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2  structures 608  species 0  interactions 987  sequences 6  architectures

Family: Tub_2 (PF04525)

Summary: Tubby C 2

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This is the Wikipedia entry entitled "Tubby protein". More...

Tubby protein Edit Wikipedia article

Tubby Protein
Tubby-1c8z-pymol.png
A tubby protein expressed in mouse brain
Identifiers
Symbol Tub
Pfam PF01167
InterPro IPR000007
PROSITE PDOC00923
SCOP 1c8z
SUPERFAMILY 1c8z
OPM superfamily 177
OPM protein 1i7e

The tubby protein is encoded by the TUB gene. It is an upstream cell signaling protein common to multicellular eukaryotes. The first tubby gene was identified in mice, and proteins that are homologous to tubby are known as "tubby-like proteins" (TULPs). They share a common and characteristic tertiary structure that consists of a beta barrel packed around an alpha helix in the central pore. The gene derives its name from its role in metabolism; mice with a mutated tubby gene develop delayed-onset obesity, sensorineural hearing loss and retinal degeneration. [1][2][3]

Structure[edit]

Tubby proteins are classified as α+β proteins and have a 12-beta stranded barrel surrounding a central alpha helix. Tubby proteins can bind the small cell signaling molecule phosphatidylinositol, which is typically localized to the cell membrane. A similar structural fold to the Tubby like proteins has been identified in the Scramblase family of proteins.[4]

Function[edit]

Tubby proteins have been implicated as transcription factors[5] and as potential signaling factors coupled to G-protein activity.[6] They are associated with neuronal differentiation and development, and in mammals are implicated in three disease processes when mutated: obesity, retinal degeneration, and hearing loss.[5] In mice, mutations in tubby proteins are known to affect life span and fat storage[7] as well as carbohydrate metabolism.[8] Tubby domains associate with cytoplasmic side of cell membranes through binding of different phosphoinositides[9]

Human proteins containing this domain[edit]

TUB; TULP1; TULP2; TULP3; TULP4;

External links[edit]

References[edit]

  1. ^ Noben-Trauth, K.; Naggert, J. K.; North, M. A.; Nishina, P. M. (1996). "A candidate gene for the mouse mutation tubby". Nature 380 (6574): 534–538. Bibcode:1996Natur.380..534N. doi:10.1038/380534a0. PMID 8606774.  edit
  2. ^ Kleyn, P. W.; Fan, W.; Kovats, S. G.; Lee, J. J.; Pulido, J. C.; Wu, Y.; Berkemeier, L. R.; Misumi, D. J.; Holmgren, L.; Charlat, O.; Woolf, E. A.; Tayber, O.; Brody, T.; Shu, P.; Hawkins, F.; Kennedy, B.; Baldini, L.; Ebeling, C.; Alperin, G. D.; Deeds, J.; Lakey, N. D.; Culpepper, J.; Chen, H.; Glücksmann-Kuis, M. A.; Carlson, G. A.; Duyk, G. M.; Moore, K. J. (1996). "Identification and characterization of the mouse obesity gene tubby: a member of a novel gene family". Cell 85 (2): 281–290. doi:10.1016/S0092-8674(00)81104-6. PMID 8612280.  edit
  3. ^ Ohlemiller, KK; Hughes, RM; Mosinger-Ogilvie, J; Speck, JD; Grosof, DH; Silverman, MS (1995). "Cochlear and retinal degeneration in the tubby mouse". Neuroreport 6 (6): 845–9. doi:10.1097/00001756-199504190-00005. PMID 7612867.  edit
  4. ^ Bateman A, Finn RD, Sims PJ, Wiedmer T, Biegert A, Söding J (January 2009). "Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors". Bioinformatics 25 (2): 159–62. doi:10.1093/bioinformatics/btn595. PMC 2639001. PMID 19010806. 
  5. ^ a b Boggon TJ, Shan WS, Santagata S, Myers SC, Shapiro L. (1999). Implication of tubby proteins as transcription factors by structure-based functional analysis. Science 286(5447):2119-25.
  6. ^ Carroll K, Gomez C, Shapiro L. (2004). Tubby proteins: the plot thickens. Nat Rev Mol Cell Biol5(1):55-63.
  7. ^ Mukhopadhyay A, Deplancke B, Walhout AJ, Tissenbaum HA. (2005). C. elegans tubby regulates life span and fat storage by two independent mechanisms. Cell Metab 2(1):35-42.
  8. ^ Wang Y, Seburn K, Bechtel L, Lee BY, Szatkiewicz JP, Nishina PM, Naggert JK. (2006). Defective carbohydrate metabolism in mice homozygous for the tubby mutation. Physiol Genomics Epub.
  9. ^ Cho, W. and Stahelin, R.V. (June 2005). "Membrane-protein interactions in cell signaling and membrane trafficking" (abstract page). Annual Review of Biophysics and Biomolecular Structure 34: 119–151. doi:10.1146/annurev.biophys.33.110502.133337. PMID 15869386. Retrieved 2007-01-23. 

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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.

Tubby C 2 Provide feedback

The structure of this family has been solved. It comprises a 12-stranded beta barrel with a central C-terminal alpha helix. This helix is thought to be a transmembrane helix. It is structurally similar to the C-terminal domain of the Tubby protein [1]. In plants it plays a role in defense against pathogens [2].

Literature references

  1. Bateman A, Finn RD, Sims PJ, Wiedmer T, Biegert A, Soding J;, Bioinformatics. 2009;25:159-162.: Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors. PUBMED:19010806 EPMC:19010806

  2. Knoth C, Eulgem T;, Plant J. 2008;55:53-64.: The oomycete response gene LURP1 is required for defense against Hyaloperonospora parasitica in Arabidopsis thaliana. PUBMED:18346188 EPMC:18346188


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007612

The structure of this domain has been solved. It comprises a 12-stranded beta barrel with a central C-terminal alpha helix. This helix is thought to be a transmembrane helix. It is structurally similar to the C-terminal domain of the Tubby protein [PUBMED:19010806]. In plants it plays a role in defense against pathogens [PUBMED:18346188].

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 Tubby_C (CL0395), which contains the following 3 members:

Scramblase Tub Tub_2

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(16)
Full
(987)
Representative proteomes NCBI
(768)
Meta
(7)
RP15
(59)
RP35
(216)
RP55
(293)
RP75
(363)
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Format an alignment

  Seed
(16)
Full
(987)
Representative proteomes NCBI
(768)
Meta
(7)
RP15
(59)
RP35
(216)
RP55
(293)
RP75
(363)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(16)
Full
(987)
Representative proteomes NCBI
(768)
Meta
(7)
RP15
(59)
RP35
(216)
RP55
(293)
RP75
(363)
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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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_4998 (release 7.5)
Previous IDs: DUF567;
Type: Family
Author: Waterfield DI, Finn RD, Eberhardt R
Number in seed: 16
Number in full: 987
Average length of the domain: 155.80 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 85.77 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.5 24.5
Trusted cut-off 24.5 24.7
Noise cut-off 24.2 24.0
Model length: 187
Family (HMM) version: 7
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 Tub_2 domain has been found. There are 2 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 seqence.

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