Papain-like proteases (or papain-like (cysteine) peptidases; abbreviated PLP or PLCP) are a large

protein family A protein family is a group of evolutionarily related proteins. In many cases, a protein family has a corresponding gene family, in which each gene encodes a corresponding protein with a 1:1 relationship. The term "protein family" should not be ...

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

enzyme An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different mol ...

s that share

structural A structure is an arrangement and organization of interrelated elements in a material object or system, or the object or system so organized. Material structures include man-made objects such as buildings and machines and natural objects such as ...

and

enzymatic An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as produc ...

properties with the group's namesake member,

papain Papain, also known as papaya proteinase I, is a cysteine protease () enzyme present in papaya (''Carica papaya'') and mountain papaya (''Vasconcellea cundinamarcensis''). It is the namesake member of the papain-like protease family. It has wi ...

. They are found in all domains of life. In animals, the group is often known as cysteine cathepsins or, in older literature, lysosomal peptidases. In the

MEROPS MEROPS is an online database for peptidases (also known as proteases, proteinases and proteolytic enzymes) and their inhibitors. The classification scheme for peptidases was published by Rawlings & Barrett in 1993, and that for protein inhibito ...

protease enzyme classification system, papain-like proteases form Clan CA. Papain-like proteases share a common catalytic dyad

active site In biology and biochemistry, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction. The active site consists of amino acid residues that form temporary bonds with the substrate, the ''binding s ...

featuring a

cysteine Cysteine (; symbol Cys or C) is a semiessential proteinogenic amino acid with the chemical formula, formula . The thiol side chain in cysteine enables the formation of Disulfide, disulfide bonds, and often participates in enzymatic reactions as ...

amino acid residue In chemistry, amines (, ) are organic compounds that contain carbon-nitrogen bonds. Amines are formed when one or more hydrogen atoms in ammonia are replaced by alkyl or aryl groups. The nitrogen atom in an amine possesses a lone pair of elec ...

that acts as a

nucleophile In chemistry, a nucleophile is a chemical species that forms bonds by donating an electron pair. All molecules and ions with a free pair of electrons or at least one pi bond can act as nucleophiles. Because nucleophiles donate electrons, they are ...

. The

human genome The human genome is a complete set of nucleic acid sequences for humans, encoded as the DNA within each of the 23 distinct chromosomes in the cell nucleus. A small DNA molecule is found within individual Mitochondrial DNA, mitochondria. These ar ...

encodes eleven cysteine

cathepsin Cathepsins (Ancient Greek ''kata-'' "down" and ''hepsein'' "boil"; abbreviated CTS) are proteases (enzymes that degrade proteins) found in all animals as well as other organisms. There are approximately a dozen members of this family, which are d ...

s which have a broad range of physiological functions. In some

parasite Parasitism is a Symbiosis, close relationship between species, where one organism, the parasite, lives (at least some of the time) on or inside another organism, the Host (biology), host, causing it some harm, and is Adaptation, adapted str ...

s papain-like proteases have roles in

host A host is a person responsible for guests at an event or for providing hospitality during it. Host may also refer to: Places * Host, Pennsylvania, a village in Berks County * Host Island, in the Wilhelm Archipelago, Antarctica People * ...

invasion, such as

cruzipain Cruzipain is a cysteine protease expressed by ''Trypanosoma cruzi''. It is classified under . Cruzipain is expressed by all strains and developmental forms of ''Trypanosoma cruzi''. It is secreted and can be found in the membrane of the parasite ...

from ''

Trypanosoma cruzi ''Trypanosoma cruzi'' is a species of parasitic euglenoids. Among the protozoa, the trypanosomes characteristically bore tissue in another organism and feed on blood (primarily) and also lymph. This behaviour causes disease or the likelihood ...

