Aminopeptidase

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3qnf.jpg
Crystal structure of the open state of human endoplasmic reticulum aminopeptidase 1 ERAP1 [1]
Identifiers
SymbolPeptidase_M1
Pfam PF01433
MEROPS M1
OPM superfamily 227
OPM protein 3mdj
CDD cd09595
Membranome 534
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary

Aminopeptidases are enzymes that catalyze the cleavage of amino acids from the N-terminus (beginning), of proteins or peptides. They are found in many organisms; in the cell, they are found in many organelles, in the cytosol (internal cellular fluid), and as membrane proteins. Aminopeptidases are used in essential cellular functions, and are often zinc metalloenzymes, containing a zinc cofactor. [2]

Contents

Aminopeptidases occur in both water-soluble and membrane-bound forms and can be found both in various cellular compartments and in the extracellular environment (outside of cells). [3] Their broad substrate specificity, their ability to strongly bind to their targets, allows them to remove beginning N-terminal amino acids from almost all unsubstituted oligopeptides. [4] For instance, Aminopeptidase N (AP-N) is particularly abundant in the brush border membranes of the kidney, the small intestine, and the placenta, and is also found in the liver. [4] AP-N is involved in the final digestion of peptides generated from the hydrolysis (cleaving) of proteins by gastric and pancreatic proteases. [5]

Some aminopeptidases are monomeric, and others are found as assemblies of relatively high mass (50 kDa) subunits. cDNA sequences are available for several aminopeptidases and a crystal structure of the open state of human endoplasmic reticulum aminopeptidase 1 is available. [1]

History

The discovery and characterization of aminopeptidases date back to the early 20th century. The term "aminopeptidase" was first introduced in 1929 by Linderstrøm-Lang and Sato in order to describe enzymes that cleave amino acids from the N-terminus of peptides. [6] [ better source needed ]

In the 1950s and 1960s, the discovery of leucine aminopeptidase (LAP) and aminopeptidase N (APN) marked important milestones in the field. LAP was found to be crucial for protein digestion, while APN was recognized for its role in the regulation of peptide-mediated effects. [4] [7] These discoveries were pivotal in understanding the physiological functions of aminopeptidases and their involvement in health and disease.[ citation needed ]

The subsequent decades[ which? ] saw extensive research into the structure, function, and mechanisms of action of various aminopeptidases. For example, the M1 family of aminopeptidases, which includes puromycin-sensitive aminopeptidase (PSA), was characterized by conserved zinc-dependent sites and exopeptidase motifs. [7] [ better source needed ] The study of PSA in different model organisms revealed its essential roles in growth and behavior. Mutations in orthologs of PSA in different species were linked to errors in meiosis and reduced viability of embryos. [7] Aminopeptidase N, also known as AP-N or CD13, was extensively characterized for its broad substrate specificity (ability to bind to its targets) and its presence in various tissues such as the brush border membranes of the kidney, small intestine, and placenta. [4] The enzyme's role in brain function and its identification as the human cluster differentiation antigen CD13 on the surface of myeloid cells further highlighted its biological significance.[ citation needed ]

Structure and classification

Aminopeptidases are a diverse group of enzymes that play crucial roles in various biological processes, including protein digestion, cell growth, and immune response. They are classified based on their substrate specificity (strength of binding) and catalytic mechanism (means of catalyzing their reaction) into two main categories: metalloaminopeptidases and cysteine aminopeptidases.[ citation needed ] Metalloaminopeptidases use a metal ion to perform their function, and cysteine aminopeptidases use a particular cysteine amino acid.

