5w56 - Revision history

OCA at 14:07, 4 October 2023

OCA — Wed, 04 Oct 2023 14:07:28 GMT

←Older revision		Revision as of 14:07, 4 October 2023
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	<StructureSection load='5w56' size='340' side='right'caption='[[5w56]], [[Resolution\|resolution]] 2.03Å' scene=''>		<StructureSection load='5w56' size='340' side='right'caption='[[5w56]], [[Resolution\|resolution]] 2.03Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w56]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pardp Pardp~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W56 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5W56 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w56]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_denitrificans_PD1222 Paracoccus denitrificans PD1222]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W56 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5W56 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GOL:GLYCEROL'>GOL</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]] 2.03Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5w57\|5w57]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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">Pden_1597 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318586 PARDP])~~</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=5w56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w56 OCA], [https://pdbe.org/5w56 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5w56 RCSB], [https://www.ebi.ac.uk/pdbsum/5w56 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5w56 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=5w56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w56 OCA], [~~http~~://pdbe.org/5w56 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5w56 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5w56 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5w56 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A1B2F3_PARDP A1B2F3_PARDP]
	<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: ~~Pardp~~]]	+	[[Category: Paracoccus denitrificans PD1222]]
-	[[Category: Avalos, D]]	+	[[Category: Avalos D]]
-	[[Category: Yukl~~, E T]]~~	+	[[Category: Yukl ET]]
-	~~[[Category: Abc transporter]]~~	+
-	~~[[Category: Metal binding protein]]~~	+
-	~~[[Category: Solute binding protein]]~~	+
-	~~[[Category: Zinc~~]]	+

OCA at 09:46, 1 January 2020

OCA — Wed, 01 Jan 2020 09:46:37 GMT

←Older revision		Revision as of 09:46, 1 January 2020
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	==Structure of Apo AztC==		==Structure of Apo AztC==
-	<StructureSection load='5w56' size='340' side='right' caption='[[5w56]], [[Resolution\|resolution]] 2.03Å' scene=''>	+	<StructureSection load='5w56' size='340' side='right'caption='[[5w56]], [[Resolution\|resolution]] 2.03Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5w56]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pardp Pardp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W56 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W56 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5w56]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pardp Pardp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W56 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W56 FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pardp]]		[[Category: Pardp]]
	[[Category: Avalos, D]]		[[Category: Avalos, D]]

OCA at 09:27, 1 November 2017

OCA — Wed, 01 Nov 2017 09:27:45 GMT

←Older revision		Revision as of 09:27, 1 November 2017
Line 3:		Line 3:
	<StructureSection load='5w56' size='340' side='right' caption='[[5w56]], [[Resolution\|resolution]] 2.03Å' scene=''>		<StructureSection load='5w56' size='340' side='right' caption='[[5w56]], [[Resolution\|resolution]] 2.03Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w56]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W56 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W56 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w56]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pardp Pardp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W56 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W56 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=GOL:GLYCEROL'>GOL</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">[[5w57\|5w57]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5w57\|5w57]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pden_1597 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318586 PARDP])</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=5w56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w56 OCA], [http://pdbe.org/5w56 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w56 RCSB], [http://www.ebi.ac.uk/pdbsum/5w56 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w56 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=5w56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w56 OCA], [http://pdbe.org/5w56 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w56 RCSB], [http://www.ebi.ac.uk/pdbsum/5w56 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w56 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Pardp]]
	[[Category: Avalos, D]]		[[Category: Avalos, D]]
	[[Category: Yukl, E T]]		[[Category: Yukl, E T]]

OCA: Protected "5w56" [edit=sysop:move=sysop]

OCA — Thu, 21 Sep 2017 04:43:26 GMT

Protected "5w56" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:43, 21 September 2017

OCA: New page: ==Structure of Apo AztC== == Structural highlights == ...
OCA — Thu, 21 Sep 2017 04:43:24 GMT
New page: ==Structure of Apo AztC== <StructureSection load='5w56' size='340' side='right' caption='5w56, resolution 2.03Å' scene=''> == Structural highlights == <table><tr>...
New page

==Structure of Apo AztC==
<StructureSection load='5w56' size='340' side='right' caption='[[5w56]], [[Resolution|resolution]] 2.03Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5w56]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W56 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W56 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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">[[5w57|5w57]]</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=5w56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w56 OCA], [http://pdbe.org/5w56 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w56 RCSB], [http://www.ebi.ac.uk/pdbsum/5w56 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w56 ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Bacteria can acquire the essential metal zinc from extremely zinc-limited environments by using ATP-binding cassette (ABC) transporters. These transporters are critical virulence factors relying on specific and high-affinity binding of zinc by a periplasmic solute-binding protein (SBP). As such, the mechanisms of zinc binding and release among bacterial SBPs are of considerable interest as antibacterial drug targets. Zinc SBPs are characterized by a flexible loop near the high-affinity zinc-binding site. The function of this structure is not always clear, and its flexibility has thus far prevented structural characterization by X-ray crystallography. Here, we present intact structures for the zinc-specific SBP AztC from the bacterium Paracoccus denitrificans in the zinc-bound and the apo states. A comparison of these structures revealed that zinc loss prompts significant structural rearrangements mediated by the formation of a sodium-binding site in the apo structure. We further show that the AztC flexible loop has no impact on zinc-binding affinity, stoichiometry, or protein structure, yet is essential for zinc transfer from the metallochaperone AztD. We also found that three His residues in the loop appear to temporarily coordinate zinc and then convey it to the high-affinity binding site. Consistent with this, mutation of any of these residues to Ala abrogated zinc transfer from AztD. Our structural and mechanistic findings conclusively identify a role for the AztC flexible loop in zinc acquisition from the metallochaperone AztD and yield critical insights into metal binding by AztC from both solution and AztD. These proteins are highly conserved in human pathogens, making this work potentially useful to the development of novel antibiotics.

Mechanisms of zinc binding to the solute binding protein AztC and transfer from the metallochaperone AztD.,Neupane DP, Avalos D, Fullam S, Roychowdhury H, Yukl ET J Biol Chem. 2017 Sep 7. pii: jbc.M117.804799. doi: 10.1074/jbc.M117.804799. PMID:28887302<ref>PMID:28887302</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5w56" style="background-color:#fffaf0;"></div>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Avalos, D]]
[[Category: Yukl, E T]]
[[Category: Abc transporter]]
[[Category: Metal binding protein]]
[[Category: Solute binding protein]]
[[Category: Zinc]]