5xvz - Revision history

OCA at 08:15, 22 November 2023

OCA — Wed, 22 Nov 2023 08:15:53 GMT

←Older revision		Revision as of 08:15, 22 November 2023
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	<StructureSection load='5xvz' size='340' side='right'caption='[[5xvz]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5xvz' size='340' side='right'caption='[[5xvz]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xvz]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_16463 Atcc 16463~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XVZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xvz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycothermus_thermophilus Mycothermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XVZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HDD:CIS-HEME+D+HYDROXYCHLORIN+GAMMA-SPIROLACTONE'>HDD</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]] 1.9Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase Catalase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HDD:CIS-HEME+D+HYDROXYCHLORIN+GAMMA-SPIROLACTONE'>HDD</scene></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=5xvz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvz OCA], [~~http~~://pdbe.org/5xvz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xvz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xvz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvz 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=5xvz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvz OCA], [https://pdbe.org/5xvz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xvz RCSB], [https://www.ebi.ac.uk/pdbsum/5xvz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/M4GGR7_9PEZI M4GGR7_9PEZI]] Occurs in almost all aerobically respiring organisms and serves to protect cells from the toxic effects of hydrogen peroxide.[RuleBase:RU004142] Serves to protect cells from the toxic effects of hydrogen peroxide.[PIRNR:PIRNR038927]	+	[https://www.uniprot.org/uniprot/M4GGR7_9PEZI M4GGR7_9PEZI] Occurs in almost all aerobically respiring organisms and serves to protect cells from the toxic effects of hydrogen peroxide.[RuleBase:RU004142] Serves to protect cells from the toxic effects of hydrogen peroxide.[PIRNR:PIRNR038927]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 16463]]
-	[[Category: Catalase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Balci, S~~]]	+	[[Category: Mycothermus thermophilus]]
-	[[Category: ~~Goc, G~~]]	+	[[Category: Balci S]]
-	[[Category: ~~Karakus, Y Yuzugullu~~]]	+	[[Category: Goc G]]
-	[[Category: Pearson~~, A R~~]]	+	[[Category: Pearson AR]]
-	[[Category: Yorke, B]]	+	[[Category: Yorke B]]
-	[[Category: ~~Lateral channel]]~~	+	[[Category: Yuzugullu Karakus Y]]
-	~~[[Category: Mutant]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Phenol oxidase~~]]	+

OCA at 06:42, 31 July 2019

OCA — Wed, 31 Jul 2019 06:42:20 GMT

←Older revision		Revision as of 06:42, 31 July 2019
Line 1:		Line 1:

	==CATPO mutant - H246W==		==CATPO mutant - H246W==
-	<StructureSection load='5xvz' size='340' side='right' caption='[[5xvz]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5xvz' size='340' side='right'caption='[[5xvz]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xvz]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XVZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xvz]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_16463 Atcc 16463]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XVZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HDD:CIS-HEME+D+HYDROXYCHLORIN+GAMMA-SPIROLACTONE'>HDD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HDD:CIS-HEME+D+HYDROXYCHLORIN+GAMMA-SPIROLACTONE'>HDD</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase Catalase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase Catalase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] </span></td></tr>
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/M4GGR7_9PEZI M4GGR7_9PEZI]] Occurs in almost all aerobically respiring organisms and serves to protect cells from the toxic effects of hydrogen peroxide.[RuleBase:RU004142] Serves to protect cells from the toxic effects of hydrogen peroxide.[PIRNR:PIRNR038927]		[[http://www.uniprot.org/uniprot/M4GGR7_9PEZI M4GGR7_9PEZI]] Occurs in almost all aerobically respiring organisms and serves to protect cells from the toxic effects of hydrogen peroxide.[RuleBase:RU004142] Serves to protect cells from the toxic effects of hydrogen peroxide.[PIRNR:PIRNR038927]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The catalase from Scytalidium thermophilum is a homotetramer containing a heme d in each active site. Although the enzyme has a classical monofunctional catalase fold, it also possesses oxidase activity towards a number of small organics, including catechol and phenol. In order to further investigate this, the crystal structure of the complex of the catalase with the classical catalase inhibitor 3-amino-1,2,4-triazole (3TR) was determined at 1.95 A resolution. Surprisingly, no binding to the heme site was observed; instead, 3TR occupies a binding site corresponding to the NADPH-binding pocket in mammalian catalases at the entrance to a lateral channel leading to the heme. Kinetic analysis of site-directed mutants supports the assignment of this pocket as the binding site for oxidase substrates.
		+
		+	Identification of the site of oxidase substrate binding in Scytalidium thermophilum catalase.,Yuzugullu Karakus Y, Goc G, Balci S, Yorke BA, Trinh CH, McPherson MJ, Pearson AR Acta Crystallogr D Struct Biol. 2018 Oct 1;74(Pt 10):979-985. doi:, 10.1107/S2059798318010628. Epub 2018 Oct 2. PMID:30289408<ref>PMID:30289408</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5xvz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Catalase 3D structures\|Catalase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 16463]]
	[[Category: Catalase]]		[[Category: Catalase]]
		+	[[Category: Large Structures]]
	[[Category: Balci, S]]		[[Category: Balci, S]]
	[[Category: Goc, G]]		[[Category: Goc, G]]