The structure of aminopeptidases varies depending on the specific enzyme, but they generally consist of a catalytic domain where the catalysis occurs and additional domains that contribute to target recognition and regulation of their functions. For instance, Aminopeptidase N (APN), a type II metalloprotease, consists of 967 amino acids with a short N-terminal cytoplasmic domain in the cytoplasm, a single transmembrane part reaching through the cellular membrane, and a large cellular ectodomain sticking out of the cell containing the active site. [8]

Metalloaminopeptidases

Metalloaminopeptidases require metal ions, such as zinc or manganese, in order to function. These enzymes can be identified by a conserved HEXXH motif in their active site. This motif is crucial for the enzyme's function, as the histidine amino acids within the motif coordinate (bind) the metal ion, which then uses hydrolysis to break the peptide bond between the first amino acid and the rest of the protein. [9] Metalloaminopeptidases are the largest and most homogenous class of aminopeptidases; the MEROPS database identifies over 35 families to be part of the MA clan. This classification, which is based on structural similarities and evolutionary relationships, indicates a common ancestral origin for these enzymes. [9] Examples of metalloaminopeptidases include aminopeptidase N (APN), leucine aminopeptidase (LAP), and aminopeptidase A (APA). [8] [10]

Cysteine aminopeptidase

Cysteine aminopeptidases, on the other hand, rely on a cysteine amino acid to perform catalysis. These enzymes are part of a broader group of cysteine proteases, all of which carve up proteins by using a nucleophilic cysteine thiol along with one or two other catalytic amino acids in a diad or triad. The triad typically consists of cysteine, histidine, and aspartate amino acids, where the cysteine acts as a nucleophile, the histidine acts as a chemical base, and the aspartate stabilizes the histidine. [11] Examples of cysteine aminopeptidases include cathepsin H and aminopeptidase B. [8]

Biological role

In general, aminopeptidases play an important role in the metabolism of both proteins and peptides. Aminopeptidases in the gastrointestinal tract, such as APN and APA, are essential for the digestion of dietary proteins. They facilitate the absorption and utilization of amino acids by cleaving them from the N-terminus of peptides. [12] These enzymes also play a role in the metabolism of bioactive peptides, including hormones and growth factors. By regulating the levels of these peptides, aminopeptidases contribute to homeostasis and physiological process modulation. [12]

Bacterial aminopeptidases

In bacteria, aminopeptidases are produced by both facultative anaerobic strains, which can respire with or without oxygen, and obligate strains, which either require or are killed by atmospheric oxygen. [13] They and can be found in many different cellular locations, for example in the cytoplasm, in membranes, associated with the cell envelope,[ clarification needed ] or secreted into the extracellular medium. [13] These enzymes are involved in the breaking down of externally supplied peptides (very short proteins) and are necessary for the final steps of protein turnover and replacement. They also participate in specific functions like the cleavage of N-terminal (beginning) methionine from newly synthesized peptide chains (methionine aminopeptidases), stabilization of ColE1-based multicopy plasmids (e.g. aminopeptidase A), and the cleavage of N-terminal pyroglutamate (e.g. pyroglutamyl aminopeptidase. [13]

Fungal aminopeptidases

Fungi, particularly species like Aspergillus oryzae and Aspergillus sojae, produce aminopeptidases that have applications in the food industry as debittering agents. [14] These enzymes are also of interest for their potential biotechnological applications. For example, leucine aminopeptidase (LAP) from Aspergillus species has been found to be thermostable and could theoretically be used to control the degree of hydrolysis and flavor development in a wide range of substances. [14]

Mammalian aminopeptidases

In mammals, aminopeptidases are produced in various tissues and organs, such as the liver, kidney, and intestine. Due to their ability to break down proteins and peptides, they are used in to help digest proteins, regulate peptide-mediated effects, and break down bioactive peptides. [4] Aminopeptidase N (AP-N) is particularly abundant in the brush border membranes of the kidney, small intestine, and placenta, and is also rich in the liver. [4] It has a broad substrate specificity (ability to bind to its targets) and is involved in the final stages of the digestion of peptides generated from breaking-up and hydrolysis of proteins by gastric and pancreatic proteases. [4]

