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0  structures 215  species 0  interactions 3446  sequences 69  architectures

Family: EDR2_C (PF07059)

Summary: Protein ENHANCED DISEASE RESISTANCE 2, C-terminal

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 "Domain of unknown function". More...

Domain of unknown function Edit Wikipedia article

A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.[1]

The DUF designation is tentative, and such families tend to be renamed to a more specific name (or merged to an existing domain) after a function is identified.[2][3]

History

The DUF naming scheme was introduced by Chris Ponting, through the addition of DUF1 and DUF2 to the SMART database.[4] These two domains were found to be widely distributed in bacterial signaling proteins. Subsequently, the functions of these domains were identified and they have since been renamed as the GGDEF domain and EAL domain respectively.[2]

Characterisation

Structural genomics programmes have attempted to understand the function of DUFs through structure determination. The structures of over 250 DUF families have been solved. This (2009) work showed that about two thirds of DUF families had a structure similar to a previously solved one and therefore likely to be divergent members of existing protein superfamilies, whereas about one third possessed a novel protein fold.[5]

Some DUF families share remote sequence homology with domains that has characterized function. Computational work can be used to link these relationships. An 2015 work was able to assign 20% of the DUFs to characterized structual superfamilies.[6] Pfam also continuously perform the (manually-verified) assignment in "clan" superfamily entries.[1]

Frequency and conservation

Protein domains and DUFs in different domains of life. Left: Annotated domains. Right: domains of unknown function. Not all overlaps shown.[7]

More than 20% of all protein domains were annotated as DUFs in 2013. About 2,700 DUFs are found in bacteria compared with just over 1,500 in eukaryotes. Over 800 DUFs are shared between bacteria and eukaryotes, and about 300 of these are also present in archaea. A total of 2,786 bacterial Pfam domains even occur in animals, including 320 DUFs.[7]

Role in biology

Many DUFs are highly conserved, indicating an important role in biology. However, many such DUFs are not essential, hence their biological role often remains unknown. For instance, DUF143 is present in most bacteria and eukaryotic genomes.[8] However, when it was deleted in Escherichia coli no obvious phenotype was detected. Later it was shown that the proteins that contain DUF143, are ribosomal silencing factors that block the assembly of the two ribosomal subunits.[8] While this function is not essential, it helps the cells to adapt to low nutrient conditions by shutting down protein biosynthesis. As a result, these proteins and the DUF only become relevant when the cells starve.[8] It is thus believed that many DUFs (or proteins of unknown function, PUFs) are only required under certain conditions.

Essential DUFs

Goodacre et al. identified 238 DUFs in 355 essential proteins (in 16 model bacterial species), most of which represent single-domain proteins, clearly establishing the biological essentiality of DUFs. These DUFs are called "essential DUFs" or eDUFs.[7]