OCA at 07:07, 4 July 2018

OCA — Wed, 04 Jul 2018 07:07:56 GMT

←Older revision		Revision as of 07:07, 4 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xvz ~~is ON HOLD until Paper Publication~~	+	==CATPO mutant - H246W==
-		+	<StructureSection load='5xvz' size='340' side='right' caption='[[5xvz]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~Authors~~: ~~Yuzugullu Karakus, Y~~., ~~Goc~~, G., ~~Balci~~, S., ~~Pearson~~, A.R., ~~Yorke~~, B.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5xvz]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XVZ FirstGlance]. <br>
-	~~Description: CATPO mutant -H246W~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HDD:CIS-HEME+D+HYDROXYCHLORIN+GAMMA-SPIROLACTONE'>HDD</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase Catalase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] </span></td></tr>
-	[[Category: ~~Pearson, A.R~~]]	+	<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=5xvz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvz OCA], [http://pdbe.org/5xvz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xvz RCSB], [http://www.ebi.ac.uk/pdbsum/5xvz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvz ProSAT]</span></td></tr>
-	[[Category: ~~Yuzugullu Karakus~~, Y]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/M4GGR7_9PEZI M4GGR7_9PEZI]] Occurs in almost all aerobically respiring organisms and serves to protect cells from the toxic effects of hydrogen peroxide.[RuleBase:RU004142] Serves to protect cells from the toxic effects of hydrogen peroxide.[PIRNR:PIRNR038927]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Catalase]]
		+	[[Category: Balci, S]]
	[[Category: Goc, G]]		[[Category: Goc, G]]
-	[[Category: ~~Balci~~, S]]	+	[[Category: Karakus, Y Yuzugullu]]
		+	[[Category: Pearson, A R]]
	[[Category: Yorke, B]]		[[Category: Yorke, B]]
		+	[[Category: Lateral channel]]
		+	[[Category: Mutant]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Phenol oxidase]]

OCA at 04:02, 6 June 2018

OCA — Wed, 06 Jun 2018 04:02:07 GMT

←Older revision		Revision as of 04:02, 6 June 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5xvz is ON HOLD	+	The entry 5xvz is ON HOLD until Paper Publication

-	Authors: Yuzugullu Karakus, Y., Goc, G., Balci, S., Pearson, A., Yorke, B.	+	Authors: Yuzugullu Karakus, Y., Goc, G., Balci, S., Pearson, A.R., Yorke, B.

	Description: CATPO mutant -H246W		Description: CATPO mutant -H246W
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Balci~~, S]]	+	[[Category: Pearson, A.R]]
		+	[[Category: Yuzugullu Karakus, Y]]
	[[Category: Goc, G]]		[[Category: Goc, G]]
		+	[[Category: Balci, S]]
	[[Category: Yorke, B]]		[[Category: Yorke, B]]
-	[[Category: Pearson, A]]
-	[[Category: Yuzugullu Karakus, Y]]

OCA at 05:44, 23 May 2018

OCA — Wed, 23 May 2018 05:44:48 GMT

←Older revision		Revision as of 05:44, 23 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5xvz is ON HOLD ~~until Paper Publication~~	+	The entry 5xvz is ON HOLD

	Authors: Yuzugullu Karakus, Y., Goc, G., Balci, S., Pearson, A., Yorke, B.		Authors: Yuzugullu Karakus, Y., Goc, G., Balci, S., Pearson, A., Yorke, B.
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	Description: CATPO mutant -H246W		Description: CATPO mutant -H246W
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Balci, S]]
	[[Category: Goc, G]]		[[Category: Goc, G]]
	[[Category: Yorke, B]]		[[Category: Yorke, B]]
-	[[Category: Balci, S]]
	[[Category: Pearson, A]]		[[Category: Pearson, A]]
	[[Category: Yuzugullu Karakus, Y]]		[[Category: Yuzugullu Karakus, Y]]

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

OCA — Wed, 27 Sep 2017 15:50:23 GMT

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

←Older revision

Revision as of 15:50, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5xvz is ON HOLD until Paper Publication Authors: Yuzugullu Karakus, Y., Goc, G., Balci, S., Pearson, A., Yorke, B. Description: CATPO mutant -H246W...

OCA — Wed, 27 Sep 2017 15:50:22 GMT

New page: '''Unreleased structure''' The entry 5xvz is ON HOLD until Paper Publication Authors: Yuzugullu Karakus, Y., Goc, G., Balci, S., Pearson, A., Yorke, B. Description: CATPO mutant -H246W...

New page

'''Unreleased structure'''

The entry 5xvz is ON HOLD until Paper Publication

Authors: Yuzugullu Karakus, Y., Goc, G., Balci, S., Pearson, A., Yorke, B.

Description: CATPO mutant -H246W
[[Category: Unreleased Structures]]
[[Category: Goc, G]]
[[Category: Yorke, B]]
[[Category: Balci, S]]
[[Category: Pearson, A]]
[[Category: Yuzugullu Karakus, Y]]