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1549  structures 1701  species 15  interactions 193252  sequences 2206  architectures

Family: WD40 (PF00400)

Summary: WD domain, G-beta repeat

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This is the Wikipedia entry entitled "WD40 repeat". More...

WD40 repeat Edit Wikipedia article

WD domain, G-beta repeat
1erj 7bladed beta propeller.png
Ribbon diagram of the C-terminal WD40 domain of Tup1 (a transcriptional corepressor in yeast), which adopts a 7-bladed beta-propeller fold. Ribbon is colored from blue (N-terminus) to red (C-terminus).[1]
Identifiers
Symbol WD40
Pfam PF00400
Pfam clan CL0186
InterPro IPR001680
PROSITE PDOC00574
SCOP 1gp2
SUPERFAMILY 1gp2
CDD cd00200

The WD40 repeat (also known as the WD or beta-transducin repeat) is a short structural motif of approximately 40 amino acids, often terminating in a tryptophan-aspartic acid (W-D) dipeptide.[2] Tandem copies of these repeats typically fold together to form a type of circular solenoid protein domain called the WD40 domain.

Structure

WD40 domain-containing proteins have 4 to 16 repeating units, all of which are thought to form a circularised beta-propeller structure (see figure to the right).[3][4] The WD40 domain is composed of several repeats, a variable region of around 20 residues at the beginning followed by a more common repeated set of residues. These repeats typically form a four stranded anti-parallel beta sheet or blade. These blades come together to form a propeller with the most common being a 7 bladed beta propeller. The blades interlock so that the last beta strand of one repeat forms with the first three of the next repeat to form the 3D blade structure.

Function

WD40-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control, autophagy and apoptosis .[5] The underlying common function of all WD40-repeat proteins is coordinating multi-protein complex assemblies, where the repeating units serve as a rigid scaffold for protein interactions. The specificity of the proteins is determined by the sequences outside the repeats themselves. Examples of such complexes are G proteins (beta subunit is a beta-propeller), TAFII transcription factor, and E3 ubiquitin ligase.[3][4]

Examples

According to the initial analysis of the human genome WD40 repeats are the eighth largest family of proteins. In all 277 proteins were identified to contain them.[6] Human genes encoding proteins containing this domain include:

See also

References

  1. ^ PDB 1erj; Sprague ER, Redd MJ, Johnson AD, Wolberger C (June 2000). "Structure of the C-terminal domain of Tup1, a corepressor of transcription in yeast". EMBO J. 19 (12): 3016–27. doi:10.1093/emboj/19.12.3016. PMC 203344. PMID 10856245. 
  2. ^ Neer EJ, Schmidt CJ, Nambudripad R, Smith TF (September 1994). "The ancient regulatory-protein family of WD-repeat proteins". Nature 371 (6495): 297–300. doi:10.1038/371297a0. PMID 8090199. 
  3. ^ a b Smith TF, Gaitatzes C, Saxena K, Neer EJ (May 1999). "The WD40 repeat: a common architecture for diverse functions". Trends Biochem. Sci. 24 (5): 181–5. doi:10.1016/S0968-0004(99)01384-5. PMID 10322433. 
  4. ^ a b Li D, Roberts R (December 2001). "WD-repeat proteins: structure characteristics, biological function, and their involvement in human diseases". Cell. Mol. Life Sci. 58 (14): 2085–97. doi:10.1007/PL00000838. PMID 11814058. 
  5. ^ Stirnimann Christian U, Petsalaki Evangelia, Russell RB, Müller CW (May 2010). "WD40 proteins propel cellular networks.". Trends Biochem. Sci. 35 (10): 565–74. doi:10.1016/j.tibs.2010.04.003. PMID 20451393. 
  6. ^ Lander ES, Linton LM, Birren B, et al. (February 2001). "Initial sequencing and analysis of the human genome". Nature 409 (6822): 860–921. doi:10.1038/35057062. PMID 11237011. 

