5uxs - Revision history

OCA at 14:30, 6 March 2024

OCA — Wed, 06 Mar 2024 14:30:16 GMT

←Older revision		Revision as of 14:30, 6 March 2024
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	<StructureSection load='5uxs' size='340' side='right'caption='[[5uxs]], [[Resolution\|resolution]] 1.42Å' scene=''>		<StructureSection load='5uxs' size='340' side='right'caption='[[5uxs]], [[Resolution\|resolution]] 1.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5uxs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UXS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5UXS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5uxs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UXS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UXS FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.421Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5uxu\|5uxu]], [[5uy0\|5uy0]], [[5uy4\|5uy4]], [[5uy5\|5uy5]], [[5uya\|5uya]], [[5uyb\|5uyb]], [[5uyd\|5uyd]], [[5uye\|5uye]], [[5uyf\|5uyf]], [[5uyg\|5uyg]], [[5uyh\|5uyh]], [[5uyc\|5uyc]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5uxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uxs OCA], [~~http~~://pdbe.org/5uxs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5uxs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5uxs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5uxs 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=5uxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uxs OCA], [https://pdbe.org/5uxs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5uxs RCSB], [https://www.ebi.ac.uk/pdbsum/5uxs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5uxs ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/YFEA_YERPE YFEA_YERPE]] Part of an ATP-driven transport system YfeABCD for chelated iron.	+	[https://www.uniprot.org/uniprot/YFEA_YERPE YFEA_YERPE] Part of an ATP-driven transport system YfeABCD for chelated iron.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Gram-negative bacteria use siderophores, outer membrane receptors, inner membrane transporters and substrate-binding proteins (SBPs) to transport transition metals through the periplasm. The SBPs share a similar protein fold that has undergone significant structural evolution to communicate with a variety of differentially regulated transporters in the cell. In Yersinia pestis, the causative agent of plague, YfeA (YPO2439, y1897), an SBP, is important for full virulence during mammalian infection. To better understand the role of YfeA in infection, crystal structures were determined under several environmental conditions with respect to transition-metal levels. Energy-dispersive X-ray spectroscopy and anomalous X-ray scattering data show that YfeA is polyspecific and can alter its substrate specificity. In minimal-media experiments, YfeA crystals grown after iron supplementation showed a threefold increase in iron fluorescence emission over the iron fluorescence emission from YfeA crystals grown from nutrient-rich conditions, and YfeA crystals grown after manganese supplementation during overexpression showed a fivefold increase in manganese fluorescence emission over the manganese fluorescence emission from YfeA crystals grown from nutrient-rich conditions. In all experiments, the YfeA crystals produced the strongest fluorescence emission from zinc and could not be manipulated otherwise. Additionally, this report documents the discovery of a novel surface metal-binding site that prefers to chelate zinc but can also bind manganese. Flexibility across YfeA crystal forms in three loops and a helix near the buried metal-binding site suggest that a structural rearrangement is required for metal loading and unloading.	+
-		+
-	Crystal structure of Yersinia pestis virulence factor YfeA reveals two polyspecific metal-binding sites.,Radka CD, DeLucas LJ, Wilson LS, Lawrenz MB, Perry RD, Aller SG Acta Crystallogr D Struct Biol. 2017 Jul 1;73(Pt 7):557-572. doi:, 10.1107/S2059798317006349. Epub 2017 Jun 30. PMID:28695856<ref>PMID:28695856</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5uxs" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Aller, S G~~]]	+	[[Category: Yersinia pestis]]
-	[[Category: ~~DeLucas, L J~~]]	+	[[Category: Aller SG]]
-	[[Category: ~~Radka, C D~~]]	+	[[Category: DeLucas LJ]]
-	[[Category: ~~Metal transport]]~~	+	[[Category: Radka CD]]
-	~~[[Category: Polyspecific]]~~	+
-	~~[[Category: Transition metal]]~~	+
-	~~[[Category: Transport~~]]	+

OCA at 08:26, 30 September 2020

OCA — Wed, 30 Sep 2020 08:26:14 GMT

←Older revision		Revision as of 08:26, 30 September 2020
Line 1:		Line 1:

