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Protein

Probable WRKY transcription factor 4

Gene

WRKY4

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Transcription factor that binds specifically to the W box (5'-(T)TGAC[CT]-3'), a frequently occurring elicitor-responsive cis-acting element. Has a positive role in resistance to necrotrophic pathogens (e.g. Botrytis cinerea), but a negative effect on plant resistance to biotrophic pathogens (e.g. Pseudomonas syringae).2 Publications

Cofactori

Zn2+2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi434 – 4341Zinc2 Publications
Metal bindingi436 – 4361Zinc2 Publications
Metal bindingi439 – 4391Zinc2 Publications
Metal bindingi463 – 4631Zinc; via pros nitrogen2 Publications
Metal bindingi465 – 4651Zinc; via tele nitrogen2 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi223 – 28765WRKY 1PROSITE-ProRule annotationAdd
BLAST
DNA bindingi403 – 46866WRKY 2PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • DNA binding Source: TAIR
  • metal ion binding Source: UniProtKB-KW
  • sequence-specific DNA binding Source: UniProtKB
  • transcription factor activity, sequence-specific DNA binding Source: TAIR
  • transcription regulatory region DNA binding Source: UniProtKB

GO - Biological processi

  • defense response Source: UniProtKB-KW
  • negative regulation of defense response to bacterium Source: UniProtKB
  • regulation of defense response to fungus Source: UniProtKB
  • response to ethylene Source: UniProtKB
  • response to jasmonic acid Source: UniProtKB
  • response to salicylic acid Source: UniProtKB
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

Plant defense, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Probable WRKY transcription factor 4
Alternative name(s):
WRKY DNA-binding protein 4
Gene namesi
Name:WRKY4
Ordered Locus Names:At1g13960
ORF Names:F16A14.18, F7A19.5
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 1

Organism-specific databases

TAIRiAT1G13960.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation1 Publication

GO - Cellular componenti

  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

Increased sensitivity to the necrotrophic fungal pathogen Botrytis cinerea.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 514514Probable WRKY transcription factor 4PRO_0000133647Add
BLAST

Proteomic databases

PaxDbiQ9XI90.
PRIDEiQ9XI90.

PTM databases

iPTMnetiQ9XI90.

Expressioni

Tissue specificityi

In young, mature and senescent leaves.1 Publication

Inductioni

By biotic and abiotic stresses such as pathogen infection (e.g. Botrytis cinerea and Pseudomonas syringae), salicylic acid (SA), jasmonic acid (JA), ethylene (ACC), liquid infiltration or spraying, and strongly during leaf senescence.3 Publications

Gene expression databases

GenevisibleiQ9XI90. AT.

Interactioni

Protein-protein interaction databases

BioGridi23196. 1 interaction.
STRINGi3702.AT1G13960.1.

Structurei

Secondary structure

1
514
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi410 – 4123Combined sources
Beta strandi418 – 4203Combined sources
Turni423 – 4264Combined sources
Beta strandi429 – 4357Combined sources
Beta strandi440 – 4489Combined sources
Turni449 – 4524Combined sources
Beta strandi453 – 4619Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WJ2NMR-A399-469[»]
2LEXNMR-A399-469[»]
ProteinModelPortaliQ9XI90.
SMRiQ9XI90. Positions 229-287, 399-469.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9XI90.

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi73 – 8412Poly-AlaAdd
BLAST

Sequence similaritiesi

Contains 2 WRKY DNA-binding domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiENOG410IDX2. Eukaryota.
ENOG410YBRT. LUCA.
HOGENOMiHOG000242409.
InParanoidiQ9XI90.
OMAiNRGSSEL.
PhylomeDBiQ9XI90.

Family and domain databases

Gene3Di2.20.25.80. 2 hits.
InterProiIPR003657. WRKY_dom.
[Graphical view]
PfamiPF03106. WRKY. 2 hits.
[Graphical view]
SMARTiSM00774. WRKY. 2 hits.
[Graphical view]
SUPFAMiSSF118290. SSF118290. 2 hits.
PROSITEiPS50811. WRKY. 2 hits.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9XI90-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MSEKEEAPST SKSTGAPSRP TLSLPPRPFS EMFFNGGVGF SPGPMTLVSN
60 70 80 90 100
MFPDSDEFRS FSQLLAGAMS SPATAAAAAA AATASDYQRL GEGTNSSSGD
110 120 130 140 150
VDPRFKQNRP TGLMISQSQS PSMFTVPPGL SPAMLLDSPS FLGLFSPVQG
160 170 180 190 200
SYGMTHQQAL AQVTAQAVQA NANMQPQTEY PPPSQVQSFS SGQAQIPTSA
210 220 230 240 250
PLPAQRETSD VTIIEHRSQQ PLNVDKPADD GYNWRKYGQK QVKGSEFPRS
260 270 280 290 300
YYKCTNPGCP VKKKVERSLD GQVTEIIYKG QHNHEPPQNT KRGNKDNTAN
310 320 330 340 350
INGSSINNNR GSSELGASQF QTNSSNKTKR EQHEAVSQAT TTEHLSEASD
360 370 380 390 400
GEEVGNGETD VREKDENEPD PKRRSTEVRI SEPAPAASHR TVTEPRIIVQ
410 420 430 440 450
TTSEVDLLDD GYRWRKYGQK VVKGNPYPRS YYKCTTPGCG VRKHVERAAT
460 470 480 490 500
DPKAVVTTYE GKHNHDLPAA KSSSHAAAAA QLRPDNRPGG LANLNQQQQQ
510
QPVARLRLKE EQTT
Length:514
Mass (Da):55,816
Last modified:May 15, 2002 - v2
Checksum:i01010F8745C420C5
GO
Isoform 2 (identifier: Q9XI90-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     112-147: GLMISQSQSPSMFTVPPGLSPAMLLDSPSFLGLFSP → AVLDLICNI

