6ir8: Difference between revisions
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==Rice WRKY/DNA complex== | ==Rice WRKY/DNA complex== | ||
<StructureSection load='6ir8' size='340' side='right' caption='[[6ir8]], [[Resolution|resolution]] 2.30Å' scene=''> | <StructureSection load='6ir8' size='340' side='right'caption='[[6ir8]], [[Resolution|resolution]] 2.30Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6ir8]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IR8 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6ir8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa_Japonica_Group Oryza sativa Japonica Group] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IR8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IR8 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <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=6ir8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ir8 OCA], [https://pdbe.org/6ir8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ir8 RCSB], [https://www.ebi.ac.uk/pdbsum/6ir8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ir8 ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/B9FNW2_ORYSJ B9FNW2_ORYSJ] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
In rice, the critical regulator of the salicylic acid signalling pathway is OsWRKY45, a transcription factor (TF) of the WRKY TF family that functions by binding to the W-box of gene promoters, but the structural basis of OsWRKY45/W-box DNA recognition is unknown. Here, we show the crystal structure of the DNA binding domain of OsWRKY45 (OsWRKY45-DBD, i.e. the WRKY and zinc finger domain) in complex with a W-box DNA. Surprisingly, two OsWRKY45-DBD molecules exchange beta4-beta5 strands to form a dimer. The domain swapping occurs at the hinge region between the beta3 and beta4 strands, and is bridged and stabilized by zinc ion via coordinating residues from different chains. The dimer contains two identical DNA binding domains that interact with the major groove of W-box DNA. In addition to hydrophobic and direct hydrogen bonds, water mediated hydrogen bonds are also involved in base-specific interaction between protein and DNA. Finally, we discussed the cause and consequence of domain swapping of OsWRKY45-DBD, and based on our work and that of previous studies present a detailed mechanism of W-box recognition by WRKY TFs. This work reveals a novel dimerization and DNA-binding mode of WRKY TFs, and an intricate picture of the WRKY/W-box DNA recognition. | |||
Structural basis of dimerization and dual W-box DNA recognition by rice WRKY domain.,Cheng X, Zhao Y, Jiang Q, Yang J, Zhao W, Taylor IA, Peng YL, Wang D, Liu J Nucleic Acids Res. 2019 Feb 20. pii: 5345154. doi: 10.1093/nar/gkz113. PMID:30783673<ref>PMID:30783673</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6ir8" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Oryza sativa Japonica Group]] | ||
[[Category: | [[Category: Synthetic construct]] | ||
[[Category: | [[Category: Cheng X]] | ||
[[Category: | [[Category: Liu J]] | ||
[[Category: | [[Category: Wang D]] | ||