteine proteases. superfamily. Within each superfamily, families are designated by their catalytic nucleophile (C = cysteine proteases).

Superfamily Families Examples
PA C3, C4, C24, 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 DmpA aminopeptidase (Ochrobactrum anthropi)
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) and calpain (Homo sapiens)
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 hepatitis C virus peptidase 2 (hepatitis C virus)
CN C9 sindbis virus-type nsP2 peptidase (sindbis virus)
CO C40 dipeptidyl-peptidase VI (Lysinibacillus sphaericus)
CP C97 DeSI-1 peptidase (Mus musculus)
unassigned C7, C8, C21, C23, C27, C36, C42, C53, C75

Catalytic mechanism

see also:catalytic triad

The first step in the reaction mechanism by which cysteine proteases catalyze the hydrolysis of peptide bonds is deprotonation 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 anionic sulfur on the 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 hydrolyzed to generate a carboxylic acid moiety on the remaining substrate fragment, while regenerating the free enzyme.

Biological importance

Cysteine proteases play multi-faceted 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 pathways and in the response to biotic and abiotic stresses.[2] In humans and other animals, they are responsible for senescence and apoptosis (programmed cell death), MHC class II immune responses, 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.[3]

In several traditional medicines, the fruits or latex of the papaya, pineapple and fig are widely used for treatment of intestinal worm infections both in humans and livestock.

Additionally, many viruses (e.g. polio, hepatitus C) express their entire genome as a singe massive polyprotein and use a protease to cleave it into functional units.


Examples of enzymes that are cysteine proteases include:


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 (e.g. lysosome) or extracellular environment (e.g. stomach). This system prevents the cell that produces the protease from being damaged by it.

Protease inhibitors are usually proteins with domains that enter or block a protease active site to prevent 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:

Potential pharmacological uses

Currently there is no widespread use of cysteine proteases as approved and effective anthelmintics but research into the subject is a promising field of study. Plant cysteine proteases isolated from these plants have been found to have high proteolytic activities that are known to digest nematode cuticles, with very low toxicity.[4] 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 acanthocephalan parasite Macracanthorynchus hirundinaceus.[5] 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.

See also


  1. ^ Domsalla A, Melzig MF (June 2008). "Occurrence and properties of proteases in plant latices". Planta Med. 74 (7): 699–711. doi:10.1055/s-2008-1074530. PMID 18496785. 
  2. ^ Grudkowska M, Zagdańska B (2004). "Multifunctional role of plant cysteine proteinases". Acta Biochim. Pol. 51 (3): 609–24. PMID 15448724. 
  3. ^ Chapman HA, Riese RJ, Shi GP (1997). "Emerging roles for cysteine proteases in human biology". Annu. Rev. Physiol. 59: 63–88. doi:10.1146/annurev.physiol.59.1.63. PMID 9074757. 
  4. ^ Stepek G, Behnke JM, Buttle DJ, Duce IR (July 2004). "Natural plant cysteine proteinases as anthelmintics?". Trends Parasitol. 20 (7): 322–7. doi:10.1016/ PMID 15193563. 
  5. ^ Behnke JM, Buttle DJ, Stepek G, Lowe A, Duce IR (2008). "Developing novel anthelmintics from plant cysteine proteinases". Parasit Vectors 1 (1): 29. doi:10.1186/1756-3305-1-29. PMC 2559997. PMID 18761736. 

External links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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

Papain Edit Wikipedia article

"Accuzyme" redirects here. For DNA polymerase and PCR mix, see Bioline Reagents.
Papain family cysteine protease
Papain cartoon.png
Papain from Carica papaya
Symbol Peptidase_C1
Pfam PF00112
InterPro IPR000668
SCOP 1aec
EC number
CAS number 9001-73-4
IntEnz IntEnz view
ExPASy NiceZyme view
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum

Papain, also known as papaya proteinase I, is a cysteine protease (EC enzyme present in papaya (Carica papaya) and mountain papaya (Vasconcellea cundinamarcensis).

