4xs6 - Revision history

OCA at 07:48, 27 September 2023

OCA — Wed, 27 Sep 2023 07:48:45 GMT

←Older revision		Revision as of 07:48, 27 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xs6]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XS6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XS6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xs6]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XS6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XS6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</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]] 3.35Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></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=4xs6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xs6 OCA], [https://pdbe.org/4xs6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xs6 RCSB], [https://www.ebi.ac.uk/pdbsum/4xs6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xs6 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=4xs6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xs6 OCA], [https://pdbe.org/4xs6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xs6 RCSB], [https://www.ebi.ac.uk/pdbsum/4xs6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xs6 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 17:49, 26 April 2023

OCA — Wed, 26 Apr 2023 17:49:47 GMT

←Older revision		Revision as of 17:49, 26 April 2023
Line 3:		Line 3:
	<StructureSection load='4xs6' size='340' side='right'caption='[[4xs6]], [[Resolution\|resolution]] 3.35Å' scene=''>		<StructureSection load='4xs6' size='340' side='right'caption='[[4xs6]], [[Resolution\|resolution]] 3.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xs6]] is a 5 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XS6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XS6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xs6]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XS6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XS6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xra\|4xra]], [[4xrd\|4xrd]], [[4xs1\|4xs1]], [[4xs4\|4xs4]], [[4xs8\|4xs8]]</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=4xs6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xs6 OCA], [https://pdbe.org/4xs6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xs6 RCSB], [https://www.ebi.ac.uk/pdbsum/4xs6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xs6 ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxiredoxin Peroxiredoxin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.15 1.11.1.15] </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=4xs6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xs6 OCA], [~~http~~://pdbe.org/4xs6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xs6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xs6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xs6 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/AHPC_SALTY AHPC_SALTY]] Directly reduces alkyl hydroperoxides with the use of electrons donated by the 57 kDa flavoprotein alkyl hydroperoxide reductase.	+	[https://www.uniprot.org/uniprot/AHPC_SALTY AHPC_SALTY] Directly reduces alkyl hydroperoxides with the use of electrons donated by the 57 kDa flavoprotein alkyl hydroperoxide reductase.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 20:

	==See Also==		==See Also==
-	*[[Thioredoxin ~~Reductase~~\|Thioredoxin ~~Reductase~~]]	+	*[[Thioredoxin reductase 3D structures\|Thioredoxin reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus typhimurium loeffler 1892]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Peroxiredoxin~~]]	+	[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
-	[[Category: Karplus~~, P A~~]]	+	[[Category: Karplus PA]]
-	[[Category: Nelson, K]]	+	[[Category: Nelson K]]
-	[[Category: Parsonage, D]]	+	[[Category: Parsonage D]]
-	[[Category: Perkins, A]]	+	[[Category: Perkins A]]
-	[[Category: Poole, L]]	+	[[Category: Poole L]]
-	~~[[Category: Conformation]]~~	+
-	~~[[Category: Lu]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Prxi~~]]	+