	==X ray structure of the periplasmic ligand binding protein YfeA from Yersinia pestis==		==X ray structure of the periplasmic ligand binding protein YfeA from Yersinia pestis==
-	<StructureSection load='5uxs' size='340' side='right' caption='[[5uxs]], [[Resolution\|resolution]] 1.42Å' scene=''>	+	<StructureSection load='5uxs' size='340' side='right'caption='[[5uxs]], [[Resolution\|resolution]] 1.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5uxs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UXS OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5UXS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5uxs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UXS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5UXS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uxu\|5uxu]], [[5uy0\|5uy0]], [[5uy4\|5uy4]], [[5uy5\|5uy5]], [[5uya\|5uya]], [[5uyb\|5uyb]], [[5uyd\|5uyd]], [[5uye\|5uye]], [[5uyf\|5uyf]], [[5uyg\|5uyg]], [[5uyh\|5uyh]], [[5uyc\|5uyc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uxu\|5uxu]], [[5uy0\|5uy0]], [[5uy4\|5uy4]], [[5uy5\|5uy5]], [[5uya\|5uya]], [[5uyb\|5uyb]], [[5uyd\|5uyd]], [[5uye\|5uye]], [[5uyf\|5uyf]], [[5uyg\|5uyg]], [[5uyh\|5uyh]], [[5uyc\|5uyc]]</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=5uxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uxs OCA], [http://pdbe.org/5uxs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uxs RCSB], [http://www.ebi.ac.uk/pdbsum/5uxs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uxs ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5uxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uxs OCA], [http://pdbe.org/5uxs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uxs RCSB], [http://www.ebi.ac.uk/pdbsum/5uxs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uxs ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Aller, S G]]		[[Category: Aller, S G]]
	[[Category: DeLucas, L J]]		[[Category: DeLucas, L J]]

OCA at 03:55, 4 August 2017

OCA — Fri, 04 Aug 2017 03:55:45 GMT

←Older revision		Revision as of 03:55, 4 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5uxs is ~~ON HOLD until Paper~~ Publication	+	==X ray structure of the periplasmic ligand binding protein YfeA from Yersinia pestis==
		+	<StructureSection load='5uxs' size='340' side='right' caption='[[5uxs]], [[Resolution\|resolution]] 1.42Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5uxs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UXS FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uxu\|5uxu]], [[5uy0\|5uy0]], [[5uy4\|5uy4]], [[5uy5\|5uy5]], [[5uya\|5uya]], [[5uyb\|5uyb]], [[5uyd\|5uyd]], [[5uye\|5uye]], [[5uyf\|5uyf]], [[5uyg\|5uyg]], [[5uyh\|5uyh]], [[5uyc\|5uyc]]</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=5uxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uxs OCA], [http://pdbe.org/5uxs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uxs RCSB], [http://www.ebi.ac.uk/pdbsum/5uxs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uxs ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/YFEA_YERPE YFEA_YERPE]] Part of an ATP-driven transport system YfeABCD for chelated iron.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Gram-negative bacteria use siderophores, outer membrane receptors, inner membrane transporters and substrate-binding proteins (SBPs) to transport transition metals through the periplasm. The SBPs share a similar protein fold that has undergone significant structural evolution to communicate with a variety of differentially regulated transporters in the cell. In Yersinia pestis, the causative agent of plague, YfeA (YPO2439, y1897), an SBP, is important for full virulence during mammalian infection. To better understand the role of YfeA in infection, crystal structures were determined under several environmental conditions with respect to transition-metal levels. Energy-dispersive X-ray spectroscopy and anomalous X-ray scattering data show that YfeA is polyspecific and can alter its substrate specificity. In minimal-media experiments, YfeA crystals grown after iron supplementation showed a threefold increase in iron fluorescence emission over the iron fluorescence emission from YfeA crystals grown from nutrient-rich conditions, and YfeA crystals grown after manganese supplementation during overexpression showed a fivefold increase in manganese fluorescence emission over the manganese fluorescence emission from YfeA crystals grown from nutrient-rich conditions. In all experiments, the YfeA crystals produced the strongest fluorescence emission from zinc and could not be manipulated otherwise. Additionally, this report documents the discovery of a novel surface metal-binding site that prefers to chelate zinc but can also bind manganese. Flexibility across YfeA crystal forms in three loops and a helix near the buried metal-binding site suggest that a structural rearrangement is required for metal loading and unloading.

-	~~Authors~~:	+	Crystal structure of Yersinia pestis virulence factor YfeA reveals two polyspecific metal-binding sites.,Radka CD, DeLucas LJ, Wilson LS, Lawrenz MB, Perry RD, Aller SG Acta Crystallogr D Struct Biol. 2017 Jul 1;73(Pt 7):557-572. doi:, 10.1107/S2059798317006349. Epub 2017 Jun 30. PMID:28695856<ref>PMID:28695856</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5uxs" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Aller, S G]]
		+	[[Category: DeLucas, L J]]
		+	[[Category: Radka, C D]]
		+	[[Category: Metal transport]]
		+	[[Category: Polyspecific]]
		+	[[Category: Transition metal]]
		+	[[Category: Transport]]

OCA at 19:29, 15 March 2017

OCA — Wed, 15 Mar 2017 19:29:36 GMT

←Older revision		Revision as of 19:29, 15 March 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Thu, 09 Mar 2017 15:04:29 GMT

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

←Older revision

Revision as of 15:04, 9 March 2017

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

OCA — Thu, 09 Mar 2017 15:04:27 GMT

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

New page

'''Unreleased structure'''

The entry 5uxs is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]