2p5q - Revision history

OCA at 09:08, 21 February 2024

OCA — Wed, 21 Feb 2024 09:08:01 GMT

←Older revision		Revision as of 09:08, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='2p5q' size='340' side='right'caption='[[2p5q]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2p5q' size='340' side='right'caption='[[2p5q]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2p5q]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Populus_balsamifera_subsp._trichocarpa_x_populus_deltoides~~ Populus ~~balsamifera subsp.~~ trichocarpa x ~~populus~~ deltoides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P5Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2p5q]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Populus_trichocarpa_x_Populus_deltoides Populus trichocarpa x Populus deltoides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P5Q FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>~~, ~~<scene name='pdbligand=CD:CADMIUM+ION'>CD</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]] 2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[2p5r\|2p5r]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">PtGPX5 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3695 Populus balsamifera subsp. trichocarpa x Populus deltoides])~~</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=2p5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p5q OCA], [https://pdbe.org/2p5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p5q RCSB], [https://www.ebi.ac.uk/pdbsum/2p5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p5q 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=2p5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p5q OCA], [https://pdbe.org/2p5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p5q RCSB], [https://www.ebi.ac.uk/pdbsum/2p5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p5q ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A3FNZ8_9ROSI A3FNZ8_9ROSI]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2p5q ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2p5q ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Glutathione peroxidases (GPXs) are a group of enzymes that regulate the levels of reactive oxygen species in cells and tissues, and protect them against oxidative damage. Contrary to most of their counterparts in animal cells, the higher plant GPX homologues identified so far possess cysteine instead of selenocysteine in their active site. Interestingly, the plant GPXs are not dependent on glutathione but rather on thioredoxin as their in vitro electron donor. We have determined the crystal structures of the reduced and oxidized form of Populus trichocarpaxdeltoides GPX5 (PtGPX5), using a selenomethionine derivative. PtGPX5 exhibits an overall structure similar to that of the known animal GPXs. PtGPX5 crystallized in the assumed physiological dimeric form, displaying a pseudo ten-stranded beta sheet core. Comparison of both redox structures indicates that a drastic conformational change is necessary to bring the two distant cysteine residues together to form an intramolecular disulfide bond. In addition, a computer model of a complex of PtGPX5 and its in vitro recycling partner thioredoxin h1 is proposed on the basis of the crystal packing of the oxidized form enzyme. A possible role of PtGPX5 as a heavy-metal sink is also discussed.
-
-	Crystal structures of a poplar thioredoxin peroxidase that exhibits the structure of glutathione peroxidases: insights into redox-driven conformational changes.,Koh CS, Didierjean C, Navrot N, Panjikar S, Mulliert G, Rouhier N, Jacquot JP, Aubry A, Shawkataly O, Corbier C J Mol Biol. 2007 Jul 13;370(3):512-29. Epub 2007 Apr 19. PMID:17531267<ref>PMID:17531267</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2p5q" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Glutathione peroxidase\|Glutathione peroxidase]]		*[[Glutathione peroxidase\|Glutathione peroxidase]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Populus ~~balsamifera subsp.~~ trichocarpa x ~~populus~~ deltoides]]	+	[[Category: Populus trichocarpa x Populus deltoides]]
-	[[Category: Aubry, A]]	+	[[Category: Aubry A]]
-	[[Category: Corbier, C]]	+	[[Category: Corbier C]]
-	[[Category: Didierjean, C]]	+	[[Category: Didierjean C]]
-	[[Category: Jacquot, J P]]	+	[[Category: Jacquot J-P]]
-	[[Category: Koh~~, C S~~]]	+	[[Category: Koh CS]]
-	[[Category: Mulliert, G]]	+	[[Category: Mulliert G]]
-	[[Category: Navrot, N]]	+	[[Category: Navrot N]]
-	[[Category: Panjikar, S]]	+	[[Category: Panjikar S]]
-	[[Category: Rouhier, N]]	+	[[Category: Rouhier N]]
-	[[Category: Shawkataly, O]]	+	[[Category: Shawkataly O]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Thioredoxin fold~~]]	+