Medicine and biotechnology

Aminopeptidase has been studied for use in treating hypertension, inflammation, and some cancers. Aminopeptidase A (APA) is implicated in blood pressure regulation by converting angiotensin II to angiotensin III. APA inhibitors are being explored as potential antihypertensive agents, offering a novel approach to managing hypertension. [12] Aminopeptidase N (APN) has been associated with the pathogenesis of inflammatory diseases such as rheumatoid arthritis and inflammatory bowel disease. Inhibitors of APN have demonstrated anti-inflammatory effects in animal models, positioning them as potential therapeutic agents for these conditions. [12] Several aminopeptidases, including APN, APA, and leucine aminopeptidase (LAP), are overexpressed in various cancers. Their involvement in tumor growth, invasion, and angiogenesis makes them attractive targets for cancer therapy. Aminopeptidase inhibitors have shown promise in preclinical studies as potential anticancer agents. [12]

Diagnostic markers

The activity and expression levels of aminopeptidases have been explored as diagnostic markers for diseases like liver disorders and cancer. Variations in these parameters can indicate pathological conditions, aiding in disease diagnosis and monitoring. [12]

Biosensors

Aminopeptidases have been utilized in creating biosensors for detecting specific amino acids or peptides. These biosensors generate a measurable signal in the presence of the target analyte, leveraging the catalytic activity of aminopeptidases. [12]

Protein sequencing

In protein sequencing, aminopeptidases are employed in the Edman degradation method. This technique involves the sequential removal and identification of the N-terminal amino acid of proteins, facilitating the elucidation of their amino acid sequence. [15]

Food industry

In the food industry, aminopeptidases from Aspergillus oryzae and Aspergillus sojae are utilized for debittering protein hydrolysates, including those used in soy sauce and miso production. These enzymes help remove bitter-tasting peptides, enhancing the flavor and palatability of these products. [15] Aminopeptidases also play a crucial role in cheese ripening by participating in the proteolysis of milk proteins. This enzymatic action contributes significantly to the development of the cheese's flavor and texture, making aminopeptidases essential in the cheese-making process. [15]

When aminopeptidases are used in food processing, it is crucial to ensure that they are food-grade and safe for consumption. Aminopeptidases from A. oryzae and A. sojae, for example, have been extensively studied and are considered safe for use in food applications. [16] It is important to handle these enzymes under conditions that prevent contamination and degradation, which could affect both the safety and quality of the food products.

Aminopeptidases require specific storage conditions to maintain their stability and enzymatic activity. For instance, human aminopeptidase A is stable at a pH range of 7.0-8.5 and can be stored at -20°C for several months without significant loss of activity. Similarly, a halotolerant intracellular protease from Bacillus subtilis strain FP-133, which exhibits aminopeptidase activity, retains full activity after being stored in 7.5% (w/v) NaCl at 4°C for 24 hours. [17] These examples indicate that aminopeptidases generally require neutral pH conditions and can be stored at low temperatures, such as -20°C or -80°C, for extended periods to preserve their activity.

See also

Related Research Articles

<span class="mw-page-title-main">Amino acid</span> Organic compounds containing amine and carboxylic groups

Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. Only these 22 appear in the genetic code of life.

<span class="mw-page-title-main">Chymotrypsin</span> Digestive enzyme

Chymotrypsin (EC 3.4.21.1, chymotrypsins A and B, alpha-chymar ophth, avazyme, chymar, chymotest, enzeon, quimar, quimotrase, alpha-chymar, alpha-chymotrypsin A, alpha-chymotrypsin) is a digestive enzyme component of pancreatic juice acting in the duodenum, where it performs proteolysis, the breakdown of proteins and polypeptides. Chymotrypsin preferentially cleaves peptide amide bonds where the side chain of the amino acid N-terminal to the scissile amide bond (the P1 position) is a large hydrophobic amino acid (tyrosine, tryptophan, and phenylalanine). These amino acids contain an aromatic ring in their side chain that fits into a hydrophobic pocket (the S1 position) of the enzyme. It is activated in the presence of trypsin. The hydrophobic and shape complementarity between the peptide substrate P1 side chain and the enzyme S1 binding cavity accounts for the substrate specificity of this enzyme. Chymotrypsin also hydrolyzes other amide bonds in peptides at slower rates, particularly those containing leucine at the P1 position.

