6rjn - Revision history

OCA at 12:21, 24 January 2024

OCA — Wed, 24 Jan 2024 12:21:47 GMT

←Older revision		Revision as of 12:21, 24 January 2024
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	<StructureSection load='6rjn' size='340' side='right'caption='[[6rjn]], [[Resolution\|resolution]] 2.29Å' scene=''>		<StructureSection load='6rjn' size='340' side='right'caption='[[6rjn]], [[Resolution\|resolution]] 2.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6rjn]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RJN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6RJN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6rjn]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Komagataella_pastoris Komagataella pastoris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RJN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RJN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.295Å</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6rjn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rjn OCA], [~~http~~://pdbe.org/6rjn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6rjn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6rjn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6rjn 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=6rjn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rjn OCA], [https://pdbe.org/6rjn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6rjn RCSB], [https://www.ebi.ac.uk/pdbsum/6rjn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6rjn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/C1PHG1_PICPA C1PHG1_PICPA]] Occurs in almost all aerobically respiring organisms and serves to protect cells from the toxic effects of hydrogen peroxide.[RuleBase:RU004142]	+	[https://www.uniprot.org/uniprot/C1PHG1_PICPA C1PHG1_PICPA] Occurs in almost all aerobically respiring organisms and serves to protect cells from the toxic effects of hydrogen peroxide.[RuleBase:RU004142]
	<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 6rjn" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6rjn" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Catalase 3D structures\|Catalase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Catalase~~]]	+	[[Category: Komagataella pastoris]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Brangbour, C]]	+	[[Category: Brangbour C]]
-	[[Category: Fernandez~~, F J~~]]	+	[[Category: Fernandez FJ]]
-	[[Category: Fulla, D]]	+	[[Category: Fulla D]]
-	[[Category: Gomez, S]]	+	[[Category: Gomez S]]
-	[[Category: Juanhuix, J]]	+	[[Category: Juanhuix J]]
-	[[Category: Lopez-Estepa, M]]	+	[[Category: Lopez-Estepa M]]
-	[[Category: Navas-Yuste, S]]	+	[[Category: Navas-Yuste S]]
-	[[Category: Payne~~, A M~~]]	+	[[Category: Payne AM]]
-	[[Category: Rivera, W]]	+	[[Category: Rivera W]]
-	[[Category: Vega~~, M C]]~~	+	[[Category: Vega MC]]
-	~~[[Category: Heme]]~~	+
-	~~[[Category: Nadp]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Pichia pastori~~]]	+

OCA at 06:47, 4 March 2020

OCA — Wed, 04 Mar 2020 06:47:56 GMT

←Older revision		Revision as of 06:47, 4 March 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6rjn is ~~ON HOLD~~	+	==Crystal structure of a Fungal Catalase at 2.3 Angstroms==
		+	<StructureSection load='6rjn' size='340' side='right'caption='[[6rjn]], [[Resolution\|resolution]] 2.29Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6rjn]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RJN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RJN FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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='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=6rjn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rjn OCA], [http://pdbe.org/6rjn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rjn RCSB], [http://www.ebi.ac.uk/pdbsum/6rjn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rjn ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/C1PHG1_PICPA C1PHG1_PICPA]] Occurs in almost all aerobically respiring organisms and serves to protect cells from the toxic effects of hydrogen peroxide.[RuleBase:RU004142]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Catalases are among the main scavengers of reactive oxygen species (ROS) present in the peroxisome, thereby preventing oxidative cellular and tissular damage. In human, multiple diseases are associated with malfunction of these organelles, which causes accumulation of ROS species and consequently the inefficient detoxification of cells. Despite intense research, much remains to be clarified about the precise molecular role of catalase in cellular homeostasis. Yeast peroxisomes and their peroxisomal catalases have been used as eukaryotic models for oxidative metabolism, ROS generation and detoxification, and associated pathologies. In order to provide reliable models for oxidative metabolism research, we have determined the high-resolution crystal structures of peroxisomal catalase from two important biotechnology and basic biology yeast models, Pichia pastoris and Kluyveromyces lactis. We have performed an extensive functional, biochemical and stability characterization of both enzymes in order to establish their differential activity profiles. Furthermore, we have analyzed the role of the peroxisomal catalase under study in the survival of yeast to oxidative burst challenges combining methanol, water peroxide, and sodium chloride. Interestingly, whereas catalase activity was induced 200-fold upon challenging the methylotrophic P. pastoris cells with methanol, the increase in catalase activity in the non-methylotrophic K. lactis was only moderate. The inhibitory effect of sodium azide and beta-mercaptoethanol over both catalases was analyzed, establishing IC50 values for both compounds that are consistent with an elevated resistance of both enzymes toward these inhibitors. Structural comparison of these two novel catalase structures allows us to rationalize the differential susceptibility to inhibitors and oxidative bursts. The inherent worth and validity of the P. pastoris and K. lactis yeast models for oxidative damage will be strengthened by the availability of reliable structural-functional information on these enzymes, which are central to our understanding of peroxisomal response toward oxidative stress.

-	~~Authors~~:	+	Peroxisomal catalases from the yeasts Pichia pastoris and Kluyveromyces lactis as models for oxidative damage in higher eukaryotes.,Gomez S, Navas-Yuste S, Payne AM, Rivera W, Lopez-Estepa M, Brangbour C, Fulla D, Juanhuix J, Fernandez FJ, Vega MC Free Radic Biol Med. 2019 Sep;141:279-290. doi:, 10.1016/j.freeradbiomed.2019.06.025. Epub 2019 Jun 22. PMID:31238127<ref>PMID:31238127</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6rjn" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Catalase]]
		+	[[Category: Large Structures]]
		+	[[Category: Brangbour, C]]
		+	[[Category: Fernandez, F J]]
		+	[[Category: Fulla, D]]
		+	[[Category: Gomez, S]]
		+	[[Category: Juanhuix, J]]
		+	[[Category: Lopez-Estepa, M]]
		+	[[Category: Navas-Yuste, S]]
		+	[[Category: Payne, A M]]
		+	[[Category: Rivera, W]]
		+	[[Category: Vega, M C]]
		+	[[Category: Heme]]
		+	[[Category: Nadp]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Pichia pastori]]

OCA: Protected "6rjn" [edit=sysop:move=sysop]

OCA — Fri, 10 May 2019 08:21:48 GMT

Protected "6rjn" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:21, 10 May 2019

OCA: New page: '''Unreleased structure''' The entry 6rjn is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Fri, 10 May 2019 08:21:46 GMT

New page: '''Unreleased structure''' The entry 6rjn is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6rjn is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]