6ide - Revision history

OCA at 10:32, 27 March 2024

OCA — Wed, 27 Mar 2024 10:32:40 GMT

←Older revision		Revision as of 10:32, 27 March 2024
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	==Crystal structure of the Vibrio cholera VqmA-Ligand-DNA complex provides molecular mechanisms for drug design==		==Crystal structure of the Vibrio cholera VqmA-Ligand-DNA complex provides molecular mechanisms for drug design==
-	<StructureSection load='6ide' size='340' side='right' caption='[[6ide]], [[Resolution\|resolution]] 2.51Å' scene=''>	+	<StructureSection load='6ide' size='340' side='right'caption='[[6ide]], [[Resolution\|resolution]] 2.51Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ide]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillo_virgola_del_koch"_trevisan_1884 "bacillo virgola del koch" trevisan 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IDE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6IDE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ide]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IDE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IDE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A1U:3,5-dimethylpyrazin-2-ol'>A1U</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]] 2.51Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6ide FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ide OCA], [~~http~~://pdbe.org/6ide PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ide RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ide PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ide ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1U:3,5-dimethylpyrazin-2-ol'>A1U</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=6ide FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ide OCA], [https://pdbe.org/6ide PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ide RCSB], [https://www.ebi.ac.uk/pdbsum/6ide PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ide ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	VqmA is a highly conserved transcriptional regulator of the quorum sensing system of Vibrio cholerae, a major human pathogen that continues to imperil human health. VqmA represses biofilm formation and plays an important role in V. cholerae pathogenicity in the human host. Despite the good understanding of VqmA's biological function, the molecular mechanisms by which its specific ligand (and effector), 3,5-dimethylpyrazine-2-ol (DPO), controls transcription of the target gene, vqmR, remain obscure. To elucidate the molecular mechanism of DPO binding, we used structural analyses and biochemical assays to study the V. cholerae VqmA-DPO-DNA complex. These analyses revealed that VqmA contains an N-terminal homodimer domain (PAS) and a C-terminal DNA binding domain (DBD). We observed that VqmA directly binds to a DPO molecule via a compact hydrophobic pocket, consisting of a six-stranded antiparallel beta-sheet and several alpha-helices. We also found that the VqmA dimer interacts with the quasi-palindromic sequence of the vqmR promoter through its DBD. The results of the biochemical studies indicated that a water atom and the VqmA residues Phe67 and Lys101 play a key role in effector recognition, which is also assisted by Tyr36 and Phe99. This is the first molecular-level view of the VqmA dimer bound to DPO and DNA. The structure-function analyses presented here improve our understanding of the complex mechanisms in the transcriptional regulation of VqmA in Vibrio spp. and may inform the design of drugs to manage V. cholerae infections.
-
-	Crystal structure of the Vibrio cholerae VqmA-ligand-DNA complex provides insight into ligand-binding mechanisms relevant for drug design.,Wu H, Li M, Guo H, Zhou H, Li B, Xu Q, Xu C, Yu F, He J J Biol Chem. 2019 Jan 4. pii: RA118.006082. doi: 10.1074/jbc.RA118.006082. PMID:30610119<ref>PMID:30610119</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6ide" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillo virgola del koch trevisan 1884~~]]	+	[[Category: Large Structures]]
-	[[Category: Guo~~, H J~~]]	+	[[Category: Vibrio cholerae]]
-	[[Category: He~~, J H~~]]	+	[[Category: Guo HJ]]
-	[[Category: Li, B]]	+	[[Category: He JH]]
-	[[Category: Li~~, M J~~]]	+	[[Category: Li B]]
-	[[Category: Wu, H]]	+	[[Category: Li MJ]]
-	[[Category: Xu~~, C Y~~]]	+	[[Category: Wu H]]
-	[[Category: Xu, Q]]	+	[[Category: Xu CY]]
-	[[Category: Yu, F]]	+	[[Category: Xu Q]]
-	[[Category: Zhou, H]]	+	[[Category: Yu F]]
-	~~[[Category: Quorum sensing]]~~	+	[[Category: Zhou H]]
-	~~[[Category: Transcription regulator]]~~	+
-	~~[[Category: Transcription-dna complex]]~~	+
-	~~[[Category: Vibrio cholera~~]]	+