<span class="mw-page-title-main">Proteolysis</span> Breakdown of proteins into smaller polypeptides or amino acids

Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids. Uncatalysed, the hydrolysis of peptide bonds is extremely slow, taking hundreds of years. Proteolysis is typically catalysed by cellular enzymes called proteases, but may also occur by intra-molecular digestion.

<span class="mw-page-title-main">Trypsin</span> Family of digestive enzymes

Trypsin is an enzyme in the first section of the small intestine that starts the digestion of protein molecules by cutting long chains of amino acids into smaller pieces. It is a serine protease from the PA clan superfamily, found in the digestive system of many vertebrates, where it hydrolyzes proteins. Trypsin is formed in the small intestine when its proenzyme form, the trypsinogen produced by the pancreas, is activated. Trypsin cuts peptide chains mainly at the carboxyl side of the amino acids lysine or arginine. It is used for numerous biotechnological processes. The process is commonly referred to as trypsinogen proteolysis or trypsinization, and proteins that have been digested/treated with trypsin are said to have been trypsinized.

<span class="mw-page-title-main">Protease</span> Enzyme that cleaves other proteins into smaller peptides

A protease is an enzyme that catalyzes proteolysis, breaking down proteins into smaller polypeptides or single amino acids, and spurring the formation of new protein products. They do this by cleaving the peptide bonds within proteins by hydrolysis, a reaction where water breaks bonds. Proteases are involved in numerous biological pathways, including digestion of ingested proteins, protein catabolism, and cell signaling.

Matrix metalloproteinases (MMPs), also known as matrix metallopeptidases or matrixins, are metalloproteinases that are calcium-dependent zinc-containing endopeptidases; other family members are adamalysins, serralysins, and astacins. The MMPs belong to a larger family of proteases known as the metzincin superfamily.

The C-terminus is the end of an amino acid chain, terminated by a free carboxyl group (-COOH). When the protein is translated from messenger RNA, it is created from N-terminus to C-terminus. The convention for writing peptide sequences is to put the C-terminal end on the right and write the sequence from N- to C-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 amine group is bonded to the carboxylic group of another amino acid, making it a chain. That leaves a free carboxylic group at one end of the peptide, called the C-terminus, and a free amine group on the other end called the N-terminus. By convention, peptide sequences are written N-terminus to C-terminus, left to right (in LTR writing systems). This correlates the translation direction to the text direction, because when a protein is translated from messenger RNA, it is created from the N-terminus to the C-terminus, as amino acids are added to the carboxyl end of the protein.

<span class="mw-page-title-main">Serine protease</span> Class of enzymes

Serine proteases 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. Serine proteases fall into two broad categories based on their structure: chymotrypsin-like (trypsin-like) or subtilisin-like.

<span class="mw-page-title-main">Metalloproteinase</span> Type of enzyme

A metalloproteinase, or metalloprotease, is any protease enzyme whose catalytic mechanism involves a metal. An example is ADAM12 which plays a significant role in the fusion of muscle cells during embryo development, in a process known as myogenesis.

<span class="mw-page-title-main">Digestive enzyme</span> Class of enzymes

Digestive enzymes take part in the chemical process of digestion, which follows the mechanical process of digestion. Food consists of macromolecules of proteins, carbohydrates, and fats that need to be broken down chemically by digestive enzymes in the mouth, stomach, pancreas, and duodenum, before being able to be absorbed into the bloodstream. Initial breakdown is achieved by chewing (mastication) and the use of digestive enzymes of saliva. Once in the stomach further mechanical churning takes place mixing the food with secreted gastric acid. Digestive gastric enzymes take part in some of the chemical process needed for absorption. Most of the enzymatic activity, and hence absorption takes place in the duodenum.

