2lex: Difference between revisions

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 ==Complex of the C-terminal WRKY domain of AtWRKY4 and a W-box DNA==
-<StructureSection load='2lex' size='340' side='right' caption='[[2lex]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2lex' size='340' side='right'caption='[[2lex]]' scene=''>
 == Structural highlights ==
-[[2lex]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LEX OCA]. <br>
+<table><tr><td colspan='2'>[[2lex]] is a 3 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=2LEX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LEX FirstGlance]. <br>
-<b>[[Ligand|Ligands:]]</b> <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>
+<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>
-<b>Resources:</b> <span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2lex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lex OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lex RCSB], [http://www.ebi.ac.uk/pdbsum/2lex PDBsum]</span><br>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2lex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lex OCA], [https://pdbe.org/2lex PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lex RCSB], [https://www.ebi.ac.uk/pdbsum/2lex PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lex ProSAT]</span></td></tr>
-== Publication Abstract from PubMed ==
+</table>
-The WRKY family transcription factors regulate plant-specific reactions that are mostly related to biotic and abiotic stresses. They share the WRKY domain that recognizes a DNA element (TTCAC[C/T]), termed W-box, in target genes. Here we determined the solution structure of the C-terminal WRKY domain of Arabidopsis WRKY4 in complex with the W-box DNA by NMR. A four-stranded beta-sheet enters the major groove of DNA in an atypical mode termed the beta-wedge, where the sheet is nearly perpendicular to the DNA helical axis. Residues in the conserved WRKYGQK motif contact with DNA bases mainly through extensive apolar contacts with thymine methyl groups. The importance of these contacts was verified by substituting the relevant T bases with U and by surface plasmon resonance (SPR) analyses of DNA binding.
+== 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).
-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. 2012 Jan 4. PMID:22219184<ref>PMID:22219184</ref>
-From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Arabidopsis thaliana]]
-[[Category: Inoue, M.]]
+[[Category: Large Structures]]
-[[Category: Kigawa, T.]]
+[[Category: Inoue M]]
-[[Category: Watanabe, S.]]
+[[Category: Kigawa T]]
-[[Category: Yamasaki, K.]]
+[[Category: Watanabe S]]
-[[Category: Yokoyama, S.]]
+[[Category: Yamasaki K]]
-[[Category: Transcription]]
+[[Category: Yokoyama S]]
-[[Category: Transcription-dna complex]]