OCA at 08:28, 6 March 2019

OCA — Wed, 06 Mar 2019 08:28:36 GMT

←Older revision		Revision as of 08:28, 6 March 2019
Line 1:		Line 1:

	==Crystal structure of the Vibrio cholera VqmA-Ligand-DNA complex provides molecular mechanisms for drug design==		==Crystal structure of the Vibrio cholera VqmA-Ligand-DNA complex provides molecular mechanisms for drug design==
-	<StructureSection load='6ide' size='340' side='right' caption='[[6ide]], [[Resolution\|resolution]] 2.51Å' scene=''>	+	<StructureSection load='6ide' size='340' side='right' caption='[[6ide]], [[Resolution\|resolution]] 2.51Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ide]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IDE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IDE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ide]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillo_virgola_del_koch"_trevisan_1884 "bacillo virgola del koch" trevisan 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IDE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IDE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A1U:3,5-dimethylpyrazin-2-ol'>A1U</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A1U:3,5-dimethylpyrazin-2-ol'>A1U</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ide FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ide OCA], [http://pdbe.org/6ide PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ide RCSB], [http://www.ebi.ac.uk/pdbsum/6ide PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ide ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ide FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ide OCA], [http://pdbe.org/6ide PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ide RCSB], [http://www.ebi.ac.uk/pdbsum/6ide PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ide ProSAT]</span></td></tr>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillo virgola del koch trevisan 1884]]
	[[Category: Guo, H J]]		[[Category: Guo, H J]]
	[[Category: He, J H]]		[[Category: He, J H]]

OCA at 12:10, 16 January 2019

OCA — Wed, 16 Jan 2019 12:10:49 GMT

←Older revision		Revision as of 12:10, 16 January 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ide is ~~ON HOLD until Sep 09 2020~~	+	==Crystal structure of the Vibrio cholera VqmA-Ligand-DNA complex provides molecular mechanisms for drug design==
		+	<StructureSection load='6ide' size='340' side='right' caption='[[6ide]], [[Resolution\|resolution]] 2.51Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6ide]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IDE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IDE FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A1U:3,5-dimethylpyrazin-2-ol'>A1U</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ide FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ide OCA], [http://pdbe.org/6ide PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ide RCSB], [http://www.ebi.ac.uk/pdbsum/6ide PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ide ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	VqmA is a highly conserved transcriptional regulator of the quorum sensing system of Vibrio cholerae, a major human pathogen that continues to imperil human health. VqmA represses biofilm formation and plays an important role in V. cholerae pathogenicity in the human host. Despite the good understanding of VqmA's biological function, the molecular mechanisms by which its specific ligand (and effector), 3,5-dimethylpyrazine-2-ol (DPO), controls transcription of the target gene, vqmR, remain obscure. To elucidate the molecular mechanism of DPO binding, we used structural analyses and biochemical assays to study the V. cholerae VqmA-DPO-DNA complex. These analyses revealed that VqmA contains an N-terminal homodimer domain (PAS) and a C-terminal DNA binding domain (DBD). We observed that VqmA directly binds to a DPO molecule via a compact hydrophobic pocket, consisting of a six-stranded antiparallel beta-sheet and several alpha-helices. We also found that the VqmA dimer interacts with the quasi-palindromic sequence of the vqmR promoter through its DBD. The results of the biochemical studies indicated that a water atom and the VqmA residues Phe67 and Lys101 play a key role in effector recognition, which is also assisted by Tyr36 and Phe99. This is the first molecular-level view of the VqmA dimer bound to DPO and DNA. The structure-function analyses presented here improve our understanding of the complex mechanisms in the transcriptional regulation of VqmA in Vibrio spp. and may inform the design of drugs to manage V. cholerae infections.

