5imc - Revision history

OCA at 14:01, 30 August 2023

OCA — Wed, 30 Aug 2023 14:01:23 GMT

←Older revision		Revision as of 14:01, 30 August 2023
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	==Xanthomonas campestris Peroxiredoxin Q - Structure F3==		==Xanthomonas campestris Peroxiredoxin Q - Structure F3==
-	<StructureSection load='5imc' size='340' side='right' caption='[[5imc]], [[Resolution\|resolution]] 1.05Å' scene=''>	+	<StructureSection load='5imc' size='340' side='right'caption='[[5imc]], [[Resolution\|resolution]] 1.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5imc]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Xancp Xancp~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IMC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5IMC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5imc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_campestris_pv._campestris_str._ATCC_33913 Xanthomonas campestris pv. campestris str. ATCC 33913]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IMC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IMC FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=FMT:FORMIC+ACID'>FMT</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='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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">[[5iiz\|5iiz]]~~, ~~[[5im9\|5im9]], [[5ima\|5ima]], [[5imd\|5imd]], [[5imf\|5imf]], [[5imv\|5imv]], [[5imz\|5imz]], [[3gkm\|3gkm]], [[3gkn\|3gkn]], [[3gkk\|3gkk]]~~<~~/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=5imc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5imc OCA], [https://pdbe.org/5imc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5imc RCSB], [https://www.ebi.ac.uk/pdbsum/5imc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5imc ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">XCC1738 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=190485 XANCP])~~</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=5imc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5imc OCA], [~~http~~://pdbe.org/5imc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5imc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5imc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5imc ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/BCP_XANCP BCP_XANCP] Thiol-specific peroxidase that catalyzes the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols, respectively. Plays a role in cell protection against oxidative stress by detoxifying peroxides and as sensor of hydrogen peroxide-mediated signaling events.<ref>PMID:19477183</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5imc" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5imc" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Bacterioferritin comigratory protein\|Bacterioferritin comigratory protein]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Xancp~~]]	+	[[Category: Large Structures]]
-	[[Category: Karplus, A]]	+	[[Category: Xanthomonas campestris pv. campestris str. ATCC 33913]]
-	[[Category: Nelson~~, K J~~]]	+	[[Category: Karplus A]]
-	[[Category: Parsonage, D]]	+	[[Category: Nelson KJ]]
-	[[Category: Perkins, A]]	+	[[Category: Parsonage D]]
-	[[Category: Poole~~, L B]]~~	+	[[Category: Perkins A]]
-	~~[[Category: Bcp]]~~	+	[[Category: Poole LB]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Peroxidase]]~~	+
-	~~[[Category: Prxq]]~~	+
-	~~[[Category: Redox~~]]	+

OCA at 10:01, 22 November 2017

OCA — Wed, 22 Nov 2017 10:01:24 GMT

←Older revision		Revision as of 10:01, 22 November 2017
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	<StructureSection load='5imc' size='340' side='right' caption='[[5imc]], [[Resolution\|resolution]] 1.05Å' scene=''>		<StructureSection load='5imc' size='340' side='right' caption='[[5imc]], [[Resolution\|resolution]] 1.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5imc]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IMC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IMC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5imc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Xancp Xancp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IMC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IMC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5iiz\|5iiz]], [[5im9\|5im9]], [[5ima\|5ima]], [[5imd\|5imd]], [[5imf\|5imf]], [[5imv\|5imv]], [[5imz\|5imz]], [[3gkm\|3gkm]], [[3gkn\|3gkn]], [[3gkk\|3gkk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5iiz\|5iiz]], [[5im9\|5im9]], [[5ima\|5ima]], [[5imd\|5imd]], [[5imf\|5imf]], [[5imv\|5imv]], [[5imz\|5imz]], [[3gkm\|3gkm]], [[3gkn\|3gkn]], [[3gkk\|3gkk]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">XCC1738 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=190485 XANCP])</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=5imc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5imc OCA], [http://pdbe.org/5imc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5imc RCSB], [http://www.ebi.ac.uk/pdbsum/5imc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5imc 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=5imc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5imc OCA], [http://pdbe.org/5imc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5imc RCSB], [http://www.ebi.ac.uk/pdbsum/5imc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5imc ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Xancp]]
	[[Category: Karplus, A]]		[[Category: Karplus, A]]
	[[Category: Nelson, K J]]		[[Category: Nelson, K J]]

