Cupin superfamily

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Cupin_1
PDB 1l3j EBI.jpg
crystal structure of oxalate decarboxylase formate complex
Identifiers
Symbol Cupin_1
Pfam PF00190
Pfam clan CL0029
InterPro IPR006045
SCOP 2phl
SUPERFAMILY 2phl
Cupin_2
PDB 1y3t EBI.jpg
crystal structure of yxag, a dioxygenase from Bacillus subtilis
Identifiers
Symbol Cupin_2
Pfam PF07883
Pfam clan CL0029
InterPro IPR013096
SCOP 1vj2
SUPERFAMILY 1vj2
Cupin_3
PDB 1rc6 EBI.jpg
crystal structure of protein ylba from E. coli, pfam duf861
Identifiers
Symbol Cupin_3
Pfam PF05899
Pfam clan CL0029
InterPro IPR008579
SCOP 1o5u
SUPERFAMILY 1o5u
Cupin_4
Identifiers
Symbol Cupin_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
Symbol Cupin_5
Pfam PF06172
Pfam clan CL0029
InterPro IPR009327
Cupin_6
Identifiers
Symbol Cupin_6
Pfam PF12852
Pfam clan CL0029
Cupin_7
Identifiers
Symbol Cupin_7
Pfam PF12973
Pfam clan CL0029

In molecular biology, the cupin superfamily of proteins is a diverse superfamily of proteins containing a conserved barrel domain, with cupa being the Latin term for a small barrel. The cupin protein superfamily includes a wide variety of enzymes, but notably contains the non-enzymatic seed storage proteins also.[1][2]

The cupin superfamily plays a role in allergy, specifically the 11 S globulins (found in legumins) and the 7S members (found in vicilins). These can be found as seed storage proteins and may be a component of normal human diet.

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.

S. sclerotiorum, better known as "white mold", is a fungal disease of many economically valuable crops such as (legumes) beans, soybeans, peanuts, etc., potato, lettuce, sunflower. 400 plant species are susceptible including stone fruits....[3][4]

T.B. 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 B. Mendel are considered the 'founders' of the modern science of nutrition.

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' ___ as 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; the word cooper is derived from Middle Dutch or Middle Low German kūper 'cooper' from kūpe 'cask', in turn from Latin cupa 'tun, 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.[5]"G-OXOs and GLPs are plant do-all proteins."[6]

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' 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. Ironically, seed storage proteins of grasses and cereals belong to the eponymous prolamin superfamily which also includes plant albumins(2S). Prolamin seed storage proteins 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. Interestingly, domesticated cereals most notably 'hexaploid' bread wheat ( pasta wheat 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.

The 'sweetest' outcome from our knowledge of germin biochemistry is that the wheat-germin gene is the obvious candidate for insertion into the American chestnut for producing a transgenic American chestnut. This tree called the "perfect tree" has no resistance to Cryphonectria parasitica, the chestnut blight fungus. [7] The fungal mycelium produce oxalic acid which eats away at the tree's bark giving it a portal into the underlying growing tissue. The xylem vessels carrying water become plugged through the chelation of calcium cations by oxalate just as in the kidney. Death is by strangulation as a canker encircles and girdles the trunk.

Transgenic American chestnut seedlings have been produced and field tested carrying the wheat germin gene for oxalate oxidase which breaks down oxalic acid the caustic chemical excreted by the invasive chestnut blight fungus.

Soybean Protein Nomenclature: Aprogress naldc.nal.usda.gov/download/31396/PDF 1. Effects of ionic strength on the ultracentrifuge pattern for water-extractable soybean proteins at pH 7.6. The terminology used most extensively in the past.

References[edit]

  1. ^ Dunwell JM (1998). "Cupins: a new superfamily of functionally diverse proteins that include germins and plant storage proteins". Biotechnol. Genet. Eng. Rev. 15: 1–32. PMID 9573603. 
  2. ^ Dunwell, J. M.; Purvis, A.; Khuri, S. (2004). "Cupins: The most functionally diverse protein superfamily?". Phytochemistry 65 (1): 7–17. doi:10.1016/j.phytochem.2003.08.016. PMID 14697267.  edit
  3. ^ http://www.broadinstitute.org/annotation/genome/sclerotinia_sclerotiorum/MultiHome.html
  4. ^ https://www.apsnet.org/edcenter/intropp/lessons/fungi/ascomycetes/Pages/WhiteMold.aspx
  5. ^ http://www.ingentaconnect.com/content/tandf/bpts/2008/00000027/00000005/art00002
  6. ^ http://www.sciencedirect.com/science/article/pii/S0981942801012852
  7. ^ http://www.susanfreinkel.com/books_American_Chestnut.html

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