5ydv - Revision history

OCA at 08:27, 22 November 2023

OCA — Wed, 22 Nov 2023 08:27:23 GMT

←Older revision		Revision as of 08:27, 22 November 2023
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	<StructureSection load='5ydv' size='340' side='right'caption='[[5ydv]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='5ydv' size='340' side='right'caption='[[5ydv]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ydv]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YDV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YDV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ydv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YDV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YDV FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=8TR:hypochlorous+acid'>8TR</scene~~>, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.752Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~qseD_2, DD95_15310, STMU2UK_04484 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=90371 "Bacillus typhimurium" Loeffler 1892])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8TR:hypochlorous+acid'>8TR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5ydv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ydv OCA], [~~http~~://pdbe.org/5ydv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ydv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ydv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ydv ProSAT]</span></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=5ydv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ydv OCA], [https://pdbe.org/5ydv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ydv RCSB], [https://www.ebi.ac.uk/pdbsum/5ydv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ydv ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q7CP75_SALTY Q7CP75_SALTY]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus typhimurium loeffler 1892]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ahn, J]]	+	[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
-	[[Category: Ha~~, N C~~]]	+	[[Category: Ahn J]]
-	[[Category: Hong, S]]	+	[[Category: Ha NC]]
-	[[Category: Jo, I]]	+	[[Category: Hong S]]
-	~~[[Category: Dna binding protein]]~~	+	[[Category: Jo I]]
-	~~[[Category: Hocl]]~~	+
-	~~[[Category: Hocl-specific transcription factor]]~~	+
-	~~[[Category: Hypochlorite]]~~	+
-	~~[[Category: Hypochlorous acid]]~~	+
-	~~[[Category: Hypt]]~~	+
-	~~[[Category: Lysr-type transcription regulator]]~~	+
-	~~[[Category: Regulatory domain~~]]	+

OCA at 06:32, 17 April 2019

OCA — Wed, 17 Apr 2019 06:32:29 GMT

←Older revision		Revision as of 06:32, 17 April 2019
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	==Regulatory domain of HypT from Salmonella typhimurium complexed with HOCl (HOCl-bound form)==		==Regulatory domain of HypT from Salmonella typhimurium complexed with HOCl (HOCl-bound form)==
-	<StructureSection load='5ydv' size='340' side='right' caption='[[5ydv]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='5ydv' size='340' side='right'caption='[[5ydv]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ydv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YDV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YDV FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ydv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YDV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YDV FirstGlance]. <br>
Line 8:		Line 8:
	<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=5ydv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ydv OCA], [http://pdbe.org/5ydv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ydv RCSB], [http://www.ebi.ac.uk/pdbsum/5ydv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ydv 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=5ydv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ydv OCA], [http://pdbe.org/5ydv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ydv RCSB], [http://www.ebi.ac.uk/pdbsum/5ydv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ydv ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Hypochlorous acid (HOCl) is generated in the immune system to kill microorganisms. In Escherichia coli, a hypochlorite-specific transcription regulator, HypT, has been characterized. HypT belongs to the LysR-type transcriptional regulator (LTTR) family that contains a DNA-binding domain (DBD) and a regulatory domain (RD). Here, we identified a hypT gene from Salmonella enterica serovar Typhimurium and determined crystal structures of the full-length HypT protein and the RD. The full-length structure reveals a type of tetrameric assembly in the LTTR family. Based on HOCl-bound and oxidation-mimicking structures, we identified a HOCl-driven methionine oxidation mechanism, in which the bound HOCl oxidizes a conserved methionine residue lining the putative ligand-binding site in the RD. Furthermore, we proposed a molecular model for the oxidized HypT, where methionine oxidation by HOCl results in a conformational change of the RD, inducing a counter rotation of the DBD dimers. Target genes that are regulated by HypT and their roles in Salmonella were also investigated. DNase I footprinting experiments revealed a DNA segment containing two pseudopalindromic motifs that are separated by approximately 100 bp, suggesting that only the oxidized structure makes a concomitant binding, forming a DNA loop. An understanding of the HypT-mediated mechanism would be helpful for controlling many pathogenic bacteria by counteracting bacterial HOCl defense mechanisms.
		+
		+	Structural basis for HOCl recognition and regulation mechanisms of HypT, a hypochlorite-specific transcriptional regulator.,Jo I, Kim D, No T, Hong S, Ahn J, Ryu S, Ha NC Proc Natl Acad Sci U S A. 2019 Feb 26;116(9):3740-3745. doi:, 10.1073/pnas.1811509116. Epub 2019 Feb 7. PMID:30733296<ref>PMID:30733296</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ydv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Bacillus typhimurium loeffler 1892]]		[[Category: Bacillus typhimurium loeffler 1892]]
		+	[[Category: Large Structures]]
	[[Category: Ahn, J]]		[[Category: Ahn, J]]
	[[Category: Ha, N C]]		[[Category: Ha, N C]]