OCA at 13:52, 21 September 2016

OCA — Wed, 21 Sep 2016 13:52:36 GMT

←Older revision		Revision as of 13:52, 21 September 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5imc is ~~ON HOLD until Paper~~ Publication	+	==Xanthomonas campestris Peroxiredoxin Q - Structure F3==
		+	<StructureSection load='5imc' size='340' side='right' caption='[[5imc]], [[Resolution\|resolution]] 1.05Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5imc]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IMC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IMC FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5iiz\|5iiz]], [[5im9\|5im9]], [[5ima\|5ima]], [[5imd\|5imd]], [[5imf\|5imf]], [[5imv\|5imv]], [[5imz\|5imz]], [[3gkm\|3gkm]], [[3gkn\|3gkn]], [[3gkk\|3gkk]]</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=5imc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5imc OCA], [http://pdbe.org/5imc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5imc RCSB], [http://www.ebi.ac.uk/pdbsum/5imc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5imc ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Peroxiredoxins (Prxs) are ubiquitous cysteine-based peroxidases that guard cells against oxidative damage, are virulence factors for pathogens, and are involved in eukaryotic redox regulatory pathways. We have analyzed catalytically active crystals to capture atomic resolution snapshots of a PrxQ subfamily enzyme (from Xanthomonas campestris) proceeding through thiolate, sulfenate, and sulfinate species. These analyses provide structures of unprecedented accuracy for seeding theoretical studies, and reveal conformational intermediates giving insight into the reaction pathway. Based on a highly non-standard geometry seen for the sulfenate intermediate, we infer that the sulfenate formation itself can strongly promote local unfolding of the active site to enhance productive catalysis. Further, these structures reveal that preventing local unfolding, in this case via crystal contacts, results in facile hyperoxidative inactivation even for Prxs normally resistant to such inactivation. This supports previous proposals that conformation-specific inhibitors may be useful for achieving selective inhibition of Prxs that are drug targets.

-	~~Authors: Perkins~~, A., Parsonage, D., Nelson, ~~K.J.~~, Poole, L.B., ~~Karplus, A~~.	+	Peroxiredoxin Catalysis at Atomic Resolution.,Perkins A, Parsonage D, Nelson KJ, Ogba OM, Cheong PH, Poole LB, Karplus PA Structure. 2016 Sep 1. pii: S0969-2126(16)30223-4. doi:, 10.1016/j.str.2016.07.012. PMID:27594682<ref>PMID:27594682</ref>

-	~~Description: Xanthomonas campestris Peroxiredoxin Q -Structure F3~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Perkins, A]]~~	+	<div class="pdbe-citations 5imc" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Karplus, A]]		[[Category: Karplus, A]]
-	[[Category: Nelson, K.J]]	+	[[Category: Nelson, K J]]
	[[Category: Parsonage, D]]		[[Category: Parsonage, D]]
-	[[Category: Poole, L.B]]	+	[[Category: Perkins, A]]
		+	[[Category: Poole, L B]]
		+	[[Category: Bcp]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Peroxidase]]
		+	[[Category: Prxq]]
		+	[[Category: Redox]]

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

OCA — Wed, 11 May 2016 00:39:10 GMT

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

←Older revision

Revision as of 00:39, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5imc is ON HOLD until Paper Publication Authors: Perkins, A., Parsonage, D., Nelson, K.J., Poole, L.B., Karplus, A. Description: Xanthomonas campes...

OCA — Wed, 11 May 2016 00:39:08 GMT

New page: '''Unreleased structure''' The entry 5imc is ON HOLD until Paper Publication Authors: Perkins, A., Parsonage, D., Nelson, K.J., Poole, L.B., Karplus, A. Description: Xanthomonas campes...

New page

'''Unreleased structure'''

The entry 5imc is ON HOLD until Paper Publication

Authors: Perkins, A., Parsonage, D., Nelson, K.J., Poole, L.B., Karplus, A.

Description: Xanthomonas campestris Peroxiredoxin Q -Structure F3
[[Category: Unreleased Structures]]
[[Category: Perkins, A]]
[[Category: Karplus, A]]
[[Category: Nelson, K.J]]
[[Category: Parsonage, D]]
[[Category: Poole, L.B]]