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0  structures 29  species 0  interactions 109  sequences 14  architectures

Family: WPP (PF13943)

Summary: WPP domain

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WPP domain Edit Wikipedia article

WPP domain
Identifiers
Symbol WPP
Pfam PF13943

The WPP domain is a protein domain thought to be exclusively found in plants, first identified in 2000.[1] The domain is about 90 amino acid residues long.

The domain is known to direct RanGAP to the nuclear envelope.[2] Non-RanGAP nuclear envelope proteins are also known to encode WPP domains, such as MFP1 attachment factor 1 (MAF1),[1] WPP1[3] and WPP2.[3]

The WPP stands for a tryptophan-proline-proline motif that is highly conserved in the domain.[1] Either deletion of the WPP domain or mutation of both the namesake tryptophan and first proline residues into alanine in the Arabidopsis thaliana protein RanGAP1 leads to mis-targeting in the majority of cells.[2]

A multiple sequence alignment of proteins containing a WPP domain showing the conserved WPP sequence motif to the left.

References[edit]

  1. ^ a b c Meier I (December 2000). "A novel link between ran signal transduction and nuclear envelope proteins in plants". Plant Physiology 124 (4): 1507–10. PMC 1539304. PMID 11115866. 
  2. ^ a b Rose A, Meier I (December 2001). "A domain unique to plant RanGAP is responsible for its targeting to the plant nuclear rim". Proceedings of the National Academy of Sciences of the United States of America 98 (26): 15377–82. doi:10.1073/pnas.261459698. PMC 65037. PMID 11752475. 
  3. ^ a b Patel S, Rose A, Meulia T, Dixit R, Cyr RJ, Meier I (December 2004). "Arabidopsis WPP-domain proteins are developmentally associated with the nuclear envelope and promote cell division". The Plant Cell 16 (12): 3260–73. doi:10.1105/tpc.104.026740. PMC 535872. PMID 15548735. 

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External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR025265

The WPP domain is thought to be exclusively found in plants. The WPP stands for a tryptophan-proline-proline motif that is highly conserved in the domain [PUBMED:11115866]. The WPP domain is known to direct RanGAP (Ran GTPase-activating protein) to the nuclear envelope [PUBMED:11752475]. RanGAP is an accessory protein for the small signaling GTPase Ran, which is involved in nucleocytoplasmic transport. Non-RanGAP nuclear envelope proteins are also known to encode WPP domains, such as MFP1 attachment factor 1 (MAF1) [PUBMED:11115866], WPP1 [PUBMED:15548735] and WPP2 [PUBMED:15548735].

Domain organisation

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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 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
(25)
Full
(109)
Representative proteomes NCBI
(111)
Meta
(2)
RP15
(10)
RP35
(39)
RP55
(50)
RP75
(65)
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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
(25)
Full
(109)
Representative proteomes NCBI
(111)
Meta
(2)
RP15
(10)
RP35
(39)
RP55
(50)
RP75
(65)
Alignment:
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Sequence:
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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
(25)
Full
(109)
Representative proteomes NCBI
(111)
Meta
(2)
RP15
(10)
RP35
(39)
RP55
(50)
RP75
(65)
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:

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Curation and family details

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Seed source: Woodcraft BJ
Previous IDs: none
Type: Domain
Author: Woodcraft BJ
Number in seed: 25
Number in full: 109
Average length of the domain: 95.70 aa
Average identity of full alignment: 43 %
Average coverage of the sequence by the domain: 27.43 %

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 20.1 20.1
Trusted cut-off 22.4 24.2
Noise cut-off 18.6 17.4
Model length: 100
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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