Kunitz domain

Last updated
Kunitz/Bovine pancreatic trypsin inhibitor domain
PDB 1kth EBI.jpg
3D structure of the C-terminal Kunitz domain from human collagen alpha-3(VI) chain. [1]
Identifiers
SymbolKunitz_BPTI
Pfam PF00014
InterPro IPR002223
PROSITE PDOC00252
SCOP2 5pti / SCOPe / SUPFAM
CDD cd00109
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary
PDB 1knt :3110-3162 2knt :3110-3162 1kth A:3110-3162

1kun :3110-3162 1bik :286-338 1shp :2-54 1jc6 A:6-58 1bf0 :6-58 1dtk :26-78 1dtx :6-58 1den :6-58 1dem :6-58 1zr0 D:35-87 1irh A:216-268 1adz :124-176 1tfx C:124-176 1d0d B:39-91 1k6u A:39-91 2fi4 I:39-91 1aal A:39-91 2kai I:39-91 1ejm D:39-91 1fak I:39-90 1bhc G:39-91 2hex C:39-91 1bth Q:39-91 3btw I:39-91 1p2q B:39-91 1bz5 C:39-91 3bth I:39-91 1oa6 5:39-91 1eaw B:39-91 3btm I:39-91 1oa5 5:39-91 2tpi I:39-91 1pit :39-91 3btd I:39-91 1b0c D:39-91 3btf I:39-91 1t8m B:39-91 1ld5 A:39-91 1bzx I:39-91 1p2j I:39-91 1uub A:39-91 3tgk I:39-91 1t7c D:39-91 1tpa I:39-91 1p2n B:39-91 1p2k I:39-91 1t8n B:39-91 1g6x A:39-91 1nag :39-91 8pti :39-91 2fi3 I:39-91 1t8o B:39-91 1k09 B:50-73 1p2m B:39-91 6pti :39-91 3tpi I:39-91 1t8l D:39-91 3btg I:39-91 3tgj I:39-91 1brb I:42-90 1jv9 A:39-91 1f7z I:39-91 1fy8 I:39-91 2ptc I:39-91 2tgp I:39-91 1mtn D:39-91 1cbw I:39-91 1jv8 A:39-91 1f5r I:39-91 7pti :39-91 3bte I:39-91 1fan :39-91 3tgi I:39-91 3btk I:39-91 5pti :39-91 1uua A:39-91 9pti :39-91 3btt I:39-91 1bpi :39-91 1p2o D:39-91 1bpt :39-91 1p2i I:39-91 4pti :39-91 1qlq A:39-91 1ld6 A:39-91 3btq I:39-91 4tpi I:39-91 1bti :39-91 1yc0 I:249-301 1ca0 I:290-342 1aap B:290-342 1taw B:290-342 1brc I:290-342 1zjd B:290-342 1bun B:30-82 1toc R:4-51

Contents

1kig I:4-60 1tap :4-60 1tcp :4-60

Kunitz domains are the active domains of proteins that inhibit the function of protein degrading enzymes or, more specifically, domains of Kunitz-type are protease inhibitors. They are relatively small with a length of about 50 to 60 amino acids and a molecular weight of 6 kDa. Examples of Kunitz-type protease inhibitors are aprotinin (bovine pancreatic trypsin inhibitor, BPTI), Alzheimer's amyloid precursor protein (APP), and tissue factor pathway inhibitor (TFPI). Kunitz STI protease inhibitor, the trypsin inhibitor initially studied by Moses Kunitz, was extracted from soybeans.

Standalone Kunitz domains are used as a framework for the development of new pharmaceutical drugs. [2]

Structure

The structure is a disulfide rich alpha+beta fold. Bovine pancreatic trypsin inhibitor is an extensively studied model structure. Certain family members are similar to the tick anticoagulant peptide (TAP, P17726 ). This is a highly selective inhibitor of factor Xa in the blood coagulation pathways. [3] TAP molecules are highly dipolar, [4] and are arranged to form a twisted two-stranded antiparallel beta sheet followed by an alpha helix. [3]

The majority of the sequences having this domain belong to the MEROPS inhibitor family I2, clan IB; the Kunitz/bovine pancreatic trypsin inhibitor family, they inhibit proteases of the S1 family [5] and are restricted to the metazoa with a single exception: Amsacta moorei entomopoxvirus, a species of poxvirus. They are short (about 50 to 60 amino acid residues) alpha/beta proteins with few secondary structures. The fold is constrained by three disulfide bonds. The type example for this family is BPTI [6] (or basic protease inhibitor), but the family includes numerous other members, [7] [8] [9] [10] such as snake venom basic protease; mammalian inter-alpha-trypsin inhibitors; trypstatin, a rat mast cell inhibitor of trypsin; a domain found in an alternatively spliced form of Alzheimer's amyloid beta-protein; domains at the C-termini of the alpha-1 and alpha-3 chains of type VI and type VII collagens; tissue factor pathway inhibitor precursor; and Kunitz STI protease inhibitor contained in legume seeds.

