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46  structures 2502  species 0  interactions 3912  sequences 57  architectures

Family: JmjC_2 (PF08007)

Summary: JmjC 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
SymbolCupin_1
PfamPF00190
Pfam clanCL0029
InterProIPR006045
SCOP22phl / SCOPe / SUPFAM
Cupin_2
PDB 1y3t EBI.jpg
crystal structure of yxag, a dioxygenase from Bacillus subtilis
Identifiers
SymbolCupin_2
PfamPF07883
Pfam clanCL0029
InterProIPR013096
SCOP21vj2 / SCOPe / SUPFAM
Cupin_3
PDB 1rc6 EBI.jpg
crystal structure of protein ylba from E. coli, pfam duf861
Identifiers
SymbolCupin_3
PfamPF05899
Pfam clanCL0029
InterProIPR008579
SCOP21o5u / SCOPe / SUPFAM
Cupin_4
Identifiers
SymbolCupin_4
PfamPF08007
Pfam clanCL0029
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
PfamPF06172
Pfam clanCL0029
InterProIPR009327
Cupin_6
Identifiers
SymbolCupin_6
PfamPF12852
Pfam clanCL0029
Cupin_7
Identifiers
SymbolCupin_7
PfamPF12973
Pfam clanCL0029

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]

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.

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

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.

JmjC domain Provide feedback

This entry includes proteins with a JmjC domain that belong to the cupin superfamily, including Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66 [1] Ribosomal oxygenase 1/2 [2,3], and 50S ribosomal protein L16 3-hydroxylase from Escherichia coli [4,5]. Proteins are bifunctional, acting as histone lysine demethylases and ribosomal histidine hydroxylases.

Literature references

  1. Kirienko NV, Fay DS;, EMBO J. 2010;29:727-739.: SLR-2 and JMJC-1 regulate an evolutionarily conserved stress-response network. PUBMED:20057358 EPMC:20057358

  2. Ge W, Wolf A, Feng T, Ho CH, Sekirnik R, Zayer A, Granatino N, Cockman ME, Loenarz C, Loik ND, Hardy AP, Claridge TDW, Hamed RB, Chowdhury R, Gong L, Robinson CV, Trudgian DC, Jiang M, Mackeen MM, Mccullagh JS, Gordiyenko Y, Thalhammer A, Yamamoto A, Yang M, Liu-Yi P, Zhang Z, Schmidt-Zachmann M, Kessler BM, Ratcliffe PJ, Preston GM, Coleman ML, Schofield CJ;, Nat Chem Biol. 2012;8:960-962.: Oxygenase-catalyzed ribosome hydroxylation occurs in prokaryotes and humans. PUBMED:23103944 EPMC:23103944

  3. Lu Y, Chang Q, Zhang Y, Beezhold K, Rojanasakul Y, Zhao H, Castranova V, Shi X, Chen F;, Cell Cycle. 2009;8:2101-2109.: Lung cancer-associated JmjC domain protein mdig suppresses formation of tri-methyl lysine 9 of histone H3. PUBMED:19502796 EPMC:19502796

  4. van Staalduinen LM, Novakowski SK, Jia Z;, J Mol Biol. 2014;426:1898-1910.: Structure and functional analysis of YcfD, a novel 2-oxoglutarate/Fe(2)(+)-dependent oxygenase involved in translational regulation in Escherichia coli. PUBMED:24530688 EPMC:24530688

  5. Chowdhury R, Sekirnik R, Brissett NC, Krojer T, Ho CH, Ng SS, Clifton IJ, Ge W, Kershaw NJ, Fox GC, Muniz JRC, Vollmar M, Phillips C, Pilka ES, Kavanagh KL, von Delft F, Oppermann U, McDonough MA, Doherty AJ, Schofield CJ;, Nature. 2014;510:422-426.: Ribosomal oxygenases are structurally conserved from prokaryotes to humans. PUBMED:24814345 EPMC:24814345


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003347

The JmjN and JmjC domains are two non-adjacent domains which have been identified in the jumonji family of transcription factors. Although it was originally suggested that the JmjN and JmjC domains always co-occur and might form a single functional unit within the folded protein, the JmjC domain was later found without the JmjN domain in organisms from bacteria to human [ PUBMED:10838566 , PUBMED:11165500 ].