-	~~Authors:~~ Wu, H., Li, M~~.J.~~, Guo, H~~.J.~~, Zhou, H., Li, B., Xu, Q., Xu, C~~.Y.~~, Yu, F., He, J.H.	+	Crystal structure of the Vibrio cholerae VqmA-ligand-DNA complex provides insight into ligand-binding mechanisms relevant for drug design.,Wu H, Li M, Guo H, Zhou H, Li B, Xu Q, Xu C, Yu F, He J J Biol Chem. 2019 Jan 4. pii: RA118.006082. doi: 10.1074/jbc.RA118.006082. PMID:30610119<ref>PMID:30610119</ref>

-	~~Description: Crystal structure~~ of the ~~Vibrio cholera VqmA~~-~~Ligand~~-~~DNA complex provides molecular mechanisms for drug design~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Zhou~~, H]]	+	<div class="pdbe-citations 6ide" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Guo~~, ~~H.J~~]]	+	== References ==
-	[[Category: He, J.H]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Guo, H J]]
		+	[[Category: He, J H]]
		+	[[Category: Li, B]]
		+	[[Category: Li, M J]]
		+	[[Category: Wu, H]]
		+	[[Category: Xu, C Y]]
	[[Category: Xu, Q]]		[[Category: Xu, Q]]
	[[Category: Yu, F]]		[[Category: Yu, F]]
-	[[Category: Wu, H]]	+	[[Category: Zhou, H]]
-	[[Category: ~~Xu, C.Y~~]]	+	[[Category: Quorum sensing]]
-	[[Category: ~~Li, M.J~~]]	+	[[Category: Transcription regulator]]
-	[[Category: ~~Li, B~~]]	+	[[Category: Transcription-dna complex]]
		+	[[Category: Vibrio cholera]]

OCA at 06:19, 10 October 2018

OCA — Wed, 10 Oct 2018 06:19:03 GMT

←Older revision		Revision as of 06:19, 10 October 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6ide is ON HOLD	+	The entry 6ide is ON HOLD until Sep 09 2020

	Authors: Wu, H., Li, M.J., Guo, H.J., Zhou, H., Li, B., Xu, Q., Xu, C.Y., Yu, F., He, J.H.		Authors: Wu, H., Li, M.J., Guo, H.J., Zhou, H., Li, B., Xu, Q., Xu, C.Y., Yu, F., He, J.H.
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Zhou, H]]		[[Category: Zhou, H]]
		+	[[Category: Guo, H.J]]
	[[Category: He, J.H]]		[[Category: He, J.H]]
	[[Category: Xu, Q]]		[[Category: Xu, Q]]
	[[Category: Yu, F]]		[[Category: Yu, F]]
-	[[Category: Li, M.J]]
-	[[Category: Guo, H.J]]
	[[Category: Wu, H]]		[[Category: Wu, H]]
	[[Category: Xu, C.Y]]		[[Category: Xu, C.Y]]
		+	[[Category: Li, M.J]]
	[[Category: Li, B]]		[[Category: Li, B]]

OCA: Protected "6ide" [edit=sysop:move=sysop]

OCA — Wed, 19 Sep 2018 18:17:45 GMT

Protected "6ide" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:17, 19 September 2018

OCA: New page: '''Unreleased structure''' The entry 6ide is ON HOLD Authors: Wu, H., Li, M.J., Guo, H.J., Zhou, H., Li, B., Xu, Q., Xu, C.Y., Yu, F., He, J.H. Description: Crystal structure of the Vi...

OCA — Wed, 19 Sep 2018 18:17:44 GMT

New page: '''Unreleased structure''' The entry 6ide is ON HOLD Authors: Wu, H., Li, M.J., Guo, H.J., Zhou, H., Li, B., Xu, Q., Xu, C.Y., Yu, F., He, J.H. Description: Crystal structure of the Vi...

New page

'''Unreleased structure'''

The entry 6ide is ON HOLD

Authors: Wu, H., Li, M.J., Guo, H.J., Zhou, H., Li, B., Xu, Q., Xu, C.Y., Yu, F., He, J.H.

Description: Crystal structure of the Vibrio cholera VqmA-Ligand-DNA complex provides molecular mechanisms for drug design
[[Category: Unreleased Structures]]
[[Category: Zhou, H]]
[[Category: He, J.H]]
[[Category: Xu, Q]]
[[Category: Yu, F]]
[[Category: Li, M.J]]
[[Category: Guo, H.J]]
[[Category: Wu, H]]
[[Category: Xu, C.Y]]
[[Category: Li, B]]