Drug development

Kunitz domains are stable as standalone peptides, able to recognise specific protein structures, and also work as competitive protease inhibitors in their free form. These properties have led to attempts at developing biopharmaceutical drugs from Kunitz domains. Candidate domains are selected from molecular libraries containing over 10 million variants with the aid of display techniques like phage display, [11] and can be produced in large scale by genetically engineered organisms.

The first of these drugs to be marketed was the kallikrein inhibitor ecallantide, used for the treatment of hereditary angioedema. [11] It was approved in the United States in 2009. [12] Another example is depelestat, an inhibitor of neutrophil elastase that has undergone Phase II clinical trials for the treatment of acute respiratory distress syndrome in 2006/2007 [13] and has also been described as a potential inhalable cystic fibrosis treatment. [14]

Examples

Human proteins containing this domain include:

Several plant protease inhibitors of the Kunitz family, the Kunitz-STI protein family, include a beta trefoil fold. [15]

Related Research Articles

<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 trypsin proteolysis or trypsinization, and proteins that have been digested/treated with trypsin are said to have been trypsinized. Trypsin was discovered in 1876 by Wilhelm Kühne and was named from the Ancient Greek word for rubbing since it was first isolated by rubbing the pancreas with glycerin.

In biology and biochemistry, protease inhibitors, or antiproteases, are molecules that inhibit the function of proteases. Many naturally occurring protease inhibitors are proteins.

Trypsinogen is the precursor form of trypsin, a digestive enzyme. It is produced by the pancreas and found in pancreatic juice, along with amylase, lipase, and chymotrypsinogen. It is cleaved to its active form, trypsin, by enteropeptidase, which is found in the intestinal mucosa. Once activated, the trypsin can cleave more trypsinogen into trypsin, a process called autoactivation. Trypsin cleaves the peptide bond on the carboxyl side of basic amino acids such as arginine and lysine.

<span class="mw-page-title-main">Beta-secretase 2</span> Enzyme found in humans

Beta-secretase 2 is an enzyme that cleaves Glu-Val-Asn-Leu!Asp-Ala-Glu-Phe in the Swedish variant of Alzheimer's amyloid precursor protein. BACE2 is a close homolog of BACE1.

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

Enteropeptidase is an enzyme produced by cells of the duodenum and is involved in digestion in humans and other animals. Enteropeptidase converts trypsinogen into its active form trypsin, resulting in the subsequent activation of pancreatic digestive enzymes. Absence of enteropeptidase results in intestinal digestion impairment.

<span class="mw-page-title-main">Dendrotoxin</span> Chemical compound

Dendrotoxins are a class of presynaptic neurotoxins produced by mamba snakes (Dendroaspis) that block particular subtypes of voltage-gated potassium channels in neurons, thereby enhancing the release of acetylcholine at neuromuscular junctions. Because of their high potency and selectivity for potassium channels, dendrotoxins have proven to be extremely useful as pharmacological tools for studying the structure and function of these ion channel proteins.

<span class="mw-page-title-main">Tissue factor pathway inhibitor</span> Single-chain polypeptide capable of inhibiting blood clotting Factor Xa

Tissue factor pathway inhibitor is a single-chain polypeptide which can reversibly inhibit factor Xa (Xa). While Xa is inhibited, the Xa-TFPI complex can subsequently also inhibit the FVIIa-tissue factor complex. TFPI contributes significantly to the inhibition of Xa in vivo, despite being present at concentrations of only 2.5 nM.

A trypsin inhibitor (TI) is a protein and a type of serine protease inhibitor (serpin) that reduces the biological activity of trypsin by controlling the activation and catalytic reactions of proteins. Trypsin is an enzyme involved in the breakdown of many different proteins, primarily as part of digestion in humans and other animals such as monogastrics and young ruminants. Serpins – including trypsin inhibitors – are irreversible and suicide substrate-like inhibitors.