Proteins containing JmjC domain are predicted to be metalloenzymes that adopt the cupin fold and are candidates for enzymes that regulate chromatin remodelling [ PUBMED:11165500 ]. The cupin fold is a flattened beta-barrel structure containing two sheets of five antiparallel beta strands that form the walls of a zinc-binding cleft. Based on the crystal structure of JmjC domain containing protein FIH and JHDM3A/JMJD2A, the JmjC domain forms an enzymatically active pocket that coordinates Fe(III) and alphaKG. Three amino-acid residues within the JmjC domain bind to the Fe(II) cofactor and two additional residues bind to alphaKG [ PUBMED:16983801 ].

JmjC domains were identified in numerous eukaryotic proteins containing domains typical of transcription factors, such as PHD, C2H2, ARID/BRIGHT and zinc fingers [ PUBMED:11165500 , PUBMED:12446723 ]. The JmjC has been shown to function in a histone demethylation mechanism that is conserved from yeast to human [ PUBMED:16362057 ]. JmjC domain proteins may be protein hydroxylases that catalyse a novel histone modification [ PUBMED:15809658 ]. The human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation [ PUBMED:20739293 ].

Domain organisation

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

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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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(26)
Full
(3912)
Representative proteomes UniProt
(16214)
RP15
(674)
RP35
(1753)
RP55
(3787)
RP75
(6479)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(26)
Full
(3912)
Representative proteomes UniProt
(16214)
RP15
(674)
RP35
(1753)
RP55
(3787)
RP75
(6479)
Alignment:
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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
(26)
Full
(3912)
Representative proteomes UniProt
(16214)
RP15
(674)
RP35
(1753)
RP55
(3787)
RP75
(6479)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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_5011 (release 16.0)
Previous IDs: DUF1701; Cupin_4;
Type: Domain
Sequence Ontology: SO:0000417
Author: Mistry J , Bateman A
Number in seed: 26
Number in full: 3912
Average length of the domain: 121.40 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 26.59 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.0 22.0
Trusted cut-off 22.0 22.0
Noise cut-off 21.9 21.9
Model length: 127
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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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 JmjC_2 domain has been found. There are 46 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0R0GUF9 View 3D Structure Click here
A0A1D6JGF3 View 3D Structure Click here
A3KP59 View 3D Structure Click here
A4I6B6 View 3D Structure Click here
A5PK74 View 3D Structure Click here
A8XEA2 View 3D Structure Click here
B0WMG3 View 3D Structure Click here
B3MSI4 View 3D Structure Click here
B4GUZ2 View 3D Structure Click here
B4I100 View 3D Structure Click here
B4JMQ2 View 3D Structure Click here
B4L6Q5 View 3D Structure Click here
B4M7P8 View 3D Structure Click here
B4NP88 View 3D Structure Click here
B4R4H1 View 3D Structure Click here
B5DUH6 View 3D Structure Click here
C3XRY1 View 3D Structure Click here
D3ZU57 View 3D Structure Click here
F1R7K2 View 3D Structure Click here
K7MK34 View 3D Structure Click here
O01658 View 3D Structure Click here
P27431 View 3D Structure Click here
P44683 View 3D Structure Click here
P46327 View 3D Structure Click here
Q16W06 View 3D Structure Click here
Q4D641 View 3D Structure Click here
Q54K96 View 3D Structure Click here
Q5EA24 View 3D Structure Click here
Q5R673 View 3D Structure Click here
Q5ZMM1 View 3D Structure Click here
Q7K4H4 View 3D Structure Click here
Q8CD15 View 3D Structure Click here
Q8CFC1 View 3D Structure Click here
Q8IUF8 View 3D Structure Click here
Q9H6W3 View 3D Structure Click here
Q9JJF3 View 3D Structure Click here