''. In plants, they are involved in host defense and in development. Studies of papain-like proteases from

prokaryote A prokaryote (; less commonly spelled procaryote) is a unicellular organism, single-celled organism whose cell (biology), cell lacks a cell nucleus, nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Ancient Gree ...

s have lagged their

eukaryotic The eukaryotes ( ) constitute the Domain (biology), domain of Eukaryota or Eukarya, organisms whose Cell (biology), cells have a membrane-bound cell nucleus, nucleus. All animals, plants, Fungus, fungi, seaweeds, and many unicellular organisms ...

counterparts. In cellular organisms they are synthesized as

preproenzyme A preproenzyme is an enzyme with two additional characteristics: "pre" refers to a signal sequence (signal peptide) which directs the enzyme to a specific organelle or subcellular localization; "pro" indicates that the enzyme is present in an inacti ...

s that are not enzymatically active until mature, and their activities are tightly regulated, often by the presence of endogenous protease inhibitors such as

cystatin The cystatins are a family of cysteine protease inhibitors which share a sequence homology and a common tertiary structure of an alpha helix lying on top of an anti-parallel beta sheet. The family is subdivided as described below. Cystatins sho ...

s. In many

RNA virus An RNA virus is a virus characterized by a ribonucleic acid (RNA) based genome. The genome can be single-stranded RNA (ssRNA) or double-stranded (Double-stranded RNA, dsRNA). Notable human diseases caused by RNA viruses include influenza, SARS, ...

es, including significant human

pathogen In biology, a pathogen (, "suffering", "passion" and , "producer of"), in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a Germ theory of d ...

s such as the

coronavirus Coronaviruses are a group of related RNA viruses that cause diseases in mammals and birds. In humans and birds, they cause respiratory tract infections that can range from mild to lethal. Mild illnesses in humans include some cases of the comm ...

SARS-CoV Severe acute respiratory syndrome–related coronavirus (SARSr-CoV or SARS-CoV'', Betacoronavirus pandemicum'')The terms ''SARSr-CoV'' and ''SARS-CoV'' are sometimes used interchangeably, especially prior to the discovery of SARS-CoV-2. This m ...

and

SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) is a strain of coronavirus that causes COVID-19, the respiratory illness responsible for the COVID-19 pandemic. The virus previously had the Novel coronavirus, provisional nam ...

, papain-like protease

protein domain In molecular biology, a protein domain is a region of a protein's Peptide, polypeptide chain that is self-stabilizing and that Protein folding, folds independently from the rest. Each domain forms a compact folded Protein tertiary structure, thre ...

s often have roles in processing of

polyprotein Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids. Protein degradation is a major regulatory mechanism of gene expression and contributes substantially to shaping mammalian proteomes. Uncatalysed, the hydrolysis o ...

s into mature

viral nonstructural protein In virology, a nonstructural protein is a protein encoded by a virus but that is not part of the viral particle. They typically include the various enzymes and transcription factors the virus uses to replicate itself, such as a viral protease ( 3CL ...

s. Many papain-like proteases are considered potential

drug target A biological target is anything within a living organism to which some other entity (like an endogenous ligand or a drug) is directed and/or binds, resulting in a change in its behavior or function. Examples of common classes of biological targets ...

Classification

The

system of protease enzyme classification defines clan CA as containing the papain-like proteases. They are thought to have a shared

evolution Evolution is the change in the heritable Phenotypic trait, characteristics of biological populations over successive generations. It occurs when evolutionary processes such as natural selection and genetic drift act on genetic variation, re ...

ary origin. As of 2021, the clan contained 45 families.

Structure

The structure of papain was among the earliest

protein structure Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid ...

s experimentally determined by

X-ray crystallography X-ray crystallography is the experimental science of determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to Diffraction, diffract in specific directions. By measuring th ...

. Many papain-like protease enzymes function as

monomer A monomer ( ; ''mono-'', "one" + '' -mer'', "part") is a molecule that can react together with other monomer molecules to form a larger polymer chain or two- or three-dimensional network in a process called polymerization. Classification Chemis ...

s, though a few, such as

cathepsin C Cathepsin C (CTSC) also known as dipeptidyl peptidase I (DPP-I) is a lysosomal exo-cysteine protease belonging to the peptidase C1 protein family, a subgroup of the cysteine cathepsins. In humans, it is encoded by the ''CTSC'' gene. Function ...

(Dipeptidyl-peptidase I), are homotetramers. The mature monomer structure is characteristically divided into two lobes or subdomains, known as the L-domain (

N-terminal The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) is the start of a protein or polypeptide, referring to the free amine group (-NH2) located at the end of a polypeptide. Within a peptide, the amin ...

) and the R-domain (

C-terminal The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal tail, carboxy tail, C-terminal end, or COOH-terminus) is the end of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group (-COOH). When t ...

), where the

is located between them. The L-domain is primarily helical while the R-domain contains

beta-sheet The beta sheet (β-sheet, also β-pleated sheet) is a common structural motif, motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone chain, backbon ...

s in a

beta-barrel In protein structures, a beta barrel (β barrel) is a beta sheet (β sheet) composed of tandem repeats that twists and coils to form a closed toroidal structure in which the first strand is bonded to the last strand (hydrogen bond). Beta-strands ...

