5ymr - Revision history

OCA at 10:24, 27 March 2024

OCA — Wed, 27 Mar 2024 10:24:14 GMT

←Older revision		Revision as of 10:24, 27 March 2024
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	<StructureSection load='5ymr' size='340' side='right'caption='[[5ymr]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='5ymr' size='340' side='right'caption='[[5ymr]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ymr]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Desvh Desvh~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YMR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YMR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ymr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._Hildenborough Desulfovibrio vulgaris str. Hildenborough]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YMR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YMR FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=8X3:2~~-~~hydroxyethylsulfonic+acid'>8X3</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.4Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~DVU_2824 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=882 DESVH])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8X3:2-hydroxyethylsulfonic+acid'>8X3</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=5ymr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ymr OCA], [~~http~~://pdbe.org/5ymr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ymr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ymr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ymr 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=5ymr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ymr OCA], [https://pdbe.org/5ymr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ymr RCSB], [https://www.ebi.ac.uk/pdbsum/5ymr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ymr ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/ISLA_DESVH ISLA_DESVH] Involved in an anaerobic respiration pathway that converts the sulfonate isethionate (2-hydroxyethanesulfonate) to ammonia, acetate and sulfide. Catalyzes the radical-mediated C-S bond cleavage of isethionate (2-hydroxyethanesulfonate) to form sulfite and acetaldehyde. Shows no activity with taurine or ethanolamine as substrates.<ref>PMID:30962433</ref>
-	~~Bacterial degradation of organosulfonates plays an important role in sulfur recycling, and has been extensively studied~~. ~~However, this process~~ in anaerobic ~~bacteria especially gut bacteria is little known despite of its potential significant impact on human health with~~ the ~~production of toxic H2S. Here~~, ~~we describe the structural~~ and ~~biochemical characterization of an oxygen-sensitive enzyme that catalyzes~~ the radical-mediated C-S bond cleavage of isethionate to form sulfite and acetaldehyde. ~~We demonstrate its involvement in pathways that enables C2 sulfonates to be used~~ as ~~terminal electron acceptors for anaerobic respiration in sulfate- and sulfite-reducing bacteria~~. Furthermore, it plays a key role in converting bile salt-derived taurine into H2S in the disease-associated gut bacterium Bilophila wadsworthia. The enzymes and transporters in these anaerobic pathways expand our understanding of microbial sulfur metabolism, and help deciphering the complex web of microbial pathways involved in the transformation of sulfur compounds in the gut.	+
-		+
-	Radical-mediated C-S bond cleavage in C2 sulfonate degradation by anaerobic bacteria.,Xing M, Wei Y, Zhou Y, Zhang J, Lin L, Hu Y, Hua G, N Nanjaraj Urs A, Liu D, Wang F, Guo C, Tong Y, Li M, Liu Y, Ang EL, Zhao H, Yuchi Z, Zhang Y Nat Commun. 2019 Apr 8;10(1):1609. doi: 10.1038/s41467-019-09618-8. PMID:30962433<ref>PMID:30962433</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5ymr" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Desvh~~]]	+	[[Category: Desulfovibrio vulgaris str. Hildenborough]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ang, E]]	+	[[Category: Ang E]]
-	[[Category: Guo, C]]	+	[[Category: Guo C]]
-	[[Category: Hu, Y]]	+	[[Category: Hu Y]]
-	[[Category: Hua, G]]	+	[[Category: Hua G]]
-	[[Category: Lin, L]]	+	[[Category: Lin L]]
-	[[Category: Wei, Y]]	+	[[Category: Wei Y]]
-	[[Category: Xing, M]]	+	[[Category: Xing M]]
-	[[Category: Yuchi, Z]]	+	[[Category: Yuchi Z]]
-	[[Category: Zhang, J]]	+	[[Category: Zhang J]]
-	[[Category: Zhang, Y]]	+	[[Category: Zhang Y]]
-	[[Category: Zhao, H]]	+	[[Category: Zhao H]]
-	~~[[Category: C-s bond cleavage]]~~	+
-	~~[[Category: Glycyl radical enzyme]]~~	+
-	~~[[Category: Isethionate]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 10:59, 2 October 2019