OCA at 20:22, 2 December 2018

OCA — Sun, 02 Dec 2018 20:22:03 GMT

←Older revision		Revision as of 20:22, 2 December 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5ydv is ~~ON HOLD until Paper Publication~~	+	==Regulatory domain of HypT from Salmonella typhimurium complexed with HOCl (HOCl-bound form)==
-		+	<StructureSection load='5ydv' size='340' side='right' caption='[[5ydv]], [[Resolution\|resolution]] 1.75Å' scene=''>
-	~~Authors~~: Jo, I., ~~Hong~~, S., ~~Ahn, J~~., Ha, N.C.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ydv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YDV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YDV FirstGlance]. <br>
-	~~Description~~: ~~Regulatory domain of HypT from Salmonella~~ typhimurium ~~complexed with HOCl (HOCl-bound form)~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8TR:hypochlorous+acid'>8TR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">qseD_2, DD95_15310, STMU2UK_04484 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892])</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=5ydv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ydv OCA], [http://pdbe.org/5ydv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ydv RCSB], [http://www.ebi.ac.uk/pdbsum/5ydv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ydv ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bacillus typhimurium loeffler 1892]]
		+	[[Category: Ahn, J]]
		+	[[Category: Ha, N C]]
	[[Category: Hong, S]]		[[Category: Hong, S]]
	[[Category: Jo, I]]		[[Category: Jo, I]]
-	[[Category: ~~Ahn, J~~]]	+	[[Category: Dna binding protein]]
-	[[Category: ~~Ha, N.C~~]]	+	[[Category: Hocl]]
		+	[[Category: Hocl-specific transcription factor]]
		+	[[Category: Hypochlorite]]
		+	[[Category: Hypochlorous acid]]
		+	[[Category: Hypt]]
		+	[[Category: Lysr-type transcription regulator]]
		+	[[Category: Regulatory domain]]

OCA: Protected "5ydv" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 16:27:09 GMT

Protected "5ydv" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:27, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5ydv is ON HOLD until Paper Publication Authors: Jo, I., Hong, S., Ahn, J., Ha, N.C. Description: Regulatory domain of HypT from Salmonella typhimu...

OCA — Wed, 27 Sep 2017 16:27:08 GMT

New page: '''Unreleased structure''' The entry 5ydv is ON HOLD until Paper Publication Authors: Jo, I., Hong, S., Ahn, J., Ha, N.C. Description: Regulatory domain of HypT from Salmonella typhimu...

New page

'''Unreleased structure'''

The entry 5ydv is ON HOLD until Paper Publication

Authors: Jo, I., Hong, S., Ahn, J., Ha, N.C.

Description: Regulatory domain of HypT from Salmonella typhimurium complexed with HOCl (HOCl-bound form)
[[Category: Unreleased Structures]]
[[Category: Hong, S]]
[[Category: Jo, I]]
[[Category: Ahn, J]]
[[Category: Ha, N.C]]