<span class="mw-page-title-main">Papain</span> Widely used enzyme extracted from papayas

Papain, also known as papaya proteinase I, is a cysteine protease enzyme present in papaya and mountain papaya. It is the namesake member of the papain-like protease family.

<span class="mw-page-title-main">Catalytic triad</span> Set of three coordinated amino acids

A catalytic triad is a set of three coordinated amino acids that can be found in the active site of some enzymes. Catalytic triads are most commonly found in hydrolase and transferase enzymes. An acid-base-nucleophile triad is a common motif for generating a nucleophilic residue for covalent catalysis. The residues form a charge-relay network to polarise and activate the nucleophile, which attacks the substrate, forming a covalent intermediate which is then hydrolysed to release the product and regenerate free enzyme. The nucleophile is most commonly a serine or cysteine amino acid, but occasionally threonine or even selenocysteine. The 3D structure of the enzyme brings together the triad residues in a precise orientation, even though they may be far apart in the sequence.

<span class="mw-page-title-main">Deubiquitinating enzyme</span>

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 ubiquitin from proteins. Ubiquitin is attached to proteins in order to regulate the degradation of proteins via the proteasome and lysosome; coordinate the cellular localisation of proteins; activate and inactivate proteins; and modulate protein-protein interactions. DUBs can reverse these effects by cleaving the peptide or isopeptide bond between ubiquitin and its substrate protein. In humans there are nearly 100 DUB genes, which can be classified into two main classes: cysteine proteases and metalloproteases. The cysteine proteases comprise ubiquitin-specific proteases (USPs), ubiquitin C-terminal hydrolases (UCHs), Machado-Josephin domain proteases (MJDs) and ovarian tumour proteases (OTU). The metalloprotease group contains only the Jab1/Mov34/Mpr1 Pad1 N-terminal+ (MPN+) (JAMM) domain proteases.

<span class="mw-page-title-main">Cysteine protease</span> Class of enzymes

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.

Gelatinases are enzymes capable of degrading gelatin through hydrolysis, playing a major role in degradation of extracellular matrix and tissue remodeling. Gelatinases are a type of matrix metalloproteinase (MMP), a family of enzymes that depend on zinc as a cofactor and can break down parts of the extracellular matrix. MMPs have multiple subgroups, including gelatinase A and gelatinase B. Gelatinases are assigned a variety of Enzyme Commission numbers: gelatinase A uses 3.4.24.24, and gelatinase B uses 3.4.24.35, in which the first three numbers are same. The first digit, 3, is the class. Class 3 enzymes are hydrolases, enzymes that catalyze hydrolysis reactions, that is, they cleave bonds in presence of water. The next digit represents sub-class 4, or proteases, which are enzymes who hydrolyze peptide bonds in proteins. The next number is the sub-subclass of 24, which consists of metalloendopeptidases which contain metal ions in their active sites, in this case zinc, which help in cleaving peptide bonds. The last part of the EC number is the serial number, identifying specific enzymes within a sub-subclass. 24 represents gelatinase A, which is a metalloproteinase that breaks down gelatin and collagen, while 35 represents gelatinase B, which hydrolyzes peptide bonds.

<span class="mw-page-title-main">Carboxypeptidase</span> Class of enzymes

A carboxypeptidase is a protease enzyme that hydrolyzes (cleaves) a peptide bond at the carboxy-terminal (C-terminal) end of a protein or peptide. This is in contrast to an aminopeptidases, which cleave peptide bonds at the N-terminus of proteins. Humans, animals, bacteria and plants contain several types of carboxypeptidases that have diverse functions ranging from catabolism to protein maturation. At least two mechanisms have been discussed.

Protein metabolism denotes the various biochemical processes responsible for the synthesis of proteins and amino acids (anabolism), and the breakdown of proteins by catabolism.

<span class="mw-page-title-main">Actinidain</span> Class of enzymes

Actinidain is a type of cysteine protease enzyme found in fruits including kiwifruit, pineapple, mango, banana, figs, and papaya. This enzyme is part of the peptidase C1 family of papain-like proteases.

