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==Crystal structure of the DNA-binding domain of the response regulator VbrR from Vibrio parahaemolyticus== | ==Crystal structure of the DNA-binding domain of the response regulator VbrR from Vibrio parahaemolyticus== | ||
<StructureSection load='7e92' size='340' side='right'caption='[[7e92]]' scene=''> | <StructureSection load='7e92' size='340' side='right'caption='[[7e92]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7E92 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7E92 FirstGlance]. <br> | <table><tr><td colspan='2'>[[7e92]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"oceanomonas_parahaemolytica"_(fujino_et_al._1951)_miyamoto_et_al._1961 "oceanomonas parahaemolytica" (fujino et al. 1951) miyamoto et al. 1961]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7E92 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7E92 FirstGlance]. <br> | ||
</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=7e92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e92 OCA], [https://pdbe.org/7e92 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e92 RCSB], [https://www.ebi.ac.uk/pdbsum/7e92 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e92 ProSAT]</span></td></tr> | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ACS84_09205, C9I78_18460, CA163_10520, CGH73_12770, D5E78_24805, F0L89_03250, F0L99_22745, WR32_19050 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=670 "Oceanomonas parahaemolytica" (Fujino et al. 1951) Miyamoto et al. 1961])</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=7e92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e92 OCA], [https://pdbe.org/7e92 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e92 RCSB], [https://www.ebi.ac.uk/pdbsum/7e92 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e92 ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
VbrK and VbrR from the gastroenteritis-causing Vibrio parahaemolyticus are a histidine kinase and response regulator, respectively, that constitute a two-component regulatory system. VbrK responds to beta-lactam antibiotics or nitrate and activates VbrR via phosphorylation. Consequently, VbrR transcriptionally regulates the expression of beta-lactamase and ExsC and contributes to the survival or virulence of V. parahaemolyticus. Due to the unavailability of the VbrR structure, it remains unclear how VbrR is activated via its N-terminal receiver domain (RD) and recognizes dsDNA via its C-terminal DNA-binding domain (DBD). To reveal the mechanism underlying VbrR-mediated activation, we generated the phosphomimetic protein (VbrR(RD-D51E)) of the VbrR RD by replacing the D51 residue at the phosphorylation site with glutamate. VbrR(RD-D51E) exhibits a beta7alpha5 structure rather than the typical beta5alpha5 structure because it contains a unique two-stranded beta-sheet. The VbrR(RD-D51E) structure represents an active state in which the D51E residue interacts with the T78 residue. As a result, the Y97 residue adopts an inward conformation, allowing VbrR(RD-D51E) to dimerize using the alpha4-beta5-alpha5 face. These activation events are facilitated by a VbrR-specific residue, R52. Further structural study demonstrated that the VbrR DBD adopts a beta-strand-decorated three-helix structure. Based on a comparative structural study, we propose that VbrR recognizes dsDNA by inserting the alpha8 helix into the major groove of dsDNA and interacting with the minor groove of dsDNA via the beta11-beta12 region. Our findings will provide a new avenue for development of new antibacterial drugs for treating V. parahaemolyticus infections. | |||
Structural analysis of the activation and DNA interactions of the response regulator VbrR from Vibrio parahaemolyticus.,Cho SY, Yoon SI Biochem Biophys Res Commun. 2021 May 28;555:102-108. doi:, 10.1016/j.bbrc.2021.03.114. Epub 2021 Apr 1. PMID:33813268<ref>PMID:33813268</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7e92" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Cho | [[Category: Cho, S Y]] | ||
[[Category: Yoon | [[Category: Yoon, S I]] | ||
[[Category: Dna-binding domain]] | |||
[[Category: Response regulator]] | |||
[[Category: Transcription]] | |||
[[Category: Transcriptional regulation]] | |||
[[Category: Vbrr]] | |||
[[Category: Vibrio parahaemolyticus]] | |||
Revision as of 13:25, 19 May 2021
Crystal structure of the DNA-binding domain of the response regulator VbrR from Vibrio parahaemolyticusCrystal structure of the DNA-binding domain of the response regulator VbrR from Vibrio parahaemolyticus
Structural highlights
Publication Abstract from PubMedVbrK and VbrR from the gastroenteritis-causing Vibrio parahaemolyticus are a histidine kinase and response regulator, respectively, that constitute a two-component regulatory system. VbrK responds to beta-lactam antibiotics or nitrate and activates VbrR via phosphorylation. Consequently, VbrR transcriptionally regulates the expression of beta-lactamase and ExsC and contributes to the survival or virulence of V. parahaemolyticus. Due to the unavailability of the VbrR structure, it remains unclear how VbrR is activated via its N-terminal receiver domain (RD) and recognizes dsDNA via its C-terminal DNA-binding domain (DBD). To reveal the mechanism underlying VbrR-mediated activation, we generated the phosphomimetic protein (VbrR(RD-D51E)) of the VbrR RD by replacing the D51 residue at the phosphorylation site with glutamate. VbrR(RD-D51E) exhibits a beta7alpha5 structure rather than the typical beta5alpha5 structure because it contains a unique two-stranded beta-sheet. The VbrR(RD-D51E) structure represents an active state in which the D51E residue interacts with the T78 residue. As a result, the Y97 residue adopts an inward conformation, allowing VbrR(RD-D51E) to dimerize using the alpha4-beta5-alpha5 face. These activation events are facilitated by a VbrR-specific residue, R52. Further structural study demonstrated that the VbrR DBD adopts a beta-strand-decorated three-helix structure. Based on a comparative structural study, we propose that VbrR recognizes dsDNA by inserting the alpha8 helix into the major groove of dsDNA and interacting with the minor groove of dsDNA via the beta11-beta12 region. Our findings will provide a new avenue for development of new antibacterial drugs for treating V. parahaemolyticus infections. Structural analysis of the activation and DNA interactions of the response regulator VbrR from Vibrio parahaemolyticus.,Cho SY, Yoon SI Biochem Biophys Res Commun. 2021 May 28;555:102-108. doi:, 10.1016/j.bbrc.2021.03.114. Epub 2021 Apr 1. PMID:33813268[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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