This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1wj2

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Solution Structure of the C-terminal WRKY Domain of AtWRKY4

Structural highlights

1wj2 is a 1 chain structure with sequence from Arabidopsis thaliana. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

WRKY4_ARATH Transcription factor. Interacts specifically with the W box (5'-(T)TGAC[CT]-3'), a frequently occurring elicitor-responsive cis-acting element (By similarity).

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The WRKY proteins comprise a major family of transcription factors that are essential in pathogen and salicylic acid responses of higher plants as well as a variety of plant-specific reactions. They share a DNA binding domain, designated as the WRKY domain, which contains an invariant WRKYGQK sequence and a CX4-5CX22-23HXH zinc binding motif. Herein, we report the NMR solution structure of the C-terminal WRKY domain of the Arabidopsis thaliana WRKY4 protein. The structure consists of a four-stranded beta-sheet, with a zinc binding pocket formed by the conserved Cys/His residues located at one end of the beta-sheet, revealing a novel zinc and DNA binding structure. The WRKYGQK residues correspond to the most N-terminal beta-strand, kinked in the middle of the sequence by the Gly residue, which enables extensive hydrophobic interactions involving the Trp residue and contributes to the structural stability of the beta-sheet. Based on a profile of NMR chemical shift perturbations, we propose that the same strand enters the DNA groove and forms contacts with the DNA bases.

Solution structure of an Arabidopsis WRKY DNA binding domain.,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 Plant Cell. 2005 Mar;17(3):944-56. Epub 2005 Feb 10. PMID:15705956^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ 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. Solution structure of an Arabidopsis WRKY DNA binding domain. Plant Cell. 2005 Mar;17(3):944-56. Epub 2005 Feb 10. PMID:15705956 doi:http://dx.doi.org/10.1105/tpc.104.026435

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1wj2"

@@ Line 1: / Line 1: @@
 ==Solution Structure of the C-terminal WRKY Domain of AtWRKY4==
-<StructureSection load='1wj2' size='340' side='right'caption='[[1wj2]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='1wj2' size='340' side='right'caption='[[1wj2]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1wj2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WJ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WJ2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1wj2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WJ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WJ2 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">WRKY4 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1wj2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wj2 OCA], [https://pdbe.org/1wj2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wj2 RCSB], [https://www.ebi.ac.uk/pdbsum/1wj2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wj2 ProSAT], [https://www.topsan.org/Proteins/RSGI/1wj2 TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/WRKY4_ARATH WRKY4_ARATH]] Transcription factor. Interacts specifically with the W box (5'-(T)TGAC[CT]-3'), a frequently occurring elicitor-responsive cis-acting element (By similarity).
+[https://www.uniprot.org/uniprot/WRKY4_ARATH WRKY4_ARATH] Transcription factor. Interacts specifically with the W box (5'-(T)TGAC[CT]-3'), a frequently occurring elicitor-responsive cis-acting element (By similarity).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
 [[Category: Large Structures]]
-[[Category: Inoue, M]]
+[[Category: Inoue M]]
-[[Category: Kigawa, T]]
+[[Category: Kigawa T]]
-[[Category: Structural genomic]]
+[[Category: Yamasaki K]]
-[[Category: Yamasaki, K]]
+[[Category: Yokoyama S]]
-[[Category: Yokoyama, S]]
-[[Category: Dna binding protein]]
-[[Category: Dna-binding domain]]
-[[Category: Rsgi]]
-[[Category: Zinc-binding]]

1wj2

From Proteopedia

Current revision

Solution Structure of the C-terminal WRKY Domain of AtWRKY4

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox