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Structural basis of dimerization and dual W-box DNA recognition by rice WRKY domain

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...

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Autores principales: Cheng, Xiankun, Zhao, Yanxiang, Jiang, Qingshan, Yang, Jun, Zhao, Wensheng, Taylor, Ian A, Peng, You-Liang, Wang, Dongli, Liu, Junfeng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6486541/
https://www.ncbi.nlm.nih.gov/pubmed/30783673
http://dx.doi.org/10.1093/nar/gkz113
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author Cheng, Xiankun
Zhao, Yanxiang
Jiang, Qingshan
Yang, Jun
Zhao, Wensheng
Taylor, Ian A
Peng, You-Liang
Wang, Dongli
Liu, Junfeng
author_facet Cheng, Xiankun
Zhao, Yanxiang
Jiang, Qingshan
Yang, Jun
Zhao, Wensheng
Taylor, Ian A
Peng, You-Liang
Wang, Dongli
Liu, Junfeng
author_sort Cheng, Xiankun
collection PubMed
description 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 β4-β5 strands to form a dimer. The domain swapping occurs at the hinge region between the β3 and β4 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.
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spelling pubmed-64865412019-05-01 Structural basis of dimerization and dual W-box DNA recognition by rice WRKY domain Cheng, Xiankun Zhao, Yanxiang Jiang, Qingshan Yang, Jun Zhao, Wensheng Taylor, Ian A Peng, You-Liang Wang, Dongli Liu, Junfeng Nucleic Acids Res Structural Biology 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 β4-β5 strands to form a dimer. The domain swapping occurs at the hinge region between the β3 and β4 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. Oxford University Press 2019-05-07 2019-02-20 /pmc/articles/PMC6486541/ /pubmed/30783673 http://dx.doi.org/10.1093/nar/gkz113 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Structural Biology
Cheng, Xiankun
Zhao, Yanxiang
Jiang, Qingshan
Yang, Jun
Zhao, Wensheng
Taylor, Ian A
Peng, You-Liang
Wang, Dongli
Liu, Junfeng
Structural basis of dimerization and dual W-box DNA recognition by rice WRKY domain
title Structural basis of dimerization and dual W-box DNA recognition by rice WRKY domain
title_full Structural basis of dimerization and dual W-box DNA recognition by rice WRKY domain
title_fullStr Structural basis of dimerization and dual W-box DNA recognition by rice WRKY domain
title_full_unstemmed Structural basis of dimerization and dual W-box DNA recognition by rice WRKY domain
title_short Structural basis of dimerization and dual W-box DNA recognition by rice WRKY domain
title_sort structural basis of dimerization and dual w-box dna recognition by rice wrky domain
topic Structural Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6486541/
https://www.ncbi.nlm.nih.gov/pubmed/30783673
http://dx.doi.org/10.1093/nar/gkz113
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