OCA at 15:16, 17 June 2021

OCA — Thu, 17 Jun 2021 15:16:44 GMT

←Older revision		Revision as of 15:16, 17 June 2021
Line 1:		Line 1:

	==Crystal structure of the poplar glutathione peroxidase 5 in the reduced form==		==Crystal structure of the poplar glutathione peroxidase 5 in the reduced form==
-	<StructureSection load='2p5q' size='340' side='right' caption='[[2p5q]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='2p5q' size='340' side='right'caption='[[2p5q]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2p5q]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Populus_balsamifera_subsp._trichocarpa_x_populus_deltoides Populus balsamifera subsp. trichocarpa x populus deltoides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P5Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2P5Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2p5q]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Populus_balsamifera_subsp._trichocarpa_x_populus_deltoides Populus balsamifera subsp. trichocarpa x populus deltoides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P5Q FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2p5r\|2p5r]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2p5r\|2p5r]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PtGPX5 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3695 Populus balsamifera subsp. trichocarpa x Populus deltoides])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PtGPX5 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3695 Populus balsamifera subsp. trichocarpa x Populus deltoides])</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=2p5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p5q OCA], [~~http~~://pdbe.org/2p5q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2p5q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2p5q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2p5q 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=2p5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p5q OCA], [https://pdbe.org/2p5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p5q RCSB], [https://www.ebi.ac.uk/pdbsum/2p5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p5q ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p5/2p5q_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p5/2p5q_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 2p5q" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2p5q" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Glutathione peroxidase\|Glutathione peroxidase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Populus balsamifera subsp. trichocarpa x populus deltoides]]		[[Category: Populus balsamifera subsp. trichocarpa x populus deltoides]]
	[[Category: Aubry, A]]		[[Category: Aubry, A]]

OCA at 09:18, 18 October 2017

OCA — Wed, 18 Oct 2017 09:18:35 GMT

←Older revision		Revision as of 09:18, 18 October 2017
Line 1:		Line 1:
		+
	==Crystal structure of the poplar glutathione peroxidase 5 in the reduced form==		==Crystal structure of the poplar glutathione peroxidase 5 in the reduced form==
	<StructureSection load='2p5q' size='340' side='right' caption='[[2p5q]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2p5q' size='340' side='right' caption='[[2p5q]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2p5r\|2p5r]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2p5r\|2p5r]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PtGPX5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3695 Populus balsamifera subsp. trichocarpa x Populus deltoides])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PtGPX5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3695 Populus balsamifera subsp. trichocarpa x Populus deltoides])</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=2p5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p5q OCA], [http://pdbe.org/2p5q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2p5q RCSB], [http://www.ebi.ac.uk/pdbsum/2p5q 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=2p5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p5q OCA], [http://pdbe.org/2p5q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2p5q RCSB], [http://www.ebi.ac.uk/pdbsum/2p5q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2p5q ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2p5q ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 2p5q" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2p5q" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Glutathione peroxidase\|Glutathione peroxidase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:12, 11 September 2015

OCA — Fri, 11 Sep 2015 12:12:33 GMT

←Older revision		Revision as of 12:12, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2p5q' size='340' side='right' caption='[[2p5q]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2p5q' size='340' side='right' caption='[[2p5q]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2p5q]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Populus_trichocarpa_x_populus_deltoides~~ Populus trichocarpa x populus deltoides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P5Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2P5Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2p5q]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Populus_balsamifera_subsp._trichocarpa_x_populus_deltoides Populus balsamifera subsp. trichocarpa x populus deltoides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P5Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2P5Q FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2p5r\|2p5r]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2p5r\|2p5r]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PtGPX5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3695 Populus trichocarpa x Populus deltoides])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PtGPX5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3695 Populus balsamifera subsp. trichocarpa x Populus deltoides])</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=2p5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p5q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2p5q RCSB], [http://www.ebi.ac.uk/pdbsum/2p5q 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=2p5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p5q OCA], [http://pdbe.org/2p5q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2p5q RCSB], [http://www.ebi.ac.uk/pdbsum/2p5q PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2p5q" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Populus trichocarpa x populus deltoides]]	+	[[Category: Populus balsamifera subsp. trichocarpa x populus deltoides]]
	[[Category: Aubry, A]]		[[Category: Aubry, A]]
	[[Category: Corbier, C]]		[[Category: Corbier, C]]