<span class="mw-page-title-main">Aprotinin</span> Antifibrinolytic molecule

The drug aprotinin, is a small protein bovine pancreatic trypsin inhibitor (BPTI), or basic trypsin inhibitor of bovine pancreas, which is an antifibrinolytic molecule that inhibits trypsin and related proteolytic enzymes. Under the trade name Trasylol, aprotinin was used as a medication administered by injection to reduce bleeding during complex surgery, such as heart and liver surgery. Its main effect is the slowing down of fibrinolysis, the process that leads to the breakdown of blood clots. The aim in its use was to decrease the need for blood transfusions during surgery, as well as end-organ damage due to hypotension as a result of marked blood loss. The drug was temporarily withdrawn worldwide in 2007 after studies suggested that its use increased the risk of complications or death; this was confirmed by follow-up studies. Trasylol sales were suspended in May 2008, except for very restricted research use. In February 2012 the European Medicines Agency (EMA) scientific committee reverted its previous standpoint regarding aprotinin, and has recommended that the suspension be lifted. Nordic became distributor of aprotinin in 2012.

<span class="mw-page-title-main">APLP2</span> Protein-coding gene in the species Homo sapiens

Amyloid-like protein 2, also known as APLP2, is a protein that in humans is encoded by the APLP2 gene. APLP2 along with APLP1 are important modulators of glucose and insulin homeostasis.

<span class="mw-page-title-main">SPINK1</span> Protein-coding gene in the species Homo sapiens

Pancreatic secretory trypsin inhibitor (PSTI) also known as serine protease inhibitor Kazal-type 1 (SPINK1) or tumor-associated trypsin inhibitor (TATI) is a protein that in humans is encoded by the SPINK1 gene.

<span class="mw-page-title-main">SPINT2</span> Protein-coding gene in the species Homo sapiens

Kunitz-type protease inhibitor 2 is an enzyme inhibitor that in humans is encoded by the SPINT2 gene. SPINT2 is a transmembrane protein with two extracellular Kunitz domains to inhibit serine proteases. This gene is a presumed tumor suppressor by inhibiting HGF activator which prevents the formation of active hepatocyte growth factor. Mutations in SPINT2 could result in congenital sodium diarrhea (CSD).

<span class="mw-page-title-main">Kunitz STI protease inhibitor</span>

Kunitz soybean trypsin inhibitor is a type of protein contained in legume seeds which functions as a protease inhibitor. Kunitz-type Soybean Trypsin Inhibitors are usually specific for either trypsin or chymotrypsin. They are thought to protect seeds against consumption by animal predators.

<span class="mw-page-title-main">Bowman–Birk protease inhibitor</span>

In molecular biology, the Bowman–Birk protease inhibitor family of proteins consists of eukaryotic proteinase inhibitors, belonging to MEROPS inhibitor family I12, clan IF. They mainly inhibit serine peptidases of the S1 family, but also inhibit S3 peptidases.

<span class="mw-page-title-main">Kazal domain</span>

The Kazal domain is an evolutionary conserved protein domain usually indicative of serine protease inhibitors. However, kazal-like domains are also seen in the extracellular part of agrins, which are not known to be protease inhibitors.

<span class="mw-page-title-main">PRSS3</span> Protein-coding gene in the species Homo sapiens

Protease, serine, 3 is a protein that in humans is encoded by the PRSS3 gene.

<span class="mw-page-title-main">WFIKKN2</span> Protein-coding gene in the species Homo sapiens

WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2 is a protein that in humans is encoded by the WFIKKN2 gene.

Kalicludine (AsKC) is a blocker of the voltage-dependent potassium channel Kv1.2 found in the snakeslocks anemone Anemonia viridis, which it uses to paralyse prey.

<span class="mw-page-title-main">Cry6Aa</span>

Cry6Aa is a toxic crystal protein generated by the bacterial family Bacillus thuringiensis during sporulation. This protein is a member of the alpha pore forming toxins family, which gives it insecticidal qualities advantageous in agricultural pest control. Each Cry protein has some level of target specificity; Cry6Aa has specific toxic action against coleopteran insects and nematodes. The corresponding B. thuringiensis gene, cry6aa, is located on bacterial plasmids. Along with several other Cry protein genes, cry6aa can be genetically recombined in Bt corn and Bt cotton so the plants produce specific toxins. Insects are developing resistance to the most commonly inserted proteins like Cry1Ac. Since Cry6Aa proteins function differently than other Cry proteins, they are combined with other proteins to decrease the development of pest resistance. Recent studies suggest this protein functions better in combination with other virulence factors such as other Cry proteins and metalloproteinases.>