-like shape, surrounded by a helix. The

enzyme substrate In chemistry, the term substrate is highly context-dependent. Broadly speaking, it can refer either to a chemical species being observed in a chemical reaction, or to a surface on which other chemical reactions or microscopy are performed. In t ...

interacts with both domains in an extended conformation. Papain-like proteases are often synthesized as

s, or enzymatically inactive precursors. A

signal peptide A signal peptide (sometimes referred to as signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short peptide (usually 16–30 amino acids long) present at the ...

at the

N-terminus The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) is the start of a protein or polypeptide, referring to the free amine group (-NH2) located at the end of a polypeptide. Within a peptide, the amin ...

, which serves as a

subcellular localization The cells of eukaryotic organisms are elaborately subdivided into functionally-distinct membrane-bound compartments. Some major constituents of eukaryotic cells are: extracellular space, plasma membrane, cytoplasm, nucleus, mitochondria, Golgi a ...

signal, is cleaved by

signal peptidase Signal peptidases are enzymes that convert secretory and some membrane proteins to their mature or pro forms by cleaving their signal peptides from their N-termini. Signal peptidases were initially observed in endoplasmic reticulum (ER)-deri ...

to form a

zymogen In biochemistry, a zymogen (), also called a proenzyme (), is an inactive precursor of an enzyme. A zymogen requires a biochemical change (such as a hydrolysis reaction revealing the active site, or changing the configuration to reveal the activ ...

Post-translational modification In molecular biology, post-translational modification (PTM) is the covalent process of changing proteins following protein biosynthesis. PTMs may involve enzymes or occur spontaneously. Proteins are created by ribosomes, which translation (biolog ...

in the form of

N-linked glycosylation ''N''-linked glycosylation is the attachment of an oligosaccharide, a carbohydrate consisting of several sugar molecules, sometimes also referred to as glycan, to a nitrogen atom (the amide nitrogen of an asparagine (Asn) residue of a protein), i ...

also occurs in parallel. The zymogen is still inactive due to the presence of a

propeptide A protein precursor, also called a pro-protein or pro-peptide, is an inactive protein (or peptide) that can be turned into an active form by post-translational modification, such as breaking off a piece of the molecule or adding on another molecule ...

which functions as an inhibitor blocking access to the active site. The propeptide is removed by

proteolysis Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids. Protein degradation is a major regulatory mechanism of gene expression and contributes substantially to shaping mammalian proteomes. Uncatalysed, the hydrolysis o ...

to form the mature enzyme.

Catalytic mechanism

Papain-like proteases have a catalytic dyad consisting of a

and a

histidine Histidine (symbol His or H) is an essential amino acid that is used in the biosynthesis of proteins. It contains an Amine, α-amino group (which is in the protonated –NH3+ form under Physiological condition, biological conditions), a carboxylic ...

residue, which form an

ion pair In chemistry, ion association is a chemical reaction whereby ions of opposite electric charge come together in solution to form a distinct chemical entity. Ion associates are classified, according to the number of ions that associate with each ...

through their charged

thiolate In organic chemistry, a thiol (; ), or thiol derivative, is any organosulfur compound of the form , where R represents an alkyl or other organic substituent. The functional group itself is referred to as either a thiol group or a sulfhydryl grou ...

and

imidazolium Imidazole (ImH) is an organic compound with the formula . It is a white or colourless solid that is soluble in water, producing a mildly alkaline solution. It can be classified as a heterocycle, specifically as a diazole. Many natural products, ...

side chains. The negatively charged cysteine thiolate functions as a

. Additional neighboring residues—

aspartate Aspartic acid (symbol Asp or D; the ionic form is known as aspartate), is an α-amino acid that is used in the biosynthesis of proteins. The L-isomer of aspartic acid is one of the 22 proteinogenic amino acids, i.e., the building blocks of protein ...

asparagine Asparagine (symbol Asn or N) is an α-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated −NH form under biological conditions), an α-carboxylic acid group (which is in the depro ...

, or

glutamine Glutamine (symbol Gln or Q) is an α-amino acid that is used in the biosynthesis of proteins. Its side chain is similar to that of glutamic acid, except the carboxylic acid group is replaced by an amide. It is classified as a charge-neutral ...