Show »
Length:487
Mass (Da):53,050
Checksum:iB046542E120086C7
GO

Sequence cautioni

The sequence AAD39282.1 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence AAF79402.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei112 – 14736GLMIS…GLFSP → AVLDLICNI in isoform 2. 1 PublicationVSP_008969Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF224703 mRNA. Translation: AAK28313.1.
AF425835 mRNA. Translation: AAL13048.1.
AC007576 Genomic DNA. Translation: AAD39282.1. Sequence problems.
AC068197 Genomic DNA. Translation: AAF79402.1. Sequence problems.
CP002684 Genomic DNA. Translation: AEE29089.1.
CP002684 Genomic DNA. Translation: AEE29090.1.
AY045676 mRNA. Translation: AAK74034.1.
BT002629 mRNA. Translation: AAO11545.1.
PIRiG86272.
RefSeqiNP_172849.1. NM_101262.2. [Q9XI90-1]
NP_849658.1. NM_179327.1. [Q9XI90-2]
UniGeneiAt.20024.

Genome annotation databases

EnsemblPlantsiAT1G13960.1; AT1G13960.1; AT1G13960. [Q9XI90-1]
GeneIDi837956.
KEGGiath:AT1G13960.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF224703 mRNA. Translation: AAK28313.1.
AF425835 mRNA. Translation: AAL13048.1.
AC007576 Genomic DNA. Translation: AAD39282.1. Sequence problems.
AC068197 Genomic DNA. Translation: AAF79402.1. Sequence problems.
CP002684 Genomic DNA. Translation: AEE29089.1.
CP002684 Genomic DNA. Translation: AEE29090.1.
AY045676 mRNA. Translation: AAK74034.1.
BT002629 mRNA. Translation: AAO11545.1.
PIRiG86272.
RefSeqiNP_172849.1. NM_101262.2. [Q9XI90-1]
NP_849658.1. NM_179327.1. [Q9XI90-2]
UniGeneiAt.20024.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WJ2NMR-A399-469[»]
2LEXNMR-A399-469[»]
ProteinModelPortaliQ9XI90.
SMRiQ9XI90. Positions 229-287, 399-469.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi23196. 1 interaction.
STRINGi3702.AT1G13960.1.

PTM databases

iPTMnetiQ9XI90.

Proteomic databases

PaxDbiQ9XI90.
PRIDEiQ9XI90.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT1G13960.1; AT1G13960.1; AT1G13960. [Q9XI90-1]
GeneIDi837956.
KEGGiath:AT1G13960.

Organism-specific databases

TAIRiAT1G13960.

Phylogenomic databases

eggNOGiENOG410IDX2. Eukaryota.
ENOG410YBRT. LUCA.
HOGENOMiHOG000242409.
InParanoidiQ9XI90.
OMAiNRGSSEL.
PhylomeDBiQ9XI90.

Miscellaneous databases

EvolutionaryTraceiQ9XI90.
PROiQ9XI90.

Gene expression databases

GenevisibleiQ9XI90. AT.

Family and domain databases

Gene3Di2.20.25.80. 2 hits.
InterProiIPR003657. WRKY_dom.
[Graphical view]
PfamiPF03106. WRKY. 2 hits.
[Graphical view]
SMARTiSM00774. WRKY. 2 hits.
[Graphical view]
SUPFAMiSSF118290. SSF118290. 2 hits.
PROSITEiPS50811. WRKY. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Evidence for an important role of WRKY DNA binding proteins in the regulation of NPR1 gene expression."
    Yu D., Chen C., Chen Z.
    Plant Cell 13:1527-1540(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), INDUCTION.
  2. "Arabidopsis thaliana transcription factor WRKY4."
    Ulker B., Kushnir S., Somssich I.E.
    Submitted (SEP-2001) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
    Strain: cv. Columbia.
    Tissue: Flower.
  3. "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
    Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K.
    , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
    Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  4. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  5. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Strain: cv. Columbia.
  6. "A new member of the Arabidopsis WRKY transcription factor family, AtWRKY6, is associated with both senescence- and defence-related processes."
    Robatzek S., Somssich I.E.
    Plant J. 28:123-133(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY, INDUCTION.
  7. "Roles of Arabidopsis WRKY3 and WRKY4 transcription factors in plant responses to pathogens."
    Lai Z., Vinod K., Zheng Z., Fan B., Chen Z.
    BMC Plant Biol. 8:68-68(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION, INDUCTION BY BIOTIC AND ABIOTIC STRESSES.
  8. Cited for: STRUCTURE BY NMR OF 399-469 IN COMPLEX WITH ZINC, COFACTOR, DNA BINDING.
  9. "Structural basis for sequence-specific DNA recognition by an Arabidopsis WRKY transcription factor."
    Yamasaki K., Kigawa T., Watanabe S., Inoue M., Yamasaki T., Seki M., Shinozaki K., Yokoyama S.
    J. Biol. Chem. 287:7683-7691(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 399-469 IN COMPLEX WITH ZINC AND W-BOX DNA, DNA BINDING, COFACTOR, FUNCTION.

Entry informationi

Entry nameiWRKY4_ARATH
AccessioniPrimary (citable) accession number: Q9XI90
Secondary accession number(s): Q93WN8, Q9LMG1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 15, 2002
Last sequence update: May 15, 2002
Last modified: June 8, 2016
This is version 113 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.