References

  1. PDB: 1KTH ; Arnoux B, Ducruix A, Prangé T (July 2002). "Anisotropic behaviour of the C-terminal Kunitz-type domain of the alpha3 chain of human type VI collagen at atomic resolution (0.9 Å)". Acta Crystallogr. D. 58 (Pt 7): 1252–4. doi:10.1107/S0907444902007333. PMID   12077460.
  2. Nixon, AE; Wood, CR (2006). "Engineered protein inhibitors of proteases". Current Opinion in Drug Discovery & Development. 9 (2): 261–8. PMID   16566296.
  3. 1 2 Antuch W, Güntert P, Billeter M, Hawthorne T, Grossenbacher H, Wüthrich K (September 1994). "NMR solution structure of the recombinant tick anticoagulant protein (rTAP), a factor Xa inhibitor from the tick Ornithodoros moubata". FEBS Lett. 352 (2): 251–7. doi:10.1016/0014-5793(94)00941-4. PMID   7925983. S2CID   2280234.
  4. St Charles R, Padmanabhan K, Arni RV, Padmanabhan KP, Tulinsky A (February 2000). "Structure of tick anticoagulant peptide at 1.6 A resolution complexed with bovine pancreatic trypsin inhibitor". Protein Sci. 9 (2): 265–72. doi:10.1110/ps.9.2.265. PMC   2144540 . PMID   10716178.
  5. Rawlings ND, Barrett AJ, Tolle DP (2004). "Evolutionary families of peptidase inhibitors". Biochem. J. 378 (Pt 3): 705–16. doi:10.1042/BJ20031825. PMC   1224039 . PMID   14705960.
  6. Wlodawer A, Housset D, Kim KS, Fuchs J, Woodward C (1991). "Crystal structure of a Y35G mutant of bovine pancreatic trypsin inhibitor". J. Mol. Biol. 220 (3): 757–770. doi:10.1016/0022-2836(91)90115-M. PMID   1714504.
  7. Salier JP (1990). "Inter-alpha-trypsin inhibitor: emergence of a family within the Kunitz-type protease inhibitor superfamily". Trends Biochem. Sci. 15 (11): 435–439. doi:10.1016/0968-0004(90)90282-G. PMID   1703675.
  8. Takahashi K, Ikeo K, Gojobori T (1992). "Evolutionary origin of a Kunitz-type trypsin inhibitor domain inserted in the amyloid beta precursor protein of Alzheimer's disease". J. Mol. Evol. 34 (6): 536–543. doi:10.1007/BF00160466. PMID   1593645. S2CID   26698630.
  9. Sprecher CA, Foster DC, Kisiel W, Mathewes S (1994). "Molecular cloning, expression, and partial characterization of a second human tissue-factor-pathway inhibitor". Proc. Natl. Acad. Sci. U.S.A. 91 (8): 3353–3357. Bibcode:1994PNAS...91.3353S. doi: 10.1073/pnas.91.8.3353 . PMC   43575 . PMID   8159751.
  10. Biemann K, Papayannopoulos IA (1992). "Amino acid sequence of a protease inhibitor isolated from Sarcophaga bullata determined by mass spectrometry". Protein Sci. 1 (2): 278–288. doi:10.1002/pro.5560010210. PMC   2142190 . PMID   1304909.
  11. 1 2 Lehmann, A (2008). "Ecallantide (DX-88), a plasma kallikrein inhibitor for the treatment of hereditary angioedema and the prevention of blood loss in on-pump cardiothoracic surgery". Expert Opinion on Biological Therapy. 8 (8): 1187–99. doi:10.1517/14712598.8.8.1187. PMID   18613770. S2CID   72623604.
  12. Dyax Corp. (2009). "Full prescibing information Kalbitor" (PDF). Retrieved 2010-05-02.
  13. Clinical trial number NCT00455767 for "Safety and Efficacy Study of Depelestat in Acute Respiratory Distress Syndrome (ARDS) Patients" at ClinicalTrials.gov
  14. Attucci, S; Gauthier, A; Korkmaz, B; Delépine, P; Martino, MF; Saudubray, F; Diot, P; Gauthier, F (2006). "EPI-hNE4, a proteolysis-resistant inhibitor of human neutrophil elastase and potential anti-inflammatory drug for treating cystic fibrosis". The Journal of Pharmacology and Experimental Therapeutics. 318 (2): 803–9. doi:10.1124/jpet.106.103440. PMID   16627747. S2CID   1771342.
  15. Azarkan M, Martinez-Rodriguez S, Buts L, Baeyens-Volant D, Garcia-Pino A (Dec 2011). "The plasticity of the β-trefoil fold constitutes an evolutionary platform for protease inhibition". The Journal of Biological Chemistry. 286 (51): 43726–34. doi: 10.1074/jbc.M111.291310 . PMC   3243510 . PMID   22027836.
This article incorporates text from the public domain Pfam and InterPro: IPR002223