External links

References

  1. ^ a b El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A, Sonnhammer EL, Hirsh L, Paladin L, Piovesan D, Tosatto SC, Finn RD (January 2019). "The Pfam protein families database in 2019". Nucleic Acids Research. 47 (D1): D427–D432. doi:10.1093/nar/gky995. PMC 6324024. PMID 30357350.
  2. ^ a b Bateman A, Coggill P, Finn RD (October 2010). "DUFs: families in search of function". Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 66 (Pt 10): 1148–52. doi:10.1107/S1744309110001685. PMC 2954198. PMID 20944204.
  3. ^ Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD (January 2012). "The Pfam protein families database". Nucleic Acids Research. 40 (Database issue): D290–301. doi:10.1093/nar/gkr1065. PMC 3245129. PMID 22127870.
  4. ^ Schultz J, Milpetz F, Bork P, Ponting CP (May 1998). "SMART, a simple modular architecture research tool: identification of signaling domains". Proceedings of the National Academy of Sciences of the United States of America. 95 (11): 5857–64. Bibcode:1998PNAS...95.5857S. doi:10.1073/pnas.95.11.5857. PMC 34487. PMID 9600884.
  5. ^ Jaroszewski L, Li Z, Krishna SS, Bakolitsa C, Wooley J, Deacon AM, Wilson IA, Godzik A (September 2009). "Exploration of uncharted regions of the protein universe". PLoS Biology. 7 (9): e1000205. doi:10.1371/journal.pbio.1000205. PMC 2744874. PMID 19787035.
  6. ^ Mudgal R, Sandhya S, Chandra N, Srinivasan N (July 2015). "De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods". Biology Direct. 10 (1): 38. doi:10.1186/s13062-015-0069-2. PMC 4520260. PMID 26228684.
  7. ^ a b c Goodacre NF, Gerloff DL, Uetz P (December 2013). "Protein domains of unknown function are essential in bacteria". mBio. 5 (1): e00744–13. doi:10.1128/mBio.00744-13. PMC 3884060. PMID 24381303.
  8. ^ a b c Häuser R, Pech M, Kijek J, Yamamoto H, Titz B, Naeve F, Tovchigrechko A, Yamamoto K, Szaflarski W, Takeuchi N, Stellberger T, Diefenbacher ME, Nierhaus KH, Uetz P (2012). Hughes D (ed.). "RsfA (YbeB) proteins are conserved ribosomal silencing factors". PLoS Genetics. 8 (7): e1002815. doi:10.1371/journal.pgen.1002815. PMC 3400551. PMID 22829778.

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.

Protein ENHANCED DISEASE RESISTANCE 2, C-terminal Provide feedback

This family represents the C-terminus (approximately 250 residues) of protein ENHANCED DISEASE RESISTANCE 2 (EDR2) from plants. EDR2 is a negative regulator of the salicylic acid (SA)-mediated resistance to pathogens, including the biotrophic powdery mildew pathogens Golovinomyces cichoracearum and Blumeria graminis, and the downy mildew pathogen Hyaloperonospora parasitica, probably by limiting the initiation of cell death and the establishment of the hypersensitive response (HR) [1,2].

Literature references

  1. Tang D, Ade J, Frye CA, Innes RW;, Plant J. 2005;44:245-257.: Regulation of plant defense responses in Arabidopsis by EDR2, a PH and START domain-containing protein. PUBMED:16212604 EPMC:16212604

  2. Vorwerk S, Schiff C, Santamaria M, Koh S, Nishimura M, Vogel J, Somerville C, Somerville S;, BMC Plant Biol. 2007;7:35.: EDR2 negatively regulates salicylic acid-based defenses and cell death during powdery mildew infections of Arabidopsis thaliana. PUBMED:17612410 EPMC:17612410


This tab holds annotation information from the InterPro database.

InterPro entry IPR009769

This entry represents the C terminus of protein ENHANCED DISEASE RESISTANCE 2 (EDR2) from plants. EDR2 is a negative regulator of the salicylic acid- (SA-) mediated resistance to pathogens, including the biotrophic powdery mildew pathogens Golovinomyces cichoracearum and Blumeria graminis, and the downy mildew pathogen Hyaloperonospora parasitica, probably by limiting the initiation of cell death and the establishment of the hypersensitive response (HR) [ PUBMED:16212604 , PUBMED:17612410 ].

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...

View options

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
(84)
Full
(3446)
Representative proteomes UniProt
(7241)
RP15
(493)
RP35
(1869)
RP55
(2881)
RP75
(3773)
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PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(84)
Full
(3446)
Representative proteomes UniProt
(7241)
RP15
(493)
RP35
(1869)
RP55
(2881)
RP75
(3773)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