—position the catalytic residues; in papain, the required catalytic residues cysteine, histidine, and aspartate are sometimes called the catalytic triad (similar to

serine protease Serine proteases (or serine endopeptidases) are enzymes that cleave peptide bonds in proteins. Serine serves as the nucleophilic amino acid at the (enzyme's) active site. They are found ubiquitously in both eukaryotes and prokaryotes. Serin ...

s). Papain-like proteases are usually

endopeptidase Endopeptidase or endoproteinase are proteolytic peptidases that break peptide bonds of nonterminal amino acids (i.e. within the molecule), in contrast to exopeptidases, which break peptide bonds from end-pieces of terminal amino acids. For this r ...

s, but some members of the group are also, or even exclusively,

exopeptidase An exopeptidase is any peptidase that catalyzes the cleavage of the terminal (or the penultimate) peptide bond; the process releases a single amino acid, dipeptide or a tripeptide from the peptide chain. Depending on whether the amino acid is r ...

s. Some viral papain-like proteases, including those of

es, can also cleave

isopeptide bond An isopeptide bond is a type of amide bond formed between a carboxyl group of one amino acid and an amino group of another. An isopeptide bond is the linkage between the side chain amino or carboxyl group of one amino acid to the α-carboxyl, α- ...

s and can function as

deubiquitinase Deubiquitinating enzymes (DUBs), also known as deubiquitinating peptidases, deubiquitinating isopeptidases, deubiquitinases, ubiquitin proteases, ubiquitin hydrolases, or ubiquitin isopeptidases, are a large group of proteases that cleave ubiquiti ...

Function

Eukaryotes

Mammals

In animals, especially in mammalian biology, members of the papain-like protease family are usually referred to as cysteine cathepsins—that is, the

members of the group of proteases known as

s (which includes cysteine,

serine Serine (symbol Ser or S) is an α-amino acid that is used in the biosynthesis of proteins. It contains an α- amino group (which is in the protonated − form under biological conditions), a carboxyl group (which is in the deprotonated − ...

, and

aspartic protease Aspartic proteases (also "aspartyl proteases", "aspartic endopeptidases") are a catalytic type of protease enzymes that use an activated water molecule bound to one or more aspartate residues for catalysis of their peptide substrates. In general, ...

s). In humans, there are 11 cysteine cathepsins: B, C, F, H, K, L, O, S, V, X, and W. Most cathepsins are expressed throughout the body, but some have narrower tissue distribution. 5tdi cathepsinK odanacatib

Although historically known as

lysosomal A lysosome () is a membrane-bound organelle that is found in all mammalian cells, with the exception of red blood cells (erythrocytes). There are normally hundreds of lysosomes in the cytosol, where they function as the cell’s degradation cent ...

proteases and studied mainly for their role in protein

catabolism Catabolism () is the set of metabolic pathways that breaks down molecules into smaller units that are either oxidized to release energy or used in other anabolic reactions. Catabolism breaks down large molecules (such as polysaccharides, lipid ...

, cysteine cathepsins have since been identified playing major roles in a number of physiological processes and disease states. As part of normal physiological processes, they are involved in key steps of

antigen presentation Antigen presentation is a vital immune process that is essential for T cell immune response triggering. Because T cells recognize only fragmented antigens displayed on cell surfaces, antigen processing must occur before the antigen fragment can ...

as part of the

adaptive immune system The adaptive immune system (AIS), also known as the acquired immune system, or specific immune system is a subsystem of the immune system that is composed of specialized cells, organs, and processes that eliminate pathogens specifically. The ac ...

, remodeling of the

extracellular matrix In biology, the extracellular matrix (ECM), also called intercellular matrix (ICM), is a network consisting of extracellular macromolecules and minerals, such as collagen, enzymes, glycoproteins and hydroxyapatite that provide structural and bio ...