External links


This article incorporates text from the public domain Pfam and InterPro IPR001680

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.

WD domain, G-beta repeat Provide feedback

No Pfam abstract.

Literature references

  1. Neer EJ, Schmidt CJ, Nambudripad R, Smith TF; , Nature 1994;371:297-300.: The ancient regulatory-protein family of WD-repeat proteins. PUBMED:8090199 EPMC:8090199


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001680

WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide. WD40 repeats usually assume a 7-8 bladed beta-propeller fold, but proteins have been found with 4 to 16 repeated units, which also form a circularised beta-propeller structure. WD-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control and apoptosis. Repeated WD40 motifs act as a site for protein-protein interaction, and proteins containing WD40 repeats are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins. The specificity of the proteins is determined by the sequences outside the repeats themselves. Examples of such complexes are G proteins (beta subunit is a beta-propeller), TAFII transcription factor, and E3 ubiquitin ligase [PUBMED:11814058, PUBMED:10322433]. In Arabidopsis spp., several WD40-containing proteins act as key regulators of plant-specific developmental events.

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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Pfam Clan

This family is a member of clan Beta_propeller (CL0186), which has the following description:

This large clan contains proteins that contain beta propellers. These are composed of between 6 and 8 repeats. The individual repeats are composed of a four stranded sheet. The clan includes families such as WD40 Pfam:PF00400 where the individual repeats are modeled. The clan also includes families where the entire propeller is modeled such as Pfam:PF02239 usually because the individual repeats are not discernible. These proteins carry out a very wide diversity of functions including catalysis.

The clan contains the following 60 members:

Apc4_WD40 Arylesterase Arylsulfotran_2 Arylsulfotrans Beta_propel CNH Coatomer_WDAD CPSF_A Cytochrom_D1 DPPIV_N DUF1513 DUF1668 DUF1900 DUF2415 DUF3312 DUF4652 DUF839 eIF2A FG-GAP FG-GAP_2 Glu_cyclase_2 Gmad1 GSDH IKI3 Kelch_1 Kelch_2 Kelch_3 Kelch_4 Kelch_5 Kelch_6 Lactonase Ldl_recept_b Lgl_C LVIVD Me-amine-dh_H MRJP Nbas_N Neisseria_PilC NHL Nucleoporin_N Nup160 PD40 Pectate_lyase22 Peptidase_S9_N Phytase-like PQQ PQQ_2 PQQ_3 RAG2 RCC1 RCC1_2 Reg_prop SBBP SBP56 SdiA-regulated SGL Str_synth TcdB_toxin_midN VCBS WD40

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...

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
(1804)
Full
(193252)
Representative proteomes NCBI
(189768)
Meta
(5414)
RP15
(44330)
RP35
(69386)
RP55
(100531)
RP75
(125805)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(1804)
Full
(193252)
Representative proteomes NCBI
(189768)
Meta
(5414)
RP15
(44330)
RP35
(69386)
RP55
(100531)
RP75
(125805)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(1804)
Full
(193252)
Representative proteomes NCBI
(189768)
Meta
(5414)
RP15
(44330)
RP35
(69386)
RP55
(100531)
RP75
(125805)
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.

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_2 (release 1.0)
Previous IDs: G-beta;
Type: Repeat
Author: Finn RD
Number in seed: 1804
Number in full: 193252
Average length of the domain: 38.20 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 20.36 %

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 21.0 12.1
Trusted cut-off 21.0 12.1
Noise cut-off 20.9 12.0
Model length: 39
Family (HMM) version: 27
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 15 interactions for this family. More...

Methyltransf_4 G-gamma P16-Arc Lipase_GDSL RGS DEP PH G-alpha Phosducin WD40 ARPC4 DUF1899 DUF1900 EZH2_WD-Binding Actin

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 WD40 domain has been found. There are 1549 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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