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
(84)
Full
(3446)
Representative proteomes UniProt
(7241)
RP15
(493)
RP35
(1869)
RP55
(2881)
RP75
(3773)
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_10173 (release 10.0)
Previous IDs: DUF1336;
Type: Domain
Sequence Ontology: SO:0000417
Author: Vella Briffa B
Number in seed: 84
Number in full: 3446
Average length of the domain: 201.40 aa
Average identity of full alignment: 34 %
Average coverage of the sequence by the domain: 37.67 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.7 24.7
Trusted cut-off 24.7 24.7
Noise cut-off 24.6 24.6
Model length: 213
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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
A0A096QUG1 View 3D Structure Click here
A0A096U797 View 3D Structure Click here
A0A0P0W3J5 View 3D Structure Click here
A0A0P0XIE5 View 3D Structure Click here
A0A0R0EZK7 View 3D Structure Click here
A0A0R0FQE3 View 3D Structure Click here
A0A0R0FYK8 View 3D Structure Click here
A0A0R0G4B3 View 3D Structure Click here
A0A0R0GBN2 View 3D Structure Click here
A0A0R0GJB2 View 3D Structure Click here
A0A0R0GY68 View 3D Structure Click here
A0A0R0HGB8 View 3D Structure Click here
A0A0R0J2M0 View 3D Structure Click here
A0A0R0KCH5 View 3D Structure Click here
A0A0R0LJE6 View 3D Structure Click here
A0A1D6F3P8 View 3D Structure Click here
A0A1D6FIT3 View 3D Structure Click here
A0A1D6GGP8 View 3D Structure Click here
A0A1D6GK73 View 3D Structure Click here
A0A1D6GK75 View 3D Structure Click here
A0A1D6GTG0 View 3D Structure Click here
A0A1D6GUT4 View 3D Structure Click here
A0A1D6GXW9 View 3D Structure Click here
A0A1D6H6Q6 View 3D Structure Click here
A0A1D6HZI8 View 3D Structure Click here
A0A1D6K613 View 3D Structure Click here
A0A1D6KNW2 View 3D Structure Click here
A0A1D6KSV2 View 3D Structure Click here
A0A1D6L074 View 3D Structure Click here
A0A1D6L5G2 View 3D Structure Click here
A0A1D6LNR8 View 3D Structure Click here
A0A1D6LTR4 View 3D Structure Click here
A0A1D6Q422 View 3D Structure Click here
A0A1D6QV93 View 3D Structure Click here
A0A1Q0XNL8 View 3D Structure Click here
B7F9A7 View 3D Structure Click here
B9DGX7 View 3D Structure Click here
C4IYK7 View 3D Structure Click here
F4IBY8 View 3D Structure Click here
F4IHT0 View 3D Structure Click here
F4JSE7 View 3D Structure Click here
F4JYC1 View 3D Structure Click here
F4KIL6 View 3D Structure Click here
F4KIL6 View 3D Structure Click here
I1J5H8 View 3D Structure Click here
I1K8K9 View 3D Structure Click here
I1LD05 View 3D Structure Click here
I1LTK2 View 3D Structure Click here
I1LZM9 View 3D Structure Click here
I1MTY2 View 3D Structure Click here
I1N607 View 3D Structure Click here
K7K1Y8 View 3D Structure Click here
K7K621 View 3D Structure Click here
K7K7Q4 View 3D Structure Click here
K7L3C8 View 3D Structure Click here
K7L8J0 View 3D Structure Click here
K7LF69 View 3D Structure Click here
K7LT55 View 3D Structure Click here
K7M363 View 3D Structure Click here
K7MCN9 View 3D Structure Click here
K7MHJ6 View 3D Structure Click here
K7N114 View 3D Structure Click here
K7N2J8 View 3D Structure Click here
Q0D9U3 View 3D Structure Click here
Q0IWY0 View 3D Structure Click here
Q2QN63 View 3D Structure Click here
Q3E7D9 View 3D Structure Click here
Q6YU77 View 3D Structure Click here
Q6Z9J1 View 3D Structure Click here
Q7EYH4 View 3D Structure Click here
Q8LPT2 View 3D Structure Click here
Q8VZF6 View 3D Structure Click here
Q94AK1 View 3D Structure Click here
Q9LEW4 View 3D Structure Click here
Q9LI95 View 3D Structure Click here
Q9SLT5 View 3D Structure Click here
Q9ZR99 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;