, differentiation of

keratinocyte Keratinocytes are the primary type of cell found in the epidermis, the outermost layer of the skin. In humans, they constitute 90% of epidermal skin cells. Basal cells in the basal layer (''stratum basale'') of the skin are sometimes referre ...

s, and processing of

peptide hormone Peptide hormones are hormones composed of peptide molecules. These hormones influence the endocrine system of animals, including humans. Most hormones are classified as either amino-acid-based hormones (amines, peptides, or proteins) or steroid h ...

s. Cysteine cathepsins have been associated with

cancer Cancer is a group of diseases involving Cell growth#Disorders, abnormal cell growth with the potential to Invasion (cancer), invade or Metastasis, spread to other parts of the body. These contrast with benign tumors, which do not spread. Po ...

and

tumor progression Tumor progression is the third and last phase in tumor development. This phase is characterised by increased growth speed and invasiveness of the tumor cells. As a result of the progression, phenotypical changes occur and the tumor becomes more agg ...

cardiovascular disease Cardiovascular disease (CVD) is any disease involving the heart or blood vessels. CVDs constitute a class of diseases that includes: coronary artery diseases (e.g. angina, heart attack), heart failure, hypertensive heart disease, rheumati ...

autoimmune disease An autoimmune disease is a condition that results from an anomalous response of the adaptive immune system, wherein it mistakenly targets and attacks healthy, functioning parts of the body as if they were foreign organisms. It is estimated tha ...

, and other human health conditions.

Cathepsin K Cathepsin K, abbreviated CTSK, is an enzyme that in humans is encoded by the ''CTSK'' gene. Function The protein encoded by this gene is a cysteine cathepsin, a lysosomal cysteine protease involved in bone remodeling and resorption. This pr ...

has a role in

bone resorption Bone resorption is resorption of bone tissue, that is, the process by which osteoclasts break down the tissue in bones and release the minerals, resulting in a transfer of calcium from bone tissue to the blood. The osteoclasts are multi-nuclea ...

and has been studied as a

for

osteoporosis Osteoporosis is a systemic skeletal disorder characterized by low bone mass, micro-architectural deterioration of bone tissue leading to more porous bone, and consequent increase in Bone fracture, fracture risk. It is the most common reason f ...

Parasites

A number of

s, including

helminth Parasitic worms, also known as helminths, are a polyphyletic group of large macroparasites; adults can generally be seen with the naked eye. Many are intestinal worms that are soil-transmitted and infect the gastrointestinal tract. Other par ...

s (parasitic worms), use papain-like proteases as mechanisms for invasion of their

hosts A host is a person responsible for guests at an event or for providing hospitality during it. Host may also refer to: Places * Host, Pennsylvania, a village in Berks County * Host Island, in the Wilhelm Archipelago, Antarctica People * ...

. Examples include ''

Toxoplasma gondii ''Toxoplasma gondii'' () is a species of parasitic alveolate that causes toxoplasmosis. Found worldwide, ''T. gondii'' is capable of infecting virtually all warm-blooded animals, but members of the cat family (felidae) are the only known d ...

'' and ''

Giardia lamblia ''Giardia duodenalis'', also known as ''Giardia intestinalis'' and ''Giardia lamblia'', is a flagellated Parasitism, parasitic protozoan microorganism of the genus ''Giardia'' that colonizes the small intestine, causing a diarrheal condition kn ...

''. In many flatworms, there are very high levels of expression of cysteine cathepsins; in the

liver fluke Liver fluke is a collective name of a polyphyletic group of parasitic trematodes under the phylum Platyhelminthes. They are principally parasites of the liver of various mammals, including humans. Capable of moving along the blood circulation, ...

Fasciola hepatica ''Fasciola hepatica'', also known as the common liver fluke or sheep liver fluke, is a parasitism, parasitic trematode (fluke (flatworm), fluke or flatworm, a type of helminth) of the class (biology), class Trematoda, phylum Platyhelminthes. It ...

'',

gene duplication Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene ...

s have produced over 20

paralog Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a sp ...

s of a cathepsin L-like enzyme. Cysteine cathepsins are also part of the normal life cycle of the unicellular parasite ''

Leishmania ''Leishmania'' () is a genus of parasitic protozoans, single-celled eukaryotic organisms of the trypanosomatid group that are responsible for the disease leishmaniasis. The parasites are transmitted by sandflies of the genus '' Phlebotomus'' ...

'', where they function as

virulence factor Virulence factors (preferably known as pathogenicity factors or effectors in botany) are cellular structures, molecules and regulatory systems that enable microbial pathogens (bacteria, viruses, fungi, and protozoa) to achieve the following: * c ...

s. The enzyme and potential

is important for the life cycle of the parasite ''

'', which causes

Chagas' disease Chagas disease, also known as American trypanosomiasis, is a tropical parasitic disease caused by ''Trypanosoma cruzi''. It is spread mostly by insects in the subfamily Triatominae, known as "kissing bugs". The symptoms change throughout the in ...

