6kgy - Revision history

OCA at 10:42, 27 March 2024

OCA — Wed, 27 Mar 2024 10:42:40 GMT

←Older revision		Revision as of 10:42, 27 March 2024
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	<StructureSection load='6kgy' size='340' side='right'caption='[[6kgy]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='6kgy' size='340' side='right'caption='[[6kgy]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kgy]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecobd Ecobd~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KGY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6KGY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kgy]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KGY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KGY FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CL:CHLORIDE+ION'>CL</scene~~>, ~~<scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</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]] 2.9Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~ECBD_3354 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=469008 ECOBD])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</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=6kgy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kgy OCA], [~~http~~://pdbe.org/6kgy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6kgy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6kgy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6kgy 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=6kgy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kgy OCA], [https://pdbe.org/6kgy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kgy RCSB], [https://www.ebi.ac.uk/pdbsum/6kgy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kgy ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/RCLA_ECOLI RCLA_ECOLI] Probably involved in reactive chlorine species (RCS) stress resistance.<ref>PMID:24078635</ref>
-	~~In response to microbial invasion, the animal immune system generates hypochlorous acid (HOCl) that kills microorganisms in the oxidative burst~~. ~~HOCl toxicity is amplified in the phagosome through import of the copper cation (Cu(2+))~~. ~~In Escherichia coli and Salmonella, the transcriptional regulator RclR senses HOCl stress and induces expression of the RclA, -B, and -C proteins,~~ involved in bacterial defenses against oxidative stress. However, the structures and biochemical roles of the Rcl proteins remain to be elucidated. In this study, we first examined the role of the flavoprotein disulfide reductase (~~FDR~~) RclA in survival of Salmonella in macrophage phagosomes, finding that RclA promotes Salmonella survival in macrophage vacuoles containing sublethal HOCl levels. To clarify the molecular mechanism, we determined the crystal structure of RclA from E.coli at 2.9 A resolution. This analysis revealed that the structure of homodimeric RclA is similar to those of typical FDRs, exhibiting two conserved cysteine residues near the flavin ring of the cofactor flavin adenine dinucleotide (FAD). Of note, we observed that Cu(2+) accelerated RclA-mediated oxidation of NADH, leading to a lowering of oxygen levels in vitro Compared with the RclA wildtype enzyme, substitution of the conserved cysteine residues lowered the specificity to Cu(2+) or substantially increased the production of superoxide anion in the absence of Cu(2+) We conclude that RclA-mediated lowering of oxygen levels could contribute to the inhibition of oxidative bursts in phagosomes. Our study sheds light on the molecular basis for how bacteria can survive HOCl stress ~~in macrophages~~.	+
-		+
-	Structure and function of the hypochlorous acid-induced flavoprotein RclA from Escherichia coli.,Baek Y, Kim J, Ahn J, Jo I, Hong S, Ryu S, Ha NC J Biol Chem. 2020 Jan 26. pii: RA119.011530. doi: 10.1074/jbc.RA119.011530. PMID:31988242<ref>PMID:~~31988242~~</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6kgy" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Ecobd]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Baek, Y]]	+	[[Category: Baek Y]]
-	[[Category: Ha, N C]]	+	[[Category: Ha N-C]]
-	~~[[Category: Cysteine disulfide]]~~	+
-	~~[[Category: Flavoprotein]]~~	+
-	~~[[Category: Hypochlorous acid]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Reductase~~]]	+

OCA at 04:37, 13 February 2020

OCA — Thu, 13 Feb 2020 04:37:55 GMT

←Older revision		Revision as of 04:37, 13 February 2020
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	<StructureSection load='6kgy' size='340' side='right'caption='[[6kgy]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='6kgy' size='340' side='right'caption='[[6kgy]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kgy]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KGY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KGY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kgy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecobd Ecobd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KGY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KGY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ECBD_3354 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=469008 ECOBD])</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=6kgy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kgy OCA], [http://pdbe.org/6kgy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kgy RCSB], [http://www.ebi.ac.uk/pdbsum/6kgy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kgy 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=6kgy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kgy OCA], [http://pdbe.org/6kgy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kgy RCSB], [http://www.ebi.ac.uk/pdbsum/6kgy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kgy ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In response to microbial invasion, the animal immune system generates hypochlorous acid (HOCl) that kills microorganisms in the oxidative burst. HOCl toxicity is amplified in the phagosome through import of the copper cation (Cu(2+)). In Escherichia coli and Salmonella, the transcriptional regulator RclR senses HOCl stress and induces expression of the RclA, -B, and -C proteins, involved in bacterial defenses against oxidative stress. However, the structures and biochemical roles of the Rcl proteins remain to be elucidated. In this study, we first examined the role of the flavoprotein disulfide reductase (FDR) RclA in survival of Salmonella in macrophage phagosomes, finding that RclA promotes Salmonella survival in macrophage vacuoles containing sublethal HOCl levels. To clarify the molecular mechanism, we determined the crystal structure of RclA from E.coli at 2.9 A resolution. This analysis revealed that the structure of homodimeric RclA is similar to those of typical FDRs, exhibiting two conserved cysteine residues near the flavin ring of the cofactor flavin adenine dinucleotide (FAD). Of note, we observed that Cu(2+) accelerated RclA-mediated oxidation of NADH, leading to a lowering of oxygen levels in vitro Compared with the RclA wildtype enzyme, substitution of the conserved cysteine residues lowered the specificity to Cu(2+) or substantially increased the production of superoxide anion in the absence of Cu(2+) We conclude that RclA-mediated lowering of oxygen levels could contribute to the inhibition of oxidative bursts in phagosomes. Our study sheds light on the molecular basis for how bacteria can survive HOCl stress in macrophages.
		+
		+	Structure and function of the hypochlorous acid-induced flavoprotein RclA from Escherichia coli.,Baek Y, Kim J, Ahn J, Jo I, Hong S, Ryu S, Ha NC J Biol Chem. 2020 Jan 26. pii: RA119.011530. doi: 10.1074/jbc.RA119.011530. PMID:31988242<ref>PMID:31988242</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6kgy" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecobd]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Baek, Y]]		[[Category: Baek, Y]]

OCA at 07:59, 5 February 2020

OCA — Wed, 05 Feb 2020 07:59:23 GMT

←Older revision		Revision as of 07:59, 5 February 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6kgy ~~is ON HOLD until Paper Publication~~	+	==HOCl-induced flavoprotein disulfide reductase RclA from Escherichia coli==
-		+	<StructureSection load='6kgy' size='340' side='right'caption='[[6kgy]], [[Resolution\|resolution]] 2.90Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6kgy]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KGY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KGY FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</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=6kgy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kgy OCA], [http://pdbe.org/6kgy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kgy RCSB], [http://www.ebi.ac.uk/pdbsum/6kgy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kgy ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Baek, Y]]
		+	[[Category: Ha, N C]]
		+	[[Category: Cysteine disulfide]]
		+	[[Category: Flavoprotein]]
		+	[[Category: Hypochlorous acid]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Reductase]]

OCA at 04:00, 21 August 2019

OCA — Wed, 21 Aug 2019 04:00:48 GMT

←Older revision		Revision as of 04:00, 21 August 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6kgy is ON HOLD	+	The entry 6kgy is ON HOLD until Paper Publication

	Authors:		Authors:

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

OCA — Wed, 17 Jul 2019 08:49:56 GMT

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

←Older revision

Revision as of 08:49, 17 July 2019

OCA: New page: '''Unreleased structure''' The entry 6kgy is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 17 Jul 2019 08:49:54 GMT

New page: '''Unreleased structure''' The entry 6kgy is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6kgy is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]