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0  structures 1609  species 0  interactions 6508  sequences 205  architectures

Family: Glyco_transf_61 (PF04577)

Summary: Glycosyltransferase 61

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.

Glycosyltransferase 61 Provide feedback

This family represents the Glycosyltransferase Family 61. Members in this family are further processed into a mature form. It includes O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2 (POMGnT2, also known as AGO61 or EOGLT) [1] and EGF domain-specific O-linked N-acetylglucosamine transferase (EOGT) [2]. This family also includes plant beta-1,2-xylosyltransferases [3].

Literature references

  1. Yoshida-Moriguchi T, Willer T, Anderson ME, Venzke D, Whyte T, Muntoni F, Lee H, Nelson SF, Yu L, Campbell KP;, Science. 2013;341:896-899.: SGK196 is a glycosylation-specific O-mannose kinase required for dystroglycan function. PUBMED:23929950 EPMC:23929950

  2. Muller R, Jenny A, Stanley P;, PLoS One. 2013;8:e62835.: The EGF repeat-specific O-GlcNAc-transferase Eogt interacts with notch signaling and pyrimidine metabolism pathways in Drosophila. PUBMED:23671640 EPMC:23671640

  3. Kajiura H, Okamoto T, Misaki R, Matsuura Y, Fujiyama K;, J Biosci Bioeng. 2012;113:48-54.: Arabidopsis beta1,2-xylosyltransferase: substrate specificity and participation in the plant-specific N-glycosylation pathway. PUBMED:22024534 EPMC:22024534


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007657

Glycosyltransferase 61 family members are further processed into a mature form. Proteins in this family includes O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2 (POMGnT2, also known as EOGTL) [ PUBMED:23929950 ] and EGF domain-specific O-linked N-acetylglucosamine transferase (EOGT) [ PUBMED:23671640 ].

This entry also includes plant beta-(1,2)-xylosyltransferase [ PUBMED:10781814 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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
(133)
Full
(6508)
Representative proteomes UniProt
(17059)
RP15
(1378)
RP35
(3487)
RP55
(5802)
RP75
(7628)
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PP/heatmap 1            

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

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

Format an alignment

  Seed
(133)
Full
(6508)
Representative proteomes UniProt
(17059)
RP15
(1378)
RP35
(3487)
RP55
(5802)
RP75
(7628)
Alignment:
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Sequence:
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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
(133)
Full
(6508)
Representative proteomes UniProt
(17059)
RP15
(1378)
RP35
(3487)
RP55
(5802)
RP75
(7628)
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_4026 (release 7.5)
Previous IDs: DUF563;
Type: Family
Sequence Ontology: SO:0100021
Author: Waterfield DI , Finn RD , Chuguransky S , Bateman A
Number in seed: 133
Number in full: 6508
Average length of the domain: 199.80 aa
Average identity of full alignment: 14 %
Average coverage of the sequence by the domain: 40.03 %

