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4  structures 1093  species 0  interactions 9557  sequences 189  architectures

Family: uDENN (PF03456)

Summary: uDENN domain

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

uDENN domain Provide feedback

This region is always found associated with PF02141. It is predicted to form an all beta domain [1].

Literature references

  1. Levivier E, Goud B, Souchet M, Calmels TP, Mornon JP, Callebaut I; , Biochem Biophys Res Commun 2001;287:688-695.: uDENN, DENN, and dDENN: indissociable domains in Rab and MAP kinases signaling pathways. PUBMED:11563850 EPMC:11563850


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005113

The tripartite DENN (after differentially expressed in neoplastic versus normal cells) domain is found in several proteins involved in Rab-mediated processes or regulation of MAPKs (Mitogen-activated preotein kinases) signaling pathways. It actually consists of three parts as the original DENN domain is always encircled on both sides by more divergent domains, called uDENN (after upstream DENN) and dDENN (for downstream DENN). The tripartite DENN domain is found associated with other domains, such as RUN, PLAT, PH, PPR, WD-40, GRAM or C1. The function of DENN domain remains to date unclear, although it appears to represent a good candidate for a GTP/GDP exchange activity [ PUBMED:11563850 , PUBMED:12906859 ].

The general characteristics of DENN domains - three regions dDENN, DENN itself, and uDENN having different patterns of sequence conservation and separated by sequences of variable length - suggest that they are composed of at least three sub-domains which may feature distinct folds but which are always associated due to functional and/or structural constraints [ PUBMED:11563850 ].

Some proteins known to contain a tripartite DENN domain are listed below:

  • Rat Rab3 GDP/GTP exchange protein (Rab3GEP)
  • Human mitogen-activated protein kinase activating protein containing death domain (MADD). It is orthologous to Rab3GEP
  • Caenorhabditis elegans regulator of presynaptic activity aex-3, the ortholog of Rab3GEP
  • Mouse Rab6 interacting protein 1 (Rab6IP1)
  • Human SET domain-binding factor 1(SBF1)
  • Human suppressor of tumoreginicity 5 (ST5)
  • Human C-MYC promoter-binding protein IRLB

This entry represents the uDENN domain.

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 PF (CL0431), which has the following description:

The families here all show the Profilin-like fold, and represent both the Profilin (actin-binding protein) (55770) and the Roadblock/LC7 domain-type (103196) superfamilies.

The clan contains the following 21 members:

Clat_adaptor_s FNIP_N Fuz_longin_1 Fuz_longin_2 Fuz_longin_3 Intu_longin_1 Intu_longin_2 Intu_longin_3 LAMTOR5 Longin Longin_2 MAPKK1_Int Nyv1_N Profilin Robl_LC7 Sedlin_N SLM4 SRP-alpha_N SRX Sybindin uDENN

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
(149)
Full
(9557)
Representative proteomes UniProt
(16968)
RP15
(1141)
RP35
(3278)
RP55
(7945)
RP75
(11355)
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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
(149)
Full
(9557)
Representative proteomes UniProt
(16968)
RP15
(1141)
RP35
(3278)
RP55
(7945)
RP75
(11355)
Alignment:
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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
(149)
Full
(9557)
Representative proteomes UniProt
(16968)
RP15
(1141)
RP35
(3278)
RP55
(7945)
RP75
(11355)
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: Callebaut I
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Callebaut I
Number in seed: 149
Number in full: 9557
Average length of the domain: 65.10 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 5.31 %

