Cupin superfamily

Last updated
Cupin_1
PDB 1l3j EBI.jpg
crystal structure of oxalate decarboxylase formate complex
Identifiers
SymbolCupin_1
Pfam PF00190
Pfam clan CL0029
InterPro IPR006045
SCOP2 2phl / SCOPe / SUPFAM
Cupin_2
PDB 1y3t EBI.jpg
crystal structure of yxag, a dioxygenase from Bacillus subtilis
Identifiers
SymbolCupin_2
Pfam PF07883
Pfam clan CL0029
InterPro IPR013096
SCOP2 1vj2 / SCOPe / SUPFAM
Cupin_3
PDB 1rc6 EBI.jpg
crystal structure of protein ylba from E. coli , pfam duf861
Identifiers
SymbolCupin_3
Pfam PF05899
Pfam clan CL0029
InterPro IPR008579
SCOP2 1o5u / SCOPe / SUPFAM
Cupin_4
Identifiers
SymbolCupin_4
Pfam PF08007
Pfam clan CL0029
Cupin_5
PDB 1yud EBI.jpg
x-ray crystal structure of protein so0799 from Shewanella oneidensis . northeast structural genomics consortium target sor12.
Identifiers
SymbolCupin_5
Pfam PF06172
Pfam clan CL0029
InterPro IPR009327
Cupin_6
Identifiers
SymbolCupin_6
Pfam PF12852
Pfam clan CL0029
Cupin_7
Identifiers
SymbolCupin_7
Pfam PF12973
Pfam clan CL0029

The cupin superfamily is a diverse superfamily of proteins named after its conserved barrel domain (cupa being the Latin term for a small barrel). The superfamily includes a wide variety of enzymes as well as non-enzymatic seed storage proteins. [1] [2]

Contents

Members of the superfamily play a role in allergy, especially seed storage proteins like 7S and 11S globulins, also known as vicilins and legumins, respectively. These proteins can be found at high concentrations in seeds of both mono- and dicotyledonous plants and are an important component of the normal human diet.

History

Thomas Burr Osborne at the end of the 19th century was the first person to systematically study seed storage proteins by their solubility characteristics. He established 4 classes of proteins: water-soluble albumins; salt soluble globulins: vicilin—typically having sedimentation coefficients, S values (a measure of the protein mass determined by sedimentation equilibrium ultracentrifugation) of about 7 Svedberg units (hence the common name 7S globulin) and legumin (11S); alcohol/water-soluble—cereal—prolamines; and a fourth class, glutelins, of difficultly soluble proteins no longer recognized and now considered low solubility prolamin or globulin storage proteins . Gluten consists of a mixture of prolamins: 'glutenin' and 'gliadin'. Osborne and his Yale colleague Lafayette Mendel are considered the 'founders' of the modern science of nutrition.

Earlier, the fungus Sclerotinia sclerotiorum (Lib.) deBary was the first oxalic acid (oxalate), secreting organism to be described as early as 1886 in Botan. Z. by A. de Barry. However, since oxalate secreting fungi are not a major threat to crop cereals no studies of this interaction were made for almost 100 years. In the early 1980s a protein dubbed 'germin' was identified in germinating wheat embryos; and in the early 1990s (1992) it was found to be an enzyme having oxalate oxidase (OXO) activity converting an oxalate substrate into carbon dioxide and hydrogen peroxide. This latter-day discovery of 'germin' was soon followed by the discovery of the 'cupin superfamily' of proteins.

Classification

Legumin and vicilin share a common evolutionary ancestor, namely, a vicilin-like protein in a fern-spore which also exhibits some characteristics of legumin. Each of these proteins contains equivalent 'subunits' indicating an evolution from a single-gene ancestor which has been duplicated during evolution. It was suggested that "germin", {first found and only known to occur in the "true cereals": barley, corn, oat, rice, and wheat} a plant enzyme, oxalate oxidase 'one-very-tough-little- protein' was such an ancestor. This hypothesis stimulated a search for the evolutionary roots of the seed storage globulins which include such food proteins as the legume soy protein—the gold standard for plant-based proteins—due to its balanced content of 7S and 11S globulin protein, other beans, the pseudocereals buckwheat, & quinoa, pumpkin seeds, cocoa, coffee, nuts, and the two cereals oats and rice.

