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3  structures 220  species 0  interactions 3051  sequences 33  architectures

Family: WRKY (PF03106)

Summary: WRKY DNA -binding domain

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WRKYdomain Edit Wikipedia article

WRKY
PDB 1wj2 EBI.jpg
solution structure of the c-terminal wrky domain of atwrky4
Identifiers
Symbol WRKY
Pfam PF03106
Pfam clan CL0274
InterPro IPR003657

In molecular biology, WRKY transcription factors are a class of sequence-specific DNA-binding transcription factors found almost exclusively in plants.[1] These transcription factors, have diverse biological functions due to their ability in regulating expression of a wide range of target genes through coordination with other DNA-binding or non-DNA-binding interacting proteins. WRKY proteins are thought to play an important role in plant defense responses, plant hormone signaling, secondary metabolism and plant responses to abiotic stress.[2]

WRKY transcription factors[edit]

The first two reports of WRKY transcription factors appeared in 1994-95 and were of ill-defined DNA binding proteins that played potential roles in the regulation of gene expression by sucrose (SPF1)[3] or during germination (ABF1 and ABF2).[4] These were followed by the identification of WRKY1, WRKY2 and WRKY3 from parsley (Petroselinum crispum) and the name WRKY (pronounced ‘worky’) was coined.[5] This report also provided the first evidence that WRKY proteins play roles in regulating plant responses to pathogens, and many reports have since shown this to be a major role of WRKY transcription factors. Increasingly, however, WRKY proteins are being shown to regulate other processes such as abiotic stress responses, seed germination, senescence and wound responses and it is becoming clear that a single WRKY transcription factor might be involved in regulating several seemingly disparate plant processes.

Structure[edit]

The WRKY domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal domain, together with a novel zinc-finger-like motif. The WRKY domain is found in one or two copies in a superfamily of plant transcription factors involved in the regulation of various physiological programs that are unique to plants, including pathogen defence, senescence, trichome development and the biosynthesis of secondary metabolites. The WRKY domain binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core of the W box is essential for function and WRKY binding.[6] Some proteins known to contain a WRKY domain include Arabidopsis thaliana ZAP1 (Zinc-dependent Activator Protein-1) and AtWRKY44/TTG2, a protein involved in trichome development and anthocyanin pigmentation; and wild oat ABF1-2, two proteins involved in the gibberelic acid-induced expression of the alpha-Amy2 gene.

Structural studies indicate that this domain is a four-stranded beta-sheet with a zinc binding pocket, forming a novel zinc and DNA binding structure.[7] The WRKYGQK residues correspond to the most N-terminal beta-strand, which enables extensive hydrophobic interactions, contributing to the structural stability of the beta-sheet.

Function[edit]

From the beginning of research into WRKY transcription factors, it was evident that they play roles in regulating several different plant processes. Recent data has led to a new insight in this area, namely that it is common for a single WRKY transcription factor to regulate transcriptional reprogramming associated with multiple plant programs. The dynamic web of signaling in which WRKY factors operate has multiple inputs and outputs.[8]

Mechanisms of action[edit]

WRKY proteins can activate or repress transcription and substantial evidence now indicates that many genes are repressed by WRKY factors bound to their promoters. The WRKY proteins themselves appear to function via numerous different interacting partners including a diverse array of protein partners, including MAP kinases, MAP kinase kinases, 14-3-3 proteins, calmodulin, histone deacetylases, resistance proteins and other WRKY transcription factors. WRKY genes also exhibit extensive autoregulation and cross-regulation that facilitates transcriptional reprogramming in a dynamic web with built in redundancy.

External links[edit]

References[edit]

