5iqx - Revision history

OCA at 14:06, 30 August 2023

OCA — Wed, 30 Aug 2023 14:06:31 GMT

←Older revision		Revision as of 14:06, 30 August 2023
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	<StructureSection load='5iqx' size='340' side='right'caption='[[5iqx]], [[Resolution\|resolution]] 1.05Å' scene=''>		<StructureSection load='5iqx' size='340' side='right'caption='[[5iqx]], [[Resolution\|resolution]] 1.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5iqx]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pseae Pseae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IQX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5IQX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5iqx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IQX FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'~~>~~HEM</scene>, <scene name='pdbligand=MLT:D~~-~~MALATE'>MLT</scene>~~, ~~<scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.05Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5iqw\|5iqw]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MLT:D-MALATE'>MLT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<~~tr id~~='~~gene~~'><~~td class="sblockLbl"~~><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">hasAp, PA3407 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])~~</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=5iqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iqx OCA], [https://pdbe.org/5iqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5iqx RCSB], [https://www.ebi.ac.uk/pdbsum/5iqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5iqx 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=5iqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iqx OCA], [~~http~~://pdbe.org/5iqx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5iqx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5iqx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5iqx ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/G3XD33_PSEAE G3XD33_PSEAE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pseae~~]]	+	[[Category: Pseudomonas aeruginosa PAO1]]
-	[[Category: Battaile~~, K P~~]]	+	[[Category: Battaile KP]]
-	[[Category: Kumar, R]]	+	[[Category: Kumar R]]
-	[[Category: Lovell, S]]	+	[[Category: Lovell S]]
-	[[Category: Rivera, M]]	+	[[Category: Rivera M]]
-	[[Category: Yao, H]]	+	[[Category: Yao H]]
-	~~[[Category: H32 loop]]~~	+
-	~~[[Category: Heme binding protein]]~~	+
-	~~[[Category: Hemophore~~]]	+

OCA at 07:37, 27 November 2019

OCA — Wed, 27 Nov 2019 07:37:56 GMT

←Older revision		Revision as of 07:37, 27 November 2019
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	==1.05A resolution structure of Holo HasAp (R33A) from Pseudomonas aeruginosa==		==1.05A resolution structure of Holo HasAp (R33A) from Pseudomonas aeruginosa==
-	<StructureSection load='5iqx' size='340' side='right' caption='[[5iqx]], [[Resolution\|resolution]] 1.05Å' scene=''>	+	<StructureSection load='5iqx' size='340' side='right'caption='[[5iqx]], [[Resolution\|resolution]] 1.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5iqx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IQX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IQX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5iqx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IQX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IQX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MLT:D-MALATE'>MLT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MLT:D-MALATE'>MLT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5iqw\|5iqw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5iqw\|5iqw]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hasAp, PA3407 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</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=5iqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iqx OCA], [http://pdbe.org/5iqx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iqx RCSB], [http://www.ebi.ac.uk/pdbsum/5iqx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iqx 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=5iqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iqx OCA], [http://pdbe.org/5iqx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iqx RCSB], [http://www.ebi.ac.uk/pdbsum/5iqx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iqx ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Pseae]]
	[[Category: Battaile, K P]]		[[Category: Battaile, K P]]
	[[Category: Kumar, R]]		[[Category: Kumar, R]]

OCA at 04:24, 21 September 2017

OCA — Thu, 21 Sep 2017 04:24:54 GMT

←Older revision		Revision as of 04:24, 21 September 2017
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MLT:D-MALATE'>MLT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MLT:D-MALATE'>MLT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5iqw\|5iqw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5iqw\|5iqw]]</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=5iqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iqx OCA], [http://pdbe.org/5iqx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iqx RCSB], [http://www.ebi.ac.uk/pdbsum/5iqx PDBsum]</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=5iqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iqx OCA], [http://pdbe.org/5iqx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iqx RCSB], [http://www.ebi.ac.uk/pdbsum/5iqx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iqx ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

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

OCA — Thu, 12 May 2016 18:51:23 GMT

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

←Older revision

Revision as of 18:51, 12 May 2016

OCA: New page: ==1.05A resolution structure of Holo HasAp (R33A) from Pseudomonas aeruginosa== == Structural highlights ==
<table><tr><td colspan='2'>[[5iqx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IQX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IQX FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MLT:D-MALATE'>MLT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5iqw|5iqw]]</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=5iqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iqx OCA], [http://pdbe.org/5iqx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iqx RCSB], [http://www.ebi.ac.uk/pdbsum/5iqx PDBsum]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Previous characterization of hemophores from Serratia marcescens (HasAs), Pseudomonas aeruginosa (HasAp), and Yersinia pestis (HasAyp) showed that hemin binds between two loops, where it is axially coordinated by H32 and Y75. The Y75 loop is structurally conserved in all three hemophores and harbors conserved ligand Y75. The other loop contains H32 in HasAs and HasAp, but a noncoordinating Q32 in HasAyp. The H32 loop in apo-HasAs and apo-HasAp is in an open conformation, which places H32 about 30 A from the hemin-binding site. Hence, hemin binding onto the Y75 loop of HasAs or HasAp triggers a large relocation of the H32 loop from an open- to a closed-loop conformation and enables coordination of the hemin-iron by H32. In comparison, the Q32 loop in apo-HasAyp is in the closed conformation, and hemin binding occurs with minimal reorganization and without coordinative interactions with the Q32 loop. Studies in crystallo and in solution have established that the open H32 loop in apo-HasAp and apo-HasAs is well structured and minimally affected by conformational dynamics. In this study we address the intriguing issue of the stability of the H32 loop in apo-HasAp and how hemin binding triggers its relocation. We address this question with a combination of NMR spectroscopy, X-ray crystallography, and molecular dynamics simulations and find that R33 is critical to the stability of the open H32 loop. Replacing R33 with A causes the H32 loop in R33A apo-HasAp to adopt a conformation similar to that of holo-HasAp. Finally, stopped-flow absorption and resonance Raman analyses of hemin binding to apo-R33A HasAp indicate that the closed H32 loop slows down the insertion of the heme inside the binding pocket, presumably as it obstructs access to the hydrophobic platform on the Y75 loop, but accelerates the completion of the heme iron coordination.

Replacing Arginine 33 for Alanine in the Hemophore HasA from Pseudomonas aeruginosa Causes Closure of the H32 Loop in the Apo-Protein.,Kumar R, Qi Y, Matsumura H, Lovell S, Yao H, Battaile KP, Im W, Moenne-Loccoz P, Rivera M Biochemistry. 2016 Apr 28. PMID:27074415<ref>PMID:27074415</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5iqx" style="background-color:#fffaf0;"></div>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Battaile, K P]]
[[Category: Kumar, R]]
[[Category: Lovell, S]]
[[Category: Rivera, M]]
[[Category: Yao, H]]
[[Category: H32 loop]]
[[Category: Heme binding protein]]
[[Category: Hemophore]]