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 22.3 22.3
Trusted cut-off 22.3 22.3
Noise cut-off 22.2 22.2
Model length: 56
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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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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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 uDENN domain has been found. There are 4 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
A0A0G2K089 View 3D Structure Click here
A0A0G2K6J1 View 3D Structure Click here
A0A0H2UKW7 View 3D Structure Click here
A0A0P0V4C5 View 3D Structure Click here
A0A0R4IBI0 View 3D Structure Click here
A0A0R4IIC4 View 3D Structure Click here
A0A1D5NSM6 View 3D Structure Click here
A0A1D6NK39 View 3D Structure Click here
A0A1D6PJS0 View 3D Structure Click here
A0A1D6QDI1 View 3D Structure Click here
A0A286Y972 View 3D Structure Click here
A0A2R8PWA9 View 3D Structure Click here
A0A2R8Q6A5 View 3D Structure Click here
A1Z7Q5 View 3D Structure Click here
A2RSQ0 View 3D Structure Click here
A6H8H2 View 3D Structure Click here
B0BNM5 View 3D Structure Click here
B8JLM2 View 3D Structure Click here
D3Z8F6 View 3D Structure Click here
D3ZLQ1 View 3D Structure Click here
D3ZX30 View 3D Structure Click here
D4A518 View 3D Structure Click here
D4A9H6 View 3D Structure Click here
E7F1J4 View 3D Structure Click here
E7F4G2 View 3D Structure Click here
E9PXF8 View 3D Structure Click here
E9Q8V6 View 3D Structure Click here
F1LTT7 View 3D Structure Click here
F1Q6K3 View 3D Structure Click here
F1QFB0 View 3D Structure Click here
F1R7P0 View 3D Structure Click here
F4IUH2 View 3D Structure Click here
F4JZV9 View 3D Structure Click here
F6NKU7 View 3D Structure Click here
G3V7Q0 View 3D Structure Click here
I1KQ47 View 3D Structure Click here
I1L1P1 View 3D Structure Click here
I1MHF0 View 3D Structure Click here
I1MSB4 View 3D Structure Click here
K7KFK6 View 3D Structure Click here
K7LZ06 View 3D Structure Click here
K7MYT4 View 3D Structure Click here
M0RAP5 View 3D Structure Click here
M0RBQ8 View 3D Structure Click here
O02626 View 3D Structure Click here
O08873 View 3D Structure Click here
O75064 View 3D Structure Click here
O95248 View 3D Structure Click here
P78524 View 3D Structure Click here
Q10RU8 View 3D Structure Click here
Q18780 View 3D Structure Click here
Q3U1T9 View 3D Structure Click here
Q3U1Y4 View 3D Structure Click here
Q54DZ1 View 3D Structure Click here
Q54GF5 View 3D Structure Click here
Q54JA6 View 3D Structure Click here
Q54JL9 View 3D Structure Click here
Q54JN1 View 3D Structure Click here
Q54VP0 View 3D Structure Click here
Q55DD7 View 3D Structure Click here
Q55FT6 View 3D Structure Click here
Q5VZ89 View 3D Structure Click here
Q68D51 View 3D Structure Click here
Q6IQ26 View 3D Structure Click here
Q6NXD8 View 3D Structure Click here
Q6P3S1 View 3D Structure Click here
Q6P9P8 View 3D Structure Click here
Q6PAL8 View 3D Structure Click here
Q6ZGD1 View 3D Structure Click here
Q6ZPE2 View 3D Structure Click here
Q6ZUT9 View 3D Structure Click here
Q7K7A5 View 3D Structure Click here
Q7Z401 View 3D Structure Click here
Q80U28 View 3D Structure Click here
Q86WG5 View 3D Structure Click here
Q8C4S8 View 3D Structure Click here
Q8CFK6 View 3D Structure Click here
Q8IV53 View 3D Structure Click here
Q8K382 View 3D Structure Click here
Q8RXA7 View 3D Structure Click here
Q8TEH3 View 3D Structure Click here
Q8WXG6 View 3D Structure Click here
Q91VV4 View 3D Structure Click here
Q924W7 View 3D Structure Click here
Q9H6A0 View 3D Structure Click here
Q9ULE3 View 3D Structure Click here
Q9VGH9 View 3D Structure Click here
Q9VXY2 View 3D Structure Click here
Q9W0E1 View 3D Structure Click here
Q9W3D3 View 3D Structure Click here
Q9Y7Q7 View 3D Structure Click here
U4PBM1 View 3D Structure Click here