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 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 128
Family (HMM) version: 16
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
A0A0P0UXB1 View 3D Structure Click here
A0A0P0UXI8 View 3D Structure Click here
A0A0P0WVV1 View 3D Structure Click here
A0A0P0Y3L4 View 3D Structure Click here
A0A0R0JCE6 View 3D Structure Click here
A0A0R0L2T1 View 3D Structure Click here
A0A1D6F303 View 3D Structure Click here
A0A1D6FD91 View 3D Structure Click here
A0A1D6FDS6 View 3D Structure Click here
A0A1D6GVR7 View 3D Structure Click here
A0A1D6GY71 View 3D Structure Click here
A0A1D6H8T8 View 3D Structure Click here
A0A1D6ILV0 View 3D Structure Click here
A0A1D6KCD6 View 3D Structure Click here
A0A1D6KIK7 View 3D Structure Click here
A0A1D6LKS7 View 3D Structure Click here
A0A1D6LTF7 View 3D Structure Click here
A0A1D6M3A4 View 3D Structure Click here
A0A1D6MMW0 View 3D Structure Click here
A0A1D6MMW3 View 3D Structure Click here
A0A1D6MMW9 View 3D Structure Click here
A0A1D6MMX0 View 3D Structure Click here
A0A1D6P0V5 View 3D Structure Click here
A0A1D6QKM8 View 3D Structure Click here
A0A1D6QUW4 View 3D Structure Click here
A0A2R8QDL9 View 3D Structure Click here
A4HUW3 View 3D Structure Click here
B4F8N2 View 3D Structure Click here
B4F8Y8 View 3D Structure Click here
B4FAX1 View 3D Structure Click here
B4FBB0 View 3D Structure Click here
B4FM83 View 3D Structure Click here
B4FZZ6 View 3D Structure Click here
B4G134 View 3D Structure Click here
C0PBI5 View 3D Structure Click here
C0PDR7 View 3D Structure Click here
C4J6G0 View 3D Structure Click here
F4ISB4 View 3D Structure Click here
F4J287 View 3D Structure Click here
I1JNB3 View 3D Structure Click here
I1K5F9 View 3D Structure Click here
I1KQG2 View 3D Structure Click here
I1KYF6 View 3D Structure Click here
I1KYF7 View 3D Structure Click here
I1N0F4 View 3D Structure Click here
I1N0F5 View 3D Structure Click here
K7L5C1 View 3D Structure Click here
K7MYB0 View 3D Structure Click here
K7U9Q2 View 3D Structure Click here
K7V917 View 3D Structure Click here
K7VCJ3 View 3D Structure Click here
K7VGB6 View 3D Structure Click here
K7VUB5 View 3D Structure Click here
K7VUX6 View 3D Structure Click here
O22225 View 3D Structure Click here
O81876 View 3D Structure Click here
Q0IP76 View 3D Structure Click here
Q0JR53 View 3D Structure Click here
Q10I20 View 3D Structure Click here
Q4D9C6 View 3D Structure Click here
Q4DA11 View 3D Structure Click here
Q4DH51 View 3D Structure Click here
Q4DJI8 View 3D Structure Click here
Q4DWC4 View 3D Structure Click here
Q4DY85 View 3D Structure Click here
Q54GL6 View 3D Structure Click here
Q5NDE5 View 3D Structure Click here
Q5NDF0 View 3D Structure Click here
Q5NDL0 View 3D Structure Click here
Q5NDL2 View 3D Structure Click here
Q5QPY4 View 3D Structure Click here
Q5VNI5 View 3D Structure Click here
Q5Z8T7 View 3D Structure Click here
Q5Z8T8 View 3D Structure Click here
Q60ES7 View 3D Structure Click here
Q69XT9 View 3D Structure Click here
Q69Y34 View 3D Structure Click here
Q6E276 View 3D Structure Click here
Q6YUL6 View 3D Structure Click here
Q6YWE6 View 3D Structure Click here
Q6YXH2 View 3D Structure Click here
Q6Z0Z4 View 3D Structure Click here
Q6Z7I3 View 3D Structure Click here
Q6ZFH6 View 3D Structure Click here
Q6ZFR0 View 3D Structure Click here
Q7XPB0 View 3D Structure Click here
Q8BW41 View 3D Structure Click here
Q8BYW9 View 3D Structure Click here
Q8GRV4 View 3D Structure Click here
Q8GXN3 View 3D Structure Click here
Q8NAT1 View 3D Structure Click here
Q8RYJ1 View 3D Structure Click here
Q9FTE0 View 3D Structure Click here
Q9FTE2 View 3D Structure Click here
Q9FWV3 View 3D Structure Click here
Q9LDH0 View 3D Structure Click here
Q9LV22 View 3D Structure Click here
Q9LV23 View 3D Structure Click here
Q9SS43 View 3D Structure Click here
Q9VQB7 View 3D Structure Click here
Q9XTX0 View 3D Structure Click here
X1WGG5 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;