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0  structures 51  species 0  interactions 318  sequences 8  architectures

Family: NUT (PF12881)

Summary: NUT protein

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NUT protein Provide feedback

This family includes the NUT protein. The gene encoding for NUT protein (Nuclear Testis protein) is found fused to BRD3 or BRD4 genes, in some aggressive types of carcinoma, due to chromosomal translocations [1-2]. Proteins of the BRD family contain two bromodomains that bind transcriptionally active chromatin through associations with acetylated histones H3 and H4 [1-2]. Such proteins are crucial for the regulation of cell cycle progression. On the other hand, little is known about NUT protein. NUT is known to have a Nuclear Export Sequence (NES) as well as a Nuclear Localisation Signal (NLS), both located towards the C-terminal end of the protein [1-2]. A fused NUT-GFP protein showed either cytoplasmic or nuclear localisation, suggesting that it is subject to nuclear/cytoplasmic shuttling. Consistent with this possibility, treatment with leptomycin B an inhibitor of CRM1-dependent nuclear export resulted in re-distribution of NUT-GFP to the nucleus [3-4]. Inspection of NUT revealed a C-terminal sequence similar to known nuclear export sequences (NES) which are often regulated by phosphorylation [3-4]. This family carries some natively unstructured sequence.

Literature references

  1. French CA, Miyoshi I, Kubonishi I, Grier HE, Perez-Atayde AR, Fletcher JA;, Cancer Res. 2003;63:304-307.: BRD4-NUT fusion oncogene: a novel mechanism in aggressive carcinoma. PUBMED:12543779 EPMC:12543779

  2. French CA, Ramirez CL, Kolmakova J, Hickman TT, Cameron MJ, Thyne ME, Kutok JL, Toretsky JA, Tadavarthy AK, Kees UR, Fletcher JA, Aster JC;, Oncogene. 2008;27:2237-2242.: BRD-NUT oncoproteins: a family of closely related nuclear proteins that block epithelial differentiation and maintain the growth of carcinoma cells. PUBMED:17934517 EPMC:17934517

  3. Fornerod M, Ohno M, Yoshida M, Mattaj IW;, Cell. 1997;90:1051-1060.: CRM1 is an export receptor for leucine-rich nuclear export signals. PUBMED:9323133 EPMC:9323133

  4. Ossareh-Nazari B, Bachelerie F, Dargemont C;, Science. 1997;278:141-144.: Evidence for a role of CRM1 in signal-mediated nuclear protein export. PUBMED:9311922 EPMC:9311922


This tab holds annotation information from the InterPro database.

InterPro entry IPR024309

This domain is found in the N-terminal region of Nuclear Testis (NUT) proteins. The NUT gene is found fused to BRD3 or BRD4 genes in some aggressive types of carcinoma, due to chromosomal translocations [PUBMED:12543779, PUBMED:17934517]. The BRD family proteins contain two bromodomains that bind transcriptionally active chromatin through associations with acetylated histones H3 and H4 [PUBMED:12543779, PUBMED:17934517]. BRD proteins are crucial for the regulation of cell cycle progression.

The function of NUT proteins is not clear. NUT proteins contain the Nuclear Export Sequence (NES) and the Nuclear Localisation Signal (NLS), both located towards the C-terminal end of the protein [PUBMED:12543779, PUBMED:17934517]. NUT-GFP protein showed either cytoplasmic or nuclear localisation, suggesting that it is subject to nuclear/cytoplasmic shuttling. Consistent with this possibility, treatment with leptomycin B an inhibitor of CRM1-dependent nuclear export resulted in re-distribution of NUT-GFP to the nucleus [PUBMED:9323133, PUBMED:9311922]. Inspection of NUT revealed a C-terminal sequence similar to known nuclear export NUT protein carries some natively unstructured sequence.

Domain organisation

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Alignments

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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
(9)
Full
(318)
Representative proteomes UniProt
(445)
NCBI
(868)
Meta
(0)
RP15
(24)
RP35
(102)
RP55
(217)
RP75
(328)
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  Seed
(9)
Full
(318)
Representative proteomes UniProt
(445)
NCBI
(868)
Meta
(0)
RP15
(24)
RP35
(102)
RP55
(217)
RP75
(328)
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
(9)
Full
(318)
Representative proteomes UniProt
(445)
NCBI
(868)
Meta
(0)
RP15
(24)
RP35
(102)
RP55
(217)
RP75
(328)
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.

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.

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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: jackhmmer:Q86Y26
Previous IDs: NUT_N;
Type: Family
Sequence Ontology: SO:0100021
Author: Zenonos ZA , Mistry J , Eberhardt R
Number in seed: 9
Number in full: 318
Average length of the domain: 417.90 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 80.88 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 28.3 27.8
Noise cut-off 19.9 24.6
Model length: 729
Family (HMM) version: 7
Download: download the raw HMM for this family

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