This search turned up a new realm: that seed storage globulin proteins (7S & 11S), as well as many other non-storage plant proteins {notably germins (G-OXOs), germin-like proteins (GLPs)} and microbial proteins belong to a vast superfamily of proteins dubbed the 'cupin superfamily' of proteins, named on the basis of a conserved beta-barrel fold (cupa the Latin term for a small barrel) originally discovered within germin and germin-like proteins from higher plants. Germin is a monocupin and 7S & 11S are each bicupins. It is a large and functionally immensely diverse 'superfamily' of proteins, numbering in the thousands, that have a common origin and whose evolution can be followed from bacteria to eukaryotes including animals and higher plants. "Cupins" are the most functionally diverse protein superfamily occurring in all spermatophytes (seed-bearing plants). " GLPs, moreover, are now known to be ubiquitous plant proteins, no longer linked only to cereal germination, but involved in plant responses to biotic and abiotic stress. [3] "G-OXOs and GLPs are plant do-all proteins". [4]

Germin of the "true cereals" is known as the 'archetypal' member of the cupin superfamily, however, it is not to be considered an empty cask or barrel but a 'jellyroll' jelly roll fold in which six monomer subunits are wrapped in three dimensions to form a barrel shape. This structure accounts for its astonishing 'refractory' nature toward various 'denaturing' agents: all germins share a remarkable stability when subjected to heat, detergents, extreme pH and resistance to broad specificity proteolytic (digestive) enzymes. Seed storage proteins of grasses and cereals belong to the eponymous prolamin superfamily which also includes plant albumins(2S). Prolamin seed storage protein so characteristic of cereals and grasses is not considered very nutritious because of its high content of the amino acid proline which it shares with gelatin and its low content of lysine, a vital amino acid.

Germin was initially identified in the early stages of wheat seed germination, thus its name. Domesticated cereals most notably 'hexaploid' bread wheat ('durum' wheat, which is used to make pasta and semolina is tetraploid) was selected by humans for its resistance to fungal pathogens. Many years later it was found to have oxalate oxidase activity generating 'antimicrobial' hydrogen peroxide from a substrate of the double-acid, oxalic acid, secreted by an invading fungus or other microbe. A reaction between oxalate and the calcium cation makes calcium oxalate, a type of 'kidney stone' in humans. Amazingly, oxalate is a metabolite of ascorbate (vitamin C), and it is worth emphasizing that ascorbate is a direct precursor of oxalate in plants.

Related Research Articles

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Sprouting is the natural process by which seeds or spores germinate and put out shoots, and already established plants produce new leaves or buds or other newly developing parts experience further growth.

The globulins are a family of globular proteins that have higher molecular weights than albumins and are insoluble in pure water but dissolve in dilute salt solutions. Some globulins are produced in the liver, while others are made by the immune system. Globulins, albumins, and fibrinogen are the major blood proteins. The normal concentration of globulins in human blood is about 2.6-3.5 g/dL.

Lipoxygenase

Lipoxygenases are a family of (non-heme) iron-containing enzymes most of which catalyze the dioxygenation of polyunsaturated fatty acids in lipids containing a cis,cis-1,4- pentadiene into cell signaling agents that serve diverse roles as autocrine signals that regulate the function of their parent cells, paracrine signals that regulate the function of nearby cells, and endocrine signals that regulate the function of distant cells.

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Nitrate reductase

Nitrate reductases are molybdoenzymes that reduce nitrate to nitrite. This reaction is critical for the production of protein in most crop plants, as nitrate is the predominant source of nitrogen in fertilized soils.

Prolamins are a group of plant storage proteins having a high proline amino acid content. They are found in plants, mainly in the seeds of cereal grains such as wheat (gliadin), barley (hordein), rye (secalin), corn (zein), sorghum (kafirin), and oats (avenin). They are characterised by a high glutamine and proline content, and have poor solubility in water. They solubilise best in strong alcohol [70-80%], light acid, and alkaline solutions. The prolamins of the tribe Triticeae, such as wheat gliadin, and related proteins are known to trigger coeliac disease, an autoimmune condition, in genetically predisposed individuals.

Wheat allergy Medical condition

Wheat allergy is an allergy to wheat which typically presents itself as a food allergy, but can also be a contact allergy resulting from occupational exposure. Like all allergies, wheat allergy involves immunoglobulin E and mast cell response. Typically the allergy is limited to the seed storage proteins of wheat. Some reactions are restricted to wheat proteins, while others can react across many varieties of seeds and other plant tissues. Wheat allergy is rare. Prevalence in adults was found to be 0.21% in a 2012 study in Japan.

Soy protein

Soy protein is a protein that is isolated from soybean. It is made from soybean meal that has been dehulled and defatted. Dehulled and defatted soybeans are processed into three kinds of high protein commercial products: soy flour, concentrates, and isolates. Soy protein isolate has been used since 1959 in foods for its functional properties.

Triticeae glutens Seed storage protein in mature wheat seeds

Gluten is the seed storage protein in mature wheat seeds. It is the sticky substance in bread wheat which allows dough to rise and retain its shape during baking. The same, or very similar, proteins are also found in related grasses within the tribe Triticeae. Seed glutens of some non-Triticeae plants have similar properties, but none can perform on a par with those of the Triticeae taxa, particularly the Triticum species. What distinguishes bread wheat from these other grass seeds is the quantity of these proteins and the level of subcomponents, with bread wheat having the highest protein content and a complex mixture of proteins derived from three grass species.