Plants

Members of the papain-like protease family play a number of important roles in

plant development Important structures in plant development are buds, shoots, roots, leaves, and flowers; plants produce these tissues and structures throughout their life from meristems located at the tips of organs, or between mature tissues. Thus, a living plant ...

, including

seed germination Germination is the process by which an organism grows from a seed or spore. The term is applied to the sprouting of a seedling from a seed of an angiosperm or gymnosperm, the growth of a sporeling from a spore, such as the spores of fungi, ...

, leaf senescence, and responding to

abiotic stress Abiotic stress is the negative impact of non-living factors on the living organisms in a specific environment. The non-living variable must influence the environment beyond its normal range of variation to adversely affect the population performan ...

. Papain-like proteases are involved in regulation of

programmed cell death Programmed cell death (PCD) sometimes referred to as cell, or cellular suicide is the death of a cell (biology), cell as a result of events inside of a cell, such as apoptosis or autophagy. PCD is carried out in a biological process, which usual ...

in plants, for example in tapetum during development of

pollen Pollen is a powdery substance produced by most types of flowers of seed plants for the purpose of sexual reproduction. It consists of pollen grains (highly reduced Gametophyte#Heterospory, microgametophytes), which produce male gametes (sperm ...

. They are also important in

plant immunity Plants are the eukaryotes that form the kingdom Plantae; they are predominantly photosynthetic. This means that they obtain their energy from sunlight, using chloroplasts derived from endosymbiosis with cyanobacteria to produce sugars fro ...

providing defense against

pests PESTS was an anonymous American activist group formed in 1986 to critique racism, tokenism, and exclusion in the art world. PESTS produced newsletters, posters, and other print material highlighting examples of discrimination in gallery represent ...

and

pathogens In biology, a pathogen (, "suffering", "passion" and , "producer of"), in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ. The term ...

. The relationship between plant papain-like proteases and pathogen responses—such as

inhibitors—have been described as an

evolutionary arms race In evolutionary biology, an evolutionary arms race is an ongoing struggle between competing sets of co-evolving genes, phenotypic and behavioral traits that develop escalating adaptations and counter-adaptations against each other, resembling the ...

. Some PLP family members in plants have culinary and commercial applications. The family's namesake member,

, is a protease derived from

papaya The papaya (, ), papaw, () or pawpaw () is the plant species ''Carica papaya'', one of the 21 accepted species in the genus '' Carica'' of the family Caricaceae, and also the name of its fruit. It was first domesticated in Mesoamerica, within ...

, used as a

meat tenderizer A meat tenderizer or meat pounder is a tool for mechanically tenderizing and flattening slabs of meat. Meat tenderizers come in at least three types: * The first, most common, is a tool that resembles a hammer or mallet made of metal or wood ...

. Similar but less widely used plant products include

bromelain Bromelain is an enzyme extract derived from the plant stem, stems of pineapples, although it exists in all parts of the fresh plant and fruit. The extract has a history of folk medicine use. As a culinary ingredient, it may be used as a Meat tender ...

from

pineapple The pineapple (''Ananas comosus'') is a Tropical vegetation, tropical plant with an edible fruit; it is the most economically significant plant in the family Bromeliaceae. The pineapple is indigenous to South America, where it has been culti ...

and

ficin Ficain also known as ficin, debricin, or higueroxyl delabarre () is a proteolytic enzyme extracted from the latex sap from the stems, leaves, and unripe fruit of the American wild fig tree '' Ficus insipida''. Ficain was originally called ficin, a ...

from

fig The fig is the edible fruit of ''Ficus carica'', a species of tree or shrub in the flowering plant family Moraceae, native to the Mediterranean region, together with western and southern Asia. It has been cultivated since ancient times and i ...

Prokaryotes

Although papain-like proteases are found in all domains of life, they have been less well-studied in

s than in

eukaryote The eukaryotes ( ) constitute the Domain (biology), domain of Eukaryota or Eukarya, organisms whose Cell (biology), cells have a membrane-bound cell nucleus, nucleus. All animals, plants, Fungus, fungi, seaweeds, and many unicellular organisms ...

s. Only a few prokaryotic PLP enzymes have been characterized by

or enzymatic studies, mostly from pathogenic bacteria, including

streptopain Streptopain, also known as streptococcal pyrogenic exotoxin B (SpeB) is a streptococcal cysteine protease. Other names include Streptococcus peptidase A, Streptococcus protease, and streptococcal cysteine proteinase. Streptopain catalyses the foll ...

from ''

Streptococcus pyogenes ''Streptococcus pyogenes'' is a species of Gram-positive, aerotolerant bacteria in the genus '' Streptococcus''. These bacteria are extracellular, and made up of non-motile and non-sporing cocci (round cells) that tend to link in chains. They ...