  1. ^ Rushton PJ, Somssich IE, Ringler P, Shen QJ (May 2010). "WRKY transcription factors". Trends Plant Sci. 15 (5): 247–58. doi:10.1016/j.tplants.2010.02.006. PMID 20304701. 
  2. ^ Cheng Y, Zhou Y, Yang Y, Chi YJ, Zhou J, Chen JY et al. (2012). "Structural and Functional Analysis of VQ Motif-Containing Proteins in Arabidopsis as Interacting Proteins of WRKY Transcription Factors.". Plant Physiol 159 (2): 810–25. doi:10.1104/pp.112.196816. PMC 3375943. PMID 22535423. 
  3. ^ Ishiguro S, Nakamura K (September 1994). "Characterization of a cDNA encoding a novel DNA-binding protein, SPF1, that recognizes SP8 sequences in the 5' upstream regions of genes coding for sporamin and beta-amylase from sweet potato". Mol. Gen. Genet. 244 (6): 563–71. PMID 7969025. 
  4. ^ Rushton, Paul; Macdonald, H., Huttly, A.K., Lazarus, C.M. and Hooley, R (1995). "Members of a new family of DNA-binding proteins bind to a conserved cis-element in the promoters of alpha-Amy2 genes". Plant Molecular Biology 29: 29: 691–702. PMID 8541496.  |accessdate= requires |url= (help)
  5. ^ Rushton PJ, Torres JT, Parniske M, Wernert P, Hahlbrock K, Somssich IE (October 1996). "Interaction of elicitor-induced DNA-binding proteins with elicitor response elements in the promoters of parsley PR1 genes". EMBO J. 15 (20): 5690–700. PMC 452313. PMID 8896462. 
  6. ^ Eulgem T, Rushton PJ, Robatzek S, Somssich IE (May 2000). "The WRKY superfamily of plant transcription factors". Trends Plant Sci. 5 (5): 199–206. doi:10.1016/S1360-1385(00)01600-9. PMID 10785665. 
  7. ^ Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Tomo Y, Hayami N, Terada T, Shirouzu M, Tanaka A, Seki M, Shinozaki K, Yokoyama S (March 2005). "Solution structure of an Arabidopsis WRKY DNA binding domain". Plant Cell 17 (3): 944–56. doi:10.1105/tpc.104.026435. PMC 1069710. PMID 15705956. 
  8. ^ Rushton, Paul. "The Lab of Dr. Paul Rushton". wordpress.com. Retrieved 17 June 2013. 

This article incorporates text from the public domain Pfam and InterPro IPR003657

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WRKY DNA -binding domain Provide feedback

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Literature references

  1. Eulgem T, Rushton PJ, Robatzek S, Somssich IE; , Trends Plant Sci 2000;5:199-206.: The WRKY superfamily of plant transcription factors. PUBMED:10785665 EPMC:10785665


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003657

The WRKY domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger- like motif. The WRKY domain is found in one or two copies in a superfamily of plant transcription factors involved in the regulation of various physiological programs that are unique to plants, including pathogen defence, senescence, trichome development and the biosynthesis of secondary metabolites. The WRKY domain binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core of the W box is essential for function and WRKY binding [PUBMED:10785665]. Some proteins known to contain a WRKY domain include Arabidopsis thaliana ZAP1 (Zinc-dependent Activator Protein-1) and AtWRKY44/TTG2, a protein involved in trichome development and anthocyanin pigmentation; and wild oat ABF1-2, two proteins involved in the gibberelic acid-induced expression of the alpha-Amy2 gene.

Structural studies indicate that this domain is a four-stranded beta-sheet with a zinc binding pocket, forming a novel zinc and DNA binding structure [PUBMED:15705956]. The WRKYGQK residues correspond to the most N-terminal beta-strand, which enables extensive hydrophobic interactions, contributing to the structural stability of the beta-sheet.

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 WRKY-GCM1 (CL0274), which contains the following 6 members:

AFT DBD_Tnp_Mut FAR1 FLYWCH GCM WRKY

Alignments

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  Seed
(34)
Full
(3051)
Representative proteomes NCBI
(2878)
Meta
(5)
RP15
(150)
RP35
(687)
RP55
(953)
RP75
(1178)
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Format an alignment

  Seed
(34)
Full
(3051)
Representative proteomes NCBI
(2878)
Meta
(5)
RP15
(150)
RP35
(687)
RP55
(953)
RP75
(1178)
Alignment:
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Sequence:
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  Seed
(34)
Full
(3051)
Representative proteomes NCBI
(2878)
Meta
(5)
RP15
(150)
RP35
(687)
RP55
(953)
RP75
(1178)
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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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: Pfam-B_85 (release 6.5)
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 34
Number in full: 3051
Average length of the domain: 54.90 aa
Average identity of full alignment: 54 %
Average coverage of the sequence by the domain: 20.61 %

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 21.0
Trusted cut-off 21.0 21.1
Noise cut-off 20.6 20.8
Model length: 60
Family (HMM) version: 10
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 WRKY domain has been found. There are 3 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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