Papain family

Papain belongs to a family of related proteins with a wide variety of activities, including endopeptidases, aminopeptidases, dipeptidyl peptidases and enzymes with both exo- and endo-peptidase activity.[1] Members of the papain family are widespread, found in baculovirus,[2] eubacteria, yeast, and practically all protozoa, plants and mammals.[1] The proteins are typically lysosomal or secreted, and proteolytic cleavage of the propeptide is required for enzyme activation, although bleomycin hydrolase is cytosolic in fungi and mammals.[3] Papain-like cysteine proteinases are essentially synthesised as inactive proenzymes (zymogens) with N-terminal propeptide regions. The activation process of these enzymes includes the removal of propeptide regions, which serve a variety of functions in vivo and in vitro. The pro-region is required for the proper folding of the newly synthesised enzyme, the inactivation of the peptidase domain and stabilisation of the enzyme against denaturing at neutral to alkaline pH conditions. Amino acid residues within the pro-region mediate their membrane association, and play a role in the transport of the proenzyme to lysosomes. Among the most notable features of propeptides is their ability to inhibit the activity of their cognate enzymes and that certain propeptides exhibit high selectivity for inhibition of the peptidases from which they originate.[4]


The papain precursor protein contains 345 amino acid residues,[5] and consists of a signal sequence (1-18), a propeptide (19-133) and the mature peptide (134-345). The amino acid numbers are based on the mature peptide. The protein is stabilised by three disulfide bridges. Its three-dimensional structure consists of two distinct structural domains with a cleft between them. This cleft contains the active site, which contains a catalytic diad that has been likened to the catalytic triad of chymotrypsin. The catalytic diad is made up of the amino acids - cysteine-25 (from which it gets its classification) and histidine-159. Aspartate-158 was thought to play a role analogous to the role of aspartate in the serine protease catalytic triad, but that has since then been disproved.[6] Nonetheless, it does appear to play a role.


The mechanism by which papain breaks peptide bonds involves the use of a catalytic triad with a deprotonated cystine. Asp-175 helps to orient the imidazole ring of His-159 to allow it to deprotonate the catalytic Cys-25. This cysteine then performs a nucleophilic attack on the carbonyl carbon of a peptide backbone. This frees the amino terminal of the peptide, and forms a covalent acyl-enzyme intermediate. The enzyme is then deacylated by a water molecule, and releases the carboxy terminal portion of the peptide. In immunology, papain is known to cleave the Fc (crystallisable) portion of immunoglobulins (antibodies) from the Fab (antigen-binding) portion.

Papain is a relatively heat resistant enzyme, with a temperature optimal range of 60-70°C.[7]

Papain prefers to cleave at: (hydrophobic)-(Arg or Lys)- cleaves here -(not Val). Hydrophobic is Ala, Val, Leu, Ile, Phe, Trp, or Tyr.[8]


Anthelmintic effect of papain on the worm Heligmosomoides bakeri.

Papain breaks down tough meat fibres, and has been used for thousands of years to tenderise meat eaten in its native South America. Meat tenderisers in powder form with papain as an active component are widely sold.

Papain can be used to dissociate cells in the first step of cell culture preparations. A ten-minute treatment of small tissue pieces (less than 1 mm cubed) will allow papain to begin breaking down the extracellular matrix molecules holding the cells together. After ten minutes, the tissue should be treated with a protease inhibitor solution to stop the protease action (if left untreated, papain's activity will lead to complete lysis of the cells). The tissue must then be triturated (passed quickly up and down through a Pasteur pipette) to break up the pieces of tissue into a single cell suspension.

It is also used as an ingredient in various enzymatic debriding preparations, notably Accuzyme. These are used in the care of some chronic wounds to clean up dead tissue.