<span class="mw-page-title-main">PA clan of proteases</span>

The PA clan is the largest group of proteases with common ancestry as identified by structural homology. Members have a chymotrypsin-like fold and similar proteolysis mechanisms but can have identity of <10%. The clan contains both cysteine and serine proteases. PA clan proteases can be found in plants, animals, fungi, eubacteria, archaea and viruses.

References

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  4. 1 2 3 4 5 6 7 Turner, Anthony J. (2013), "Aminopeptidase N", Handbook of Proteolytic Enzymes, Elsevier, pp. 397–403, doi:10.1016/b978-0-12-382219-2.00079-x, ISBN   978-0-12-382219-2
  5. ↑ Sanz, Yolanda (2007), "Aminopeptidases", Industrial Enzymes, Dordrecht: Springer Netherlands, pp. 243–260, doi:10.1007/1-4020-5377-0_15, ISBN   978-1-4020-5376-4
  6. ↑ Bala, Sandeep Chowdary; Haque, Neshatul; Pillalamarri, Vijaykumar; Reddi, Ravikumar; Kashyap, Rajnandani; Marapaka, Anil Kumar; Addlagatta, Anthony (2019-05-15). "Discovery of a new class of type 1 methionine aminopeptidases that have relaxed substrate specificity". International Journal of Biological Macromolecules . 129: 523–529. doi:10.1016/j.ijbiomac.2019.02.055. ISSN   0141-8130. PMID   30763644. S2CID   73436841.
  7. 1 2 3 Su, Shanchun; Pan, Baoliang; Hu, Yanxin; Wang, Ming (2019-11-12). "Characterization of aminopeptidase encoding gene anp-1 and its association with development in Caenorhabditis elegans". PeerJ. 7: e7944. doi: 10.7717/peerj.7944 . ISSN   2167-8359. PMC   6857582 . PMID   31737443.
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  10. ↑ Silbernagl, Stefan; Gekle, Michael (2008), "Amino Acids, Oligopeptides, and Hyperaminoacidurias", Seldin and Giebisch's The Kidney, Elsevier, pp. 2021–2044, doi:10.1016/b978-012088488-9.50075-9, ISBN   978-0-12-088488-9
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  14. 1 2 Nampoothiri, K.M.; Nagy, V.; Kovacs, K.; Szakacs, G.; Pandey, A. (December 2005). "l-leucine aminopeptidase production by filamentous Aspergillus fungi". Letters in Applied Microbiology. 41 (6): 498–504. doi:10.1111/j.1472-765x.2005.01789.x. ISSN   0266-8254. PMID   16305677.
  15. 1 2 3 Wang, Yawei; Zhao, Puying; Zhou, Ying; Hu, Xiaomin; Xiong, Hairong (2023-01-10). "From bitter to delicious: properties and uses of microbial aminopeptidases". World Journal of Microbiology and Biotechnology. 39 (3): 72. doi:10.1007/s11274-022-03501-3. ISSN   0959-3993. PMID   36625962.
  16. ↑ Adam Salifou; Christian Tétédé Rodrigue Konfo; Alexandrine Bokossa; Nicodème Worou Chabi; Fidèle Paul Tchobo; Mohamed Mansourou Soumanou (2023-11-30). "Innovative approaches in food processing: enhancing quality, preservation, and safety through advanced technologies: A review". World Journal of Advanced Research and Reviews. 20 (2): 637–648. doi: 10.30574/wjarr.2023.20.2.2297 . ISSN   2581-9615.
  17. ↑ Setyorini, Endang; Kim, Young-Ju; Takenaka, Shinji; Murakami, Shuichiro; Aoki, Kenji (2006-07-17). "Purification and characterization of a halotolerant intracellular protease from Bacillus subtilis strain FP-133". Journal of Basic Microbiology. 46 (4): 294–304. doi:10.1002/jobm.200510086. ISSN   0233-111X. PMID   16847833.
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