OCA at 16:44, 19 January 2015

OCA — Mon, 19 Jan 2015 16:44:26 GMT

←Older revision		Revision as of 16:44, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2p5q]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Populus_trichocarpa_x_populus_deltoides Populus trichocarpa x populus deltoides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P5Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2P5Q FirstGlance]. <br>		<table><tr><td colspan='2'>[[2p5q]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Populus_trichocarpa_x_populus_deltoides Populus trichocarpa x populus deltoides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P5Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2P5Q FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2p5r\|2p5r]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2p5r\|2p5r]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PtGPX5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3695 Populus trichocarpa x Populus deltoides])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PtGPX5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3695 Populus trichocarpa x Populus deltoides])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2p5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p5q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2p5q RCSB], [http://www.ebi.ac.uk/pdbsum/2p5q 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=2p5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p5q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2p5q RCSB], [http://www.ebi.ac.uk/pdbsum/2p5q PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Populus trichocarpa x populus deltoides]]		[[Category: Populus trichocarpa x populus deltoides]]
-	[[Category: Aubry, A.]]	+	[[Category: Aubry, A]]
-	[[Category: Corbier, C.]]	+	[[Category: Corbier, C]]
-	[[Category: Didierjean, C.]]	+	[[Category: Didierjean, C]]
-	[[Category: Jacquot, J P.]]	+	[[Category: Jacquot, J P]]
-	[[Category: Koh, C S.]]	+	[[Category: Koh, C S]]
-	[[Category: Mulliert, G.]]	+	[[Category: Mulliert, G]]
-	[[Category: Navrot, N.]]	+	[[Category: Navrot, N]]
-	[[Category: Panjikar, S.]]	+	[[Category: Panjikar, S]]
-	[[Category: Rouhier, N.]]	+	[[Category: Rouhier, N]]
-	[[Category: Shawkataly, O.]]	+	[[Category: Shawkataly, O]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Thioredoxin fold]]		[[Category: Thioredoxin fold]]

OCA at 08:45, 29 September 2014

OCA — Mon, 29 Sep 2014 08:45:39 GMT

←Older revision		Revision as of 08:45, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2p5q.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the poplar glutathione peroxidase 5 in the reduced form==
		+	<StructureSection load='2p5q' size='340' side='right' caption='[[2p5q]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2p5q]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Populus_trichocarpa_x_populus_deltoides Populus trichocarpa x populus deltoides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P5Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2P5Q FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2p5r\|2p5r]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PtGPX5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3695 Populus trichocarpa x Populus deltoides])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2p5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p5q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2p5q RCSB], [http://www.ebi.ac.uk/pdbsum/2p5q PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p5/2p5q_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Glutathione peroxidases (GPXs) are a group of enzymes that regulate the levels of reactive oxygen species in cells and tissues, and protect them against oxidative damage. Contrary to most of their counterparts in animal cells, the higher plant GPX homologues identified so far possess cysteine instead of selenocysteine in their active site. Interestingly, the plant GPXs are not dependent on glutathione but rather on thioredoxin as their in vitro electron donor. We have determined the crystal structures of the reduced and oxidized form of Populus trichocarpaxdeltoides GPX5 (PtGPX5), using a selenomethionine derivative. PtGPX5 exhibits an overall structure similar to that of the known animal GPXs. PtGPX5 crystallized in the assumed physiological dimeric form, displaying a pseudo ten-stranded beta sheet core. Comparison of both redox structures indicates that a drastic conformational change is necessary to bring the two distant cysteine residues together to form an intramolecular disulfide bond. In addition, a computer model of a complex of PtGPX5 and its in vitro recycling partner thioredoxin h1 is proposed on the basis of the crystal packing of the oxidized form enzyme. A possible role of PtGPX5 as a heavy-metal sink is also discussed.