''; xylellain, from the plant pathogen ''

Xylella fastidiosa ''Xylella fastidiosa'' is an aerobic, Gram-negative bacterium of the genus ''Xylella''. It is a plant pathogen, that grows in the water transport tissues of plants ( xylem vessels) and is transmitted exclusively by xylem sap-feeding insects suc ...

''; Cwp84 from ''

Clostridioides difficile ''Clostridioides difficile'' ( syn. ''Clostridium difficile'') is a bacterium known for causing serious diarrheal infections, and may also cause colon cancer. It is known also as ''C. difficile'', or ''C. diff'' (), and is a Gram-positive spec ...

''; and Lpg2622 from ''

Legionella pneumophila ''Legionella pneumophila'', the primary causative agent for Legionnaires' disease, Legionnaire's disease, is an Aerobic organism, aerobic, pleomorphic, Flagellum, flagellated, non-spore-forming, Gram-negative bacteria, Gram-negative bacterium. ' ...

''.

Viruses

The papain-like protease family includes a number of

s that are found in large

s expressed by

es. Among the best studied viral PLPs are nidoviral papain-like protease domains from

nidovirus ''Nidovirales'' is an order of enveloped, positive-strand RNA viruses which infect vertebrates and invertebrates. Host organisms include mammals, birds, reptiles, amphibians, fish, arthropods, molluscs, and helminths. The order includes the fami ...

es, particularly those from

es. These PLPs are responsible for several cleavage events that process a large polyprotein into

s, although they perform fewer cleavages than the

3C-like protease The 3C-like protease (3CLpro) or main protease (Mpro), formally known as C30 endopeptidase or 3-chymotrypsin-like protease, is the main protease found in coronaviruses. It cleaves the coronavirus polyprotein at eleven conserved sites. It is a c ...

(also known as the main protease). Coronavirus PLPs are multifunctional enzymes that can also act as

s (cleaving the

ubiquitin Ubiquitin is a small (8.6 kDa) regulatory protein found in most tissues of eukaryotic organisms, i.e., it is found ''ubiquitously''. It was discovered in 1975 by Gideon Goldstein and further characterized throughout the late 1970s and 19 ...

) and "deISGylating enzymes" with analogous activity against the

ubiquitin-like protein Ubiquitin-like proteins (UBLs) are a family of small proteins involved in post-translational modification of other proteins in a cell (biology), cell, usually with a regulatory protein, regulatory function. The UBL protein family derives its name ...

ISG15. In human pathogens including

MERS-CoV Middle East respiratory syndrome–related coronavirus (MERS-CoV, ''Betacoronavirus cameli'') or EMC/2012 ( HCoV-EMC/2012), is the virus that causes Middle East respiratory syndrome (MERS). It is a species of coronavirus which infects humans, ba ...

, and

, the PLP domain is essential for

viral replication Viral replication is the formation of biological viruses during the infection process in the target host cells. Viruses must first get into the cell before viral replication can occur. Through the generation of abundant copies of its genome ...

and is therefore considered a

for the development of

antiviral drug Antiviral drugs are a class of medication used for treating viral infections. Most antivirals target specific viruses, while a broad-spectrum antiviral is effective against a wide range of viruses. Antiviral drugs are a class of antimicrobials ...

s. One such experimental antiviral medication, Jun12682, is being studied as a potential treatment for COVID-19, and it is believed to work by inhibiting SARS-CoV-2 papain-like protease (PLpro). The surface zone of SARS-CoV-2 PLpro participating in binding of cellular proteins can also be targeted by bioactive molecules, such as

glycyrrhizinic acid Glycyrrhizin (glycyrrhizic acid or glycyrrhizinic acid) is the chief sweet-tasting constituent of ''Glycyrrhiza glabra'' (liquorice) root. Structurally, it is a saponin used as an emulsifier and gel-forming agent in foodstuffs and cosmetics. I ...

, thus potentially preventing protein-protein complexation.

References

{{reflist, 30em Proteases Protein superfamilies