OCA at 15:47, 28 August 2019

OCA — Wed, 28 Aug 2019 15:47:03 GMT

←Older revision		Revision as of 15:47, 28 August 2019
Line 11:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/AHPC_SALTY AHPC_SALTY]] Directly reduces alkyl hydroperoxides with the use of electrons donated by the 57 kDa flavoprotein alkyl hydroperoxide reductase.		[[http://www.uniprot.org/uniprot/AHPC_SALTY AHPC_SALTY]] Directly reduces alkyl hydroperoxides with the use of electrons donated by the 57 kDa flavoprotein alkyl hydroperoxide reductase.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	AIMS: Peroxiredoxins (Prxs) are ubiquitous cysteine-based peroxidases involved in oxidant defense and signal transduction. Despite much study, the precise roles of conserved residues remain poorly defined. In this study, we carried out extensive functional and structural characterization of 10 variants of such residues in a model decameric bacterial Prx. RESULTS: Three active site proximal mutations of Salmonella typhimurium AhpC, T43V, R119A, and E49Q, lowered catalytic efficiency with hydrogen peroxide by 4-5 orders of magnitude, but did not affect reactivity toward their reductant, AhpF. pKa values of the peroxidatic cysteine were also shifted up by 1-1.3 pH units for these and a decamer disruption mutant, T77I. Except for the decamer-stabilizing T77V, all mutations destabilized decamers in the reduced form. In the oxidized form, three mutants-T77V, T43A, and T43S-exhibited stabilized decamers and were more efficiently reduced by AhpF than wild-type AhpC. Crystal structures of most mutants were solved and many showed alterations in stability of the fully folded active site loop. INNOVATION: This is the first study of Prx mutants to comprehensively assess the effects of mutations on catalytic activities, the active site cysteine pKa, and the protein structure and oligomeric status. CONCLUSION: The Arg119 side chain must be properly situated for efficient catalysis, but for other debilitating variants, the functional defects could be explained by structural perturbations and/or associated decamer destabilization rather than direct effects. This underscores the importance of our comprehensive approach. A remarkable new finding was the preference of the reductant for decamers. Antioxid. Redox Signal. 28, 521-536.
		+
		+	Experimentally Dissecting the Origins of Peroxiredoxin Catalysis.,Nelson KJ, Perkins A, Van Swearingen AED, Hartman S, Brereton AE, Parsonage D, Salsbury FR Jr, Karplus PA, Poole LB Antioxid Redox Signal. 2018 Mar 1;28(7):521-536. doi: 10.1089/ars.2016.6922. Epub, 2017 Apr 4. PMID:28375740<ref>PMID:28375740</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4xs6" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Thioredoxin Reductase\|Thioredoxin Reductase]]		*[[Thioredoxin Reductase\|Thioredoxin Reductase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 23:40, 5 June 2019

OCA — Wed, 05 Jun 2019 23:40:55 GMT

←Older revision		Revision as of 23:40, 5 June 2019
Line 1:		Line 1:
		+
	==Salmonella typhimurium AhpC W81F mutant==		==Salmonella typhimurium AhpC W81F mutant==
-	<StructureSection load='4xs6' size='340' side='right' caption='[[4xs6]], [[Resolution\|resolution]] 3.35Å' scene=''>	+	<StructureSection load='4xs6' size='340' side='right'caption='[[4xs6]], [[Resolution\|resolution]] 3.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xs6]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XS6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XS6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xs6]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XS6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XS6 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xra\|4xra]], [[4xrd\|4xrd]], [[4xs1\|4xs1]], [[4xs4\|4xs4]], [[4xs8\|4xs8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xra\|4xra]], [[4xrd\|4xrd]], [[4xs1\|4xs1]], [[4xs4\|4xs4]], [[4xs8\|4xs8]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxiredoxin Peroxiredoxin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.15 1.11.1.15] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxiredoxin Peroxiredoxin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.15 1.11.1.15] </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=4xs6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xs6 OCA], [http://pdbe.org/4xs6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xs6 RCSB], [http://www.ebi.ac.uk/pdbsum/4xs6 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=4xs6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xs6 OCA], [http://pdbe.org/4xs6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xs6 RCSB], [http://www.ebi.ac.uk/pdbsum/4xs6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xs6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/AHPC_SALTY AHPC_SALTY]] Directly reduces alkyl hydroperoxides with the use of electrons donated by the 57 kDa flavoprotein alkyl hydroperoxide reductase.		[[http://www.uniprot.org/uniprot/AHPC_SALTY AHPC_SALTY]] Directly reduces alkyl hydroperoxides with the use of electrons donated by the 57 kDa flavoprotein alkyl hydroperoxide reductase.
		+
		+	==See Also==
		+	*[[Thioredoxin Reductase\|Thioredoxin Reductase]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus typhimurium loeffler 1892]]
		+	[[Category: Large Structures]]
	[[Category: Peroxiredoxin]]		[[Category: Peroxiredoxin]]
	[[Category: Karplus, P A]]		[[Category: Karplus, P A]]