OCA — Wed, 02 Oct 2019 10:59:02 GMT

←Older revision		Revision as of 10:59, 2 October 2019
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	<StructureSection load='5ymr' size='340' side='right'caption='[[5ymr]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='5ymr' size='340' side='right'caption='[[5ymr]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ymr]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YMR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YMR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ymr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Desvh Desvh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YMR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YMR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8X3:2-hydroxyethylsulfonic+acid'>8X3</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8X3:2-hydroxyethylsulfonic+acid'>8X3</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DVU_2824 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 DESVH])</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=5ymr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ymr OCA], [http://pdbe.org/5ymr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ymr RCSB], [http://www.ebi.ac.uk/pdbsum/5ymr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ymr 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=5ymr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ymr OCA], [http://pdbe.org/5ymr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ymr RCSB], [http://www.ebi.ac.uk/pdbsum/5ymr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ymr ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacterial degradation of organosulfonates plays an important role in sulfur recycling, and has been extensively studied. However, this process in anaerobic bacteria especially gut bacteria is little known despite of its potential significant impact on human health with the production of toxic H2S. Here, we describe the structural and biochemical characterization of an oxygen-sensitive enzyme that catalyzes the radical-mediated C-S bond cleavage of isethionate to form sulfite and acetaldehyde. We demonstrate its involvement in pathways that enables C2 sulfonates to be used as terminal electron acceptors for anaerobic respiration in sulfate- and sulfite-reducing bacteria. Furthermore, it plays a key role in converting bile salt-derived taurine into H2S in the disease-associated gut bacterium Bilophila wadsworthia. The enzymes and transporters in these anaerobic pathways expand our understanding of microbial sulfur metabolism, and help deciphering the complex web of microbial pathways involved in the transformation of sulfur compounds in the gut.
		+
		+	Radical-mediated C-S bond cleavage in C2 sulfonate degradation by anaerobic bacteria.,Xing M, Wei Y, Zhou Y, Zhang J, Lin L, Hu Y, Hua G, N Nanjaraj Urs A, Liu D, Wang F, Guo C, Tong Y, Li M, Liu Y, Ang EL, Zhao H, Yuchi Z, Zhang Y Nat Commun. 2019 Apr 8;10(1):1609. doi: 10.1038/s41467-019-09618-8. PMID:30962433<ref>PMID:30962433</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ymr" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Desvh]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Ang, E]]		[[Category: Ang, E]]

OCA at 07:40, 20 March 2019

OCA — Wed, 20 Mar 2019 07:40:06 GMT

←Older revision		Revision as of 07:40, 20 March 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5ymr ~~is ON HOLD until Apr 22 2020~~	+	==The Crystal Structure of IseG==
-		+	<StructureSection load='5ymr' size='340' side='right'caption='[[5ymr]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ymr]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YMR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YMR FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8X3:2-hydroxyethylsulfonic+acid'>8X3</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=5ymr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ymr OCA], [http://pdbe.org/5ymr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ymr RCSB], [http://www.ebi.ac.uk/pdbsum/5ymr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ymr ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Ang, E]]
		+	[[Category: Guo, C]]
		+	[[Category: Hu, Y]]
		+	[[Category: Hua, G]]
		+	[[Category: Lin, L]]
		+	[[Category: Wei, Y]]
		+	[[Category: Xing, M]]
		+	[[Category: Yuchi, Z]]
		+	[[Category: Zhang, J]]
		+	[[Category: Zhang, Y]]
		+	[[Category: Zhao, H]]
		+	[[Category: C-s bond cleavage]]
		+	[[Category: Glycyl radical enzyme]]
		+	[[Category: Isethionate]]
		+	[[Category: Lyase]]

OCA at 05:56, 30 January 2019

OCA — Wed, 30 Jan 2019 05:56:02 GMT

←Older revision		Revision as of 05:56, 30 January 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ymr is ON HOLD until ~~Jan~~ 22 2020	+	The entry 5ymr is ON HOLD until Apr 22 2020

	Authors:		Authors:

OCA at 06:02, 26 September 2018

OCA — Wed, 26 Sep 2018 06:02:58 GMT

←Older revision		Revision as of 06:02, 26 September 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ymr is ON HOLD until ~~Paper Publication~~	+	The entry 5ymr is ON HOLD until Jan 22 2020

	Authors:		Authors:

OCA at 06:26, 8 November 2017

OCA — Wed, 08 Nov 2017 06:26:22 GMT

←Older revision		Revision as of 06:26, 8 November 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ymr is ON HOLD	+	The entry 5ymr is ON HOLD until Paper Publication

	Authors:		Authors:

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

OCA — Wed, 01 Nov 2017 04:45:37 GMT

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

←Older revision

Revision as of 04:45, 1 November 2017

OCA: New page: '''Unreleased structure''' The entry 5ymr is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 01 Nov 2017 04:45:36 GMT

New page: '''Unreleased structure''' The entry 5ymr is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5ymr is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]