Papain is also used in some toothpastes and mint sweets as a tooth whitener; however, its whitening effect is minimal, because the papain is present in low concentrations and is quickly diluted by saliva. It would take several months of use to have a noticeable effect.[9]

It is the main ingredient of Papacarie, a gel used for chemomechanical dental caries removal. It does not require drilling and does not interfere in the bond strength of restorative materials to dentin.[10]

Papain has been known to interfere with urine drug tests for cannabinoids.[11] It is found in some drug detox products.


The papain-digested antibody: two Fab fragments and an Fc fragment.

An antibody digested by papain yields three fragments: two 50 kDa Fab fragments and one 50kDa Fc fragment. The papain-digested antibody is unable to promote agglutination, precipitation, opsonization, and lysis.


Papain is usually produced as a crude, dried material by collecting the latex from the fruit of the papaya tree. The latex is collected after scoring the neck of the fruit, where it may either dry on the fruit or drip into a container. This latex is then further dried. It is now classified as a dried, crude material. A purification step is necessary to remove contaminating substances. This purification consists of the solubilization and extraction of the active papain enzyme system through a government-registered process. This purified papain may be supplied as powder or as liquid.

US restrictions on marketing

On September 23, 2008, the US Food and Drug Administration (FDA) warned companies to stop marketing ophthalmic balanced salt solutions and topical drug products containing papain by November 4, 2008. The FDA said, "Papain-containing drug products in topical form historically have been marketed without approval...".[12] According to the FDA's statement on the subject, "These unapproved products have put consumers' health in jeopardy, from reports of permanent vision loss with unapproved balanced salt solutions to a serious drop in blood pressure and increased heart rate from the topical papain products," said Janet Woodcock, M.D., director for the Center for Drug Evaluation and Research. In the same FDA announcement, the FDA states the following:

Unapproved topical papain products

Topical drug ointments containing papain are used to remove dead or contaminated tissue in acute and chronic lesions, such as diabetic ulcers, pressure ulcers, varicose ulcers, and traumatic infected wounds. Trade names for these products include Accuzyme, Allanfil, Allanzyme, Ethezyme, Gladase, Kovia, Panafil, Pap Urea, and Ziox. Other products are marketed under the names of the active ingredients, for instance, papain-urea ointment.

In 2008 the FDA announced its intention to take action against these products because it had received reports of serious adverse events in patients using products containing papain. Reports included hypersensitivity (allergic) reactions that lead to hypotension (low blood pressure) and tachycardia (rapid heart rate). In addition, people allergic to latex can also be allergic to papaya, the source of papain, implying that people with latex sensitivity may be at increased risk of suffering an adverse reaction to a topical papain drug product.

FDA recommended that people with concerns about using topical papain preparations contact their health care provider about discontinuing use. There are a number of FDA-approved topical products that have been found safe and effective as wound-healing agents and do not contain papain.