OCA at 02:29, 28 January 2016

OCA — Thu, 28 Jan 2016 02:29:45 GMT

←Older revision		Revision as of 02:29, 28 January 2016
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Salmonella typhimurium AhpC W81F mutant==
-		+	<StructureSection load='4xs6' size='340' side='right' caption='[[4xs6]], [[Resolution\|resolution]] 3.35Å' scene=''>
-	~~The entry~~ 4xs6 is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4xs6]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XS6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XS6 FirstGlance]. <br>
-	~~Authors~~: ~~Perkins~~, A., ~~Nelson~~, ~~K., Parsonage~~, D.~~, Poole, L~~., ~~Karplus, P~~.A.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
-		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xra\|4xra]], [[4xrd\|4xrd]], [[4xs1\|4xs1]], [[4xs4\|4xs4]], [[4xs8\|4xs8]]</td></tr>
-	~~Description~~: ~~Salmonella typhimurium AhpC W81F mutant~~	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxiredoxin Peroxiredoxin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.15 1.11.1.15] </span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=4xs6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xs6 OCA], [http://pdbe.org/4xs6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xs6 RCSB], [http://www.ebi.ac.uk/pdbsum/4xs6 PDBsum]</span></td></tr>
-	[~~[Category~~: ~~Poole~~, L]]	+	</table>
-	[[~~Category~~: ~~Perkins, A~~]]	+	== Function ==
-	[[Category: ~~Karplus, P.A~~]]	+	[[http://www.uniprot.org/uniprot/AHPC_SALTY AHPC_SALTY]] Directly reduces alkyl hydroperoxides with the use of electrons donated by the 57 kDa flavoprotein alkyl hydroperoxide reductase.
-	[[Category: ~~Parsonage~~, D]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Peroxiredoxin]]
		+	[[Category: Karplus, P A]]
	[[Category: Nelson, K]]		[[Category: Nelson, K]]
		+	[[Category: Parsonage, D]]
		+	[[Category: Perkins, A]]
		+	[[Category: Poole, L]]
		+	[[Category: Conformation]]
		+	[[Category: Lu]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Prxi]]

OCA at 10:05, 18 March 2015

OCA — Wed, 18 Mar 2015 10:05:13 GMT

←Older revision		Revision as of 10:05, 18 March 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xs6 is ON HOLD	+	The entry 4xs6 is ON HOLD until Paper Publication

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

OCA at 14:45, 7 February 2015

OCA — Sat, 07 Feb 2015 14:45:59 GMT

←Older revision		Revision as of 14:45, 7 February 2015
Line 3:		Line 3:
	The entry 4xs6 is ON HOLD		The entry 4xs6 is ON HOLD

-	Authors: Perkins, A., Nelson, K., Parsonage, D., Poole, L., Karplus, P. A.	+	Authors: Perkins, A., Nelson, K., Parsonage, D., Poole, L., Karplus, P.A.

	Description: Salmonella typhimurium AhpC W81F mutant		Description: Salmonella typhimurium AhpC W81F mutant
Line 9:		Line 9:
	[[Category: Poole, L]]		[[Category: Poole, L]]
	[[Category: Perkins, A]]		[[Category: Perkins, A]]
		+	[[Category: Karplus, P.A]]
	[[Category: Parsonage, D]]		[[Category: Parsonage, D]]
	[[Category: Nelson, K]]		[[Category: Nelson, K]]
-	[[Category: Karplus, P. A]]

OCA: Protected "4xs6" [edit=sysop:move=sysop]

OCA — Wed, 28 Jan 2015 15:46:38 GMT

Protected "4xs6" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:46, 28 January 2015

OCA: New page: '''Unreleased structure''' The entry 4xs6 is ON HOLD Authors: Perkins, A., Nelson, K., Parsonage, D., Poole, L., Karplus, P. A. Description: Salmonella typhimurium AhpC W81F mutant [[C...

OCA — Wed, 28 Jan 2015 15:46:37 GMT

New page: '''Unreleased structure''' The entry 4xs6 is ON HOLD Authors: Perkins, A., Nelson, K., Parsonage, D., Poole, L., Karplus, P. A. Description: Salmonella typhimurium AhpC W81F mutant [[C...

New page

'''Unreleased structure'''

The entry 4xs6 is ON HOLD

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

Description: Salmonella typhimurium AhpC W81F mutant
[[Category: Unreleased Structures]]
[[Category: Poole, L]]
[[Category: Perkins, A]]
[[Category: Parsonage, D]]
[[Category: Nelson, K]]
[[Category: Karplus, P. A]]