Glutelins are a class of propain prolamin proteins found in the endosperm of certain seeds of the grass family. They constitute a major component of the protein composite collectively referred to as gluten. Glutenin is the most common glutelin, as it is found in wheat and is responsible for some of the refined baking properties in bread wheat. The glutelins of barley and rye have also been identified. Glutelins are the primary form of energy storage in the endosperm of rice grains.

Storage proteins serve as biological reserves of metal ions and amino acids, used by organisms. They are found in plant seeds, egg whites, and milk.

Kelch motif

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In molecular biology, the BURP domain is a ~230-amino acid protein domain, which has been named for the four members of the group initially identified, BNM2, USP, RD22, and PG1beta. It is found in the C-terminal part of a number of plant cell wall proteins, which are defined not only by the BURP domain, but also by the overall similarity in their modular construction. The BURP domain proteins consists of either three or four modules: (i) an N-terminal hydrophobic domain - a presumptive transit peptide, joined to (ii) a short conserved segment or other short segment, (iii) an optional segment consisting of repeated units which is unique to each member, and (iv) the C-terminal BURP domain. Although the BURP domain proteins share primary structural features, their expression patterns and the conditions under which they are expressed differ. The presence of the conserved BURP domain in diverse plant proteins suggests an important role for this domain. It is possible that the BURP domain represents a general motif for localization of proteins within the cell wall matrix. The other structural domains associated with the BURP domain may specify other target sites for intermolecular interactions.

Multicopper oxidase Class of enzymes

In molecular biology, multicopper oxidases are enzymes which oxidise their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre; dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water. There are three spectroscopically different copper centres found in multicopper oxidases: type 1, type 2 and type 3. Multicopper oxidases consist of 2, 3 or 6 of these homologous domains, which also share homology with the cupredoxins azurin and plastocyanin. Structurally, these domains consist of a cupredoxin-like fold, a beta-sandwich consisting of 7 strands in 2 beta-sheets, arranged in a Greek-key beta-barrel. Multicopper oxidases include:

Glucose-methanol-choline oxidoreductase family

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HD domain

In molecular biology, the HD domain is a conserved protein domain, named after the conserved histidine (H) and/or aspartate (D) amino acid residues. It is found in a superfamily of enzymes with a predicted or known phosphohydrolase activity. These enzymes appear to be involved in nucleic acid metabolism, signal transduction and possibly other functions in bacteria, archaea and eukaryotes. The fact that all the highly conserved residues in the HD superfamily are histidines or aspartates suggests that coordination of divalent cations is essential for the activity of these proteins.

Pea protein

Pea protein is a type of food. It is a source of protein derived and extracted in powder form from the yellow and green split peas, Pisum sativum, classified in the legume food group. It can be used as a supplement to increase an individual's protein or other nutrient intake, or as a substitute for other food products. It is also used as a functional ingredient in food-manufacturing, such as a thickener, foaming agent, or an emulsifier.

YjeF N terminal protein domain

In molecular biology, the YjeF N terminal is a protein domain found in the N-terminal of the protein, EDC3. The YjeF N-terminal domains occur either as single proteins or fusions with other domains and are commonly associated with enzymes. They help assemble the processing body (P-body) in preparation for mRNAdecay. Structural homology indicated it may have some similarity to the enzyme family, hydrolase.

References

  1. Dunwell JM (1998). "Cupins: a new superfamily of functionally diverse proteins that include germins and plant storage proteins". Biotechnology & Genetic Engineering Reviews. 15: 1–32. doi: 10.1080/02648725.1998.10647950 . PMID   9573603.
  2. Dunwell JM, Purvis A, Khuri S (January 2004). "Cupins: the most functionally diverse protein superfamily?". Phytochemistry. 65 (1): 7–17. doi:10.1016/j.phytochem.2003.08.016. PMID   14697267.
  3. Dunwell J, Gibbings JG, Mahmood T, Saqlan Naqvi S (2008-09-01). "Germin and Germin-like Proteins: Evolution, Structure, and Function" (PDF). Critical Reviews in Plant Sciences. 27 (5): 342–375. doi:10.1080/07352680802333938. S2CID   83885115.
  4. Bernier, François; Berna, Anne (July 2001). "Germins and germin-like proteins: Plant do-all proteins. But what do they do exactly?". Plant Physiology and Biochemistry. 39 (7–8): 545–554. doi:10.1016/S0981-9428(01)01285-2.
This article incorporates text from the public domain Pfam and InterPro: IPR013096
This article incorporates text from the public domain Pfam and InterPro: IPR006045
This article incorporates text from the public domain Pfam and InterPro: IPR009327
This article incorporates text from the public domain Pfam and InterPro: IPR008579