5ima - Revision history

OCA at 14:01, 30 August 2023

2023-08-30T14:01:22Z

←Older revision		Revision as of 14:01, 30 August 2023
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	==Xanthomonas campestris Peroxiredoxin Q - Structure F2==		==Xanthomonas campestris Peroxiredoxin Q - Structure F2==
-	<StructureSection load='5ima' size='340' side='right' caption='[[5ima]], [[Resolution\|resolution]] 1.04Å' scene=''>	+	<StructureSection load='5ima' size='340' side='right'caption='[[5ima]], [[Resolution\|resolution]] 1.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ima]] 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=5IMA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5IMA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ima]] 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=5IMA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IMA 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]] 1.04Å</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]], [[5imc\|5imc]], [[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=5ima FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ima OCA], [https://pdbe.org/5ima PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ima RCSB], [https://www.ebi.ac.uk/pdbsum/5ima PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ima 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=5ima FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ima OCA], [~~http~~://pdbe.org/5ima PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ima RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ima PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ima 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 5ima" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ima" 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

2017-11-22T10:01:24Z

←Older revision		Revision as of 10:01, 22 November 2017
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	<StructureSection load='5ima' size='340' side='right' caption='[[5ima]], [[Resolution\|resolution]] 1.04Å' scene=''>		<StructureSection load='5ima' size='340' side='right' caption='[[5ima]], [[Resolution\|resolution]] 1.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ima]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IMA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IMA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ima]] 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=5IMA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IMA 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]], [[5imc\|5imc]], [[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]], [[5imc\|5imc]], [[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=5ima FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ima OCA], [http://pdbe.org/5ima PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ima RCSB], [http://www.ebi.ac.uk/pdbsum/5ima PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ima 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=5ima FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ima OCA], [http://pdbe.org/5ima PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ima RCSB], [http://www.ebi.ac.uk/pdbsum/5ima PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ima 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

2016-09-21T13:52:32Z

←Older revision		Revision as of 13:52, 21 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ima is ~~ON HOLD until Paper~~ Publication	+	==Xanthomonas campestris Peroxiredoxin Q - Structure F2==
		+	<StructureSection load='5ima' size='340' side='right' caption='[[5ima]], [[Resolution\|resolution]] 1.04Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ima]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IMA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IMA 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]], [[5imc\|5imc]], [[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=5ima FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ima OCA], [http://pdbe.org/5ima PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ima RCSB], [http://www.ebi.ac.uk/pdbsum/5ima PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ima 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 F2~~	+	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 5ima" 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 "5ima" [edit=sysop:move=sysop]

2016-05-11T00:39:03Z

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

←Older revision

Revision as of 00:39, 11 May 2016

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

2016-05-11T00:39:02Z

New page: '''Unreleased structure''' The entry 5ima 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 5ima 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 F2
[[Category: Unreleased Structures]]
[[Category: Perkins, A]]
[[Category: Karplus, A]]
[[Category: Nelson, K.J]]
[[Category: Parsonage, D]]
[[Category: Poole, L.B]]