Human cysteine proteases from papain family


See also


  1. ^ a b Rawlings ND, Barrett AJ (1994). "Families of cysteine peptidases". Meth. Enzymol. 244: 461–486. doi:10.1016/0076-6879(94)44034-4. PMID 7845226. 
  2. ^ Rawlings ND, Barrett AJ (1993). "Evolutionary families of peptidases". Biochem. J. 290: 205–218. PMC 1132403. PMID 8439290. 
  3. ^ Sebti SM, Lazo JS, DeLeon JC (1987). "Purification, characterization, and amino acid composition of rabbit pulmonary bleomycin hydrolase". Biochemistry 26 (14): 4213–4219. doi:10.1021/bi00388a006. PMID 3117099. 
  4. ^ Yamamoto Y, Takahashi SY, Kurata M, Watabe S, Murakami R (2002). "Novel cysteine proteinase inhibitors homologous to the proregions of cysteine proteinases". Curr Protein Pept Sci 3 (2): 231–238. doi:10.2174/1389203024605331. PMID 12188906. 
  5. ^ "UniProt P00784: Papain precursor - Carica papaya (Papaya)". UniProtKB. 
  6. ^ Ménard R, Khouri HE, Plouffe C, Dupras R, Ripoll D, Vernet T, Tessier DC, Lalberté F, Thomas DY, Storer AC (July 1990). "A protein engineering study of the role of aspartate 158 in the catalytic mechanism of papain". Biochemistry 29 (28): 6706–13. doi:10.1021/bi00480a021. PMID 2397208. 
  7. ^
  8. ^
  9. ^ Chakravarthy P, Acharya S (October 2012). "Efficacy of extrinsic stain removal by novel dentifrice containing papain and bromelain extracts". J Young Pharm 4 (4): 245–9. doi:10.4103/0975-1483.104368. PMC 3573376. PMID 23493413. 
  10. ^ Lopes MC, Mascarini RC, da Silva BM, Flório FM, Basting RT (2007). "Effect of a papain-based gel for chemomechanical caries removal on dentin shear bond strength". J Dent Child (Chic) 74 (2): 93–7. PMID 18477426. 
  11. ^ Section of Toxicology, Department of Pharmacology, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, 37614, USA. Papain: a novel urine adulterant. 
  12. ^ Shuren J (2008-09-22). "Topical Drug Products Containing Papain; Enforcement Action Dates". United States Food and Drug Administration, Department of Health and Human Services. 

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.

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External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000668

In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold:

  • Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.
  • Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases.

In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding.

Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad [PUBMED:11517925].

This group of proteins belong to the peptidase family C1, sub-family C1A (papain family, clan CA). It includes proteins classed as non-peptidase homologs. These are have either been shown experimentally to lack peptidase activity or lack one or more of the active site residues.

The papain family has a wide variety of activities, including broad-range (papain) and narrow-range endo-peptidases, aminopeptidases, dipeptidyl peptidases and enzymes with both exo- and endo-peptidase activity [PUBMED:7845226]. Members of the papain family are widespread, found in baculovirus [PUBMED:8439290], eubacteria, yeast, and practically all protozoa, plants and mammals [PUBMED:7845226]. The proteins are typically lysosomal or secreted, and proteolytic cleavage of the propeptide is required for enzyme activation, although bleomycin hydrolase is cytosolic in fungi and mammals [PUBMED:3117099]. Papain-like cysteine proteinases are essentially synthesised as inactive proenzymes (zymogens) with N-terminal propeptide regions. The activation process of these enzymes includes the removal of propeptide regions. The propeptide regions serve a variety of functions in vivo and in vitro. The pro-region is required for the proper folding of the newly synthesised enzyme, the inactivation of the peptidase domain and stabilisation of the enzyme against denaturing at neutral to alkaline pH conditions. Amino acid residues within the pro-region mediate their membrane association, and play a role in the transport of the proenzyme to lysosomes. Among the most notable features of propeptides is their ability to inhibit the activity of their cognate enzymes and that certain propeptides exhibit high selectivity for inhibition of the peptidases from which they originate [PUBMED:12188906].

The catalytic residues of papain are Cys-25 and His-159, other important residues being Gln-19, which helps form the 'oxyanion hole', and Asn-175, which orientates the imidazole ring of His-159.

Gene Ontology

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Domain organisation

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MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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Curation and family details

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Seed source: Prosite
Previous IDs: Cys-protease;
Type: Domain
Author: Sonnhammer ELL
Number in seed: 157
Number in full: 7017
Average length of the domain: 199.90 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 53.16 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.7 20.7
Trusted cut-off 20.7 20.7
Noise cut-off 20.6 20.6
Model length: 219
Family (HMM) version: 18
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Species distribution

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There are 5 interactions for this family. More...

Inhibitor_I42 Inhibitor_I29 Peptidase_C1 CathepsinC_exc Cystatin


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_C1 domain has been found. There are 373 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 seqence.

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