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21  structures 101  species 1  interaction 253  sequences 4  architectures

Family: Whirly (PF08536)

Summary: Whirly transcription factor

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This is the Wikipedia entry entitled "Whirly". More...

Whirly Edit Wikipedia article

Whirly
Identifiers
Symbol Whirly
Pfam PF08536
InterPro IPR013742

In molecular biology the protein domain Whirly is a transcription factor commonly found in plants. This means they aid the transcription of genes from DNA into a complementary copy of mRNA. In particular, in plants, they aid the transcription of plant defence genes.[1]

Function

The function of Whirly proteins is to regulate the expression of genes that aid defence. They are transcription factors which bind to single stranded DNA in order to regulate gene expression. When a pathogen enters, salicylic acid is released as a signalling molecule which affects Whirly, allowing the expression of defence genes to occur.[1]

Structure

This protein contains 10 beta strands and 2 alpha helices.[2]

History

PBF-2 was the first protein in the Whirly family to be discovered.[1] In the past, the protein has also been named p24.[3]

References

  1. ^ a b c Desveaux D, Maréchal A, Brisson N (February 2005). "Whirly transcription factors: defense gene regulation and beyond". Trends Plant Sci. 10 (2): 95–102. doi:10.1016/j.tplants.2004.12.008. PMID 15708347. 
  2. ^ Cappadocia L, Maréchal A, Parent JS, Lepage E, Sygusch J, Brisson N (June 2010). "Crystal structures of DNA-Whirly complexes and their role in Arabidopsis organelle genome repair". Plant Cell. 22 (6): 1849–67. doi:10.1105/tpc.109.071399. PMC 2910959Freely accessible. PMID 20551348. 
  3. ^ Desveaux D, Allard J, Brisson N, Sygusch J (July 2002). "A new family of plant transcription factors displays a novel ssDNA-binding surface". Nat. Struct. Biol. 9 (7): 512–7. doi:10.1038/nsb814. PMID 12080340. 

External links

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.

Whirly transcription factor Provide feedback

This family contains the plant whirly transcription factors.

Literature references

  1. Desveaux D, Despres C, Joyeux A, Subramaniam R, Brisson N; , Plant Cell 2000;12:1477-1489.: PBF-2 is a novel single-stranded DNA binding factor implicated in PR-10a gene activation in potato. PUBMED:10948264 EPMC:10948264

  2. Desveaux D, Marechal A, Brisson N; , Trends Plant Sci. 2005;10:95-102.: Whirly transcription factors: defense gene regulation and beyond. PUBMED:15708347 EPMC:15708347

  3. Desveaux D, Allard J, Brisson N, Sygusch J; , Nat Struct Biol. 2002;9:512-517.: A new family of plant transcription factors displays a novel ssDNA-binding surface. PUBMED:12080340 EPMC:12080340


This tab holds annotation information from the InterPro database.

InterPro entry IPR013742

This is a family of plant transcription factors.

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 sPC4_like (CL0609), which has the following description:

According to SCOP this superfamily contains a helix-swapped dimer of beta(4)-alpha motifs. Members of this superfamily are ssDNA binding domains found transcriptional regulators.

The clan contains the following 7 members:

DUF1818 DUF3276 MRP PC4 PurA SsgA Whirly

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, the UniProtKB sequence database, 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
(24)
Full
(253)
Representative proteomes UniProt
(389)
NCBI
(509)
Meta
(4)
RP15
(36)
RP35
(112)
RP55
(187)
RP75
(226)
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PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(24)
Full
(253)
Representative proteomes UniProt
(389)
NCBI
(509)
Meta
(4)
RP15
(36)
RP35
(112)
RP55
(187)
RP75
(226)
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
(24)
Full
(253)
Representative proteomes UniProt
(389)
NCBI
(509)
Meta
(4)
RP15
(36)
RP35
(112)
RP55
(187)
RP75
(226)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: manual
Previous IDs: Plant_TF;
Type: Domain
Author: Mistry J, Pachon DMR
Number in seed: 24
Number in full: 253
Average length of the domain: 123.50 aa
Average identity of full alignment: 43 %
Average coverage of the sequence by the domain: 49.04 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.0 20.0
Trusted cut-off 20.4 20.4
Noise cut-off 19.9 19.5
Model length: 136
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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Interactions

There is 1 interaction for this family. More...

Whirly

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 Whirly domain has been found. There are 21 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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