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229  structures 4001  species 3  interactions 20335  sequences 127  architectures

Family: Cupin_2 (PF07883)

Summary: Cupin domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Cupin superfamily". More...

Cupin superfamily Edit Wikipedia article

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

  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

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Cupin domain Provide feedback

This family represents the conserved barrel domain of the 'cupin' superfamily [1] ('cupa' is the Latin term for a small barrel).

Literature references

  1. Dunwell JM; , Biotechnol Genet Eng Rev 1998;15:1-32.: Cupins: a new superfamily of functionally diverse proteins that include germins and plant storage proteins. PUBMED:9573603 EPMC:9573603


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013096

This family represents the conserved barrel domain of the cupin superfamily [PUBMED:9573603] (cupa is the Latin term for a small barrel).

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Cupin (CL0029), which has the following description:

This clan represents the conserved barrel domain of the 'cupin' superfamily [1] ('cupa' is the Latin term for a small barrel). The cupin fold is found in a wide variety of enzymes, but notably contains the non-enzymatic seed storage proteins also.

The clan contains the following 53 members:

2OG-Fe_Oxy_2 2OG-FeII_Oxy 2OG-FeII_Oxy_2 2OG-FeII_Oxy_3 2OG-FeII_Oxy_4 2OG-FeII_Oxy_5 3-HAO AraC_binding AraC_binding_2 AraC_N ARD Asp_Arg_Hydrox Auxin_BP CDO_I CENP-C_C CsiD Cupin_1 Cupin_2 Cupin_3 Cupin_4 Cupin_5 Cupin_6 Cupin_7 Cupin_8 dTDP_sugar_isom DUF1255 DUF1479 DUF1498 DUF1637 DUF1971 DUF386 DUF4437 Ectoine_synth EutQ FdtA FTO_NTD GPI HgmA HutD JmjC KduI MannoseP_isomer Ofd1_CTDD Oxygenase-NA PhyH Pirin Pirin_C PMI_typeI Pox_C4_C10 TauD Tet_JBP VIT VIT_2

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(156)
Full
(20335)
Representative proteomes NCBI
(26569)
Meta
(7119)
RP15
(1857)
RP35
(3867)
RP55
(5218)
RP75
(6298)
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Format an alignment

  Seed
(156)
Full
(20335)
Representative proteomes NCBI
(26569)
Meta
(7119)
RP15
(1857)
RP35
(3867)
RP55
(5218)
RP75
(6298)
Alignment:
Format:
Order:
Sequence:
Gaps:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(156)
Full
(20335)
Representative proteomes NCBI
(26569)
Meta
(7119)
RP15
(1857)
RP35
(3867)
RP55
(5218)
RP75
(6298)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_81 (release 15.0)
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 156
Number in full: 20335
Average length of the domain: 70.00 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 38.76 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.5 21.6
Trusted cut-off 21.5 21.6
Noise cut-off 21.4 21.5
Model length: 71
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 3 interactions for this family. More...

Cupin_2 HTH_3 Cupin_3

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Cupin_2 domain has been found. There are 229 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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