-	~~{{STRUCTURE_2p5q\| PDB=2p5q \| SCENE= }}~~	+	Crystal structures of a poplar thioredoxin peroxidase that exhibits the structure of glutathione peroxidases: insights into redox-driven conformational changes.,Koh CS, Didierjean C, Navrot N, Panjikar S, Mulliert G, Rouhier N, Jacquot JP, Aubry A, Shawkataly O, Corbier C J Mol Biol. 2007 Jul 13;370(3):512-29. Epub 2007 Apr 19. PMID:17531267<ref>PMID:17531267</ref>

-	~~===Crystal structure~~ of the ~~poplar glutathione peroxidase 5 in the reduced form===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17531267}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2p5q]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Populus_trichocarpa_x_populus_deltoides Populus trichocarpa x populus deltoides]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2P5Q OCA].~~	+

	==See Also==		==See Also==
	*[[Glutathione peroxidase\|Glutathione peroxidase]]		*[[Glutathione peroxidase\|Glutathione peroxidase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:017531267<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Populus trichocarpa x populus deltoides]]		[[Category: Populus trichocarpa x populus deltoides]]
	[[Category: Aubry, A.]]		[[Category: Aubry, A.]]

OCA at 18:48, 20 October 2012

OCA — Sat, 20 Oct 2012 18:48:28 GMT

←Older revision		Revision as of 18:48, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2p5q]] is a 4 chain structure ~~of [[Glutathione peroxidase]]~~ with sequence from [http://en.wikipedia.org/wiki/Populus_trichocarpa_x_populus_deltoides Populus trichocarpa x populus deltoides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P5Q OCA].	+	[[2p5q]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Populus_trichocarpa_x_populus_deltoides Populus trichocarpa x populus deltoides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P5Q OCA].

	==See Also==		==See Also==

OCA: Protected "2p5q" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 05:18:08 GMT

Protected "2p5q" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:18, 27 July 2012

OCA at 05:18, 27 July 2012

OCA — Fri, 27 Jul 2012 05:18:07 GMT

←Older revision		Revision as of 05:18, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2p5q.png\|left\|200px]]		[[Image:2p5q.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2p5q", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2p5q\| PDB=2p5q \| SCENE= }}		{{STRUCTURE_2p5q\| PDB=2p5q \| SCENE= }}

	===Crystal structure of the poplar glutathione peroxidase 5 in the reduced form===		===Crystal structure of the poplar glutathione peroxidase 5 in the reduced form===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17531267}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17531267 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17531267}}		{{ABSTRACT_PUBMED_17531267}}

	==About this Structure==		==About this Structure==
-	~~2P5Q~~ is a 4 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Populus_trichocarpa_x_populus_deltoides Populus trichocarpa x populus deltoides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P5Q OCA].	+	[[2p5q]] is a 4 chain structure of [[Glutathione peroxidase]] with sequence from [http://en.wikipedia.org/wiki/Populus_trichocarpa_x_populus_deltoides Populus trichocarpa x populus deltoides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P5Q OCA].
		+
		+	==See Also==
		+	*[[Glutathione peroxidase\|Glutathione peroxidase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17531267~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017531267</ref><references group="xtra"/>
	[[Category: Populus trichocarpa x populus deltoides]]		[[Category: Populus trichocarpa x populus deltoides]]
	[[Category: Aubry, A.]]		[[Category: Aubry, A.]]
Line 35:		Line 26:
	[[Category: Rouhier, N.]]		[[Category: Rouhier, N.]]
	[[Category: Shawkataly, O.]]		[[Category: Shawkataly, O.]]
		+	[[Category: Oxidoreductase]]
	[[Category: Thioredoxin fold]]		[[Category: Thioredoxin fold]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 21:32:05 2009''

OCA at 19:32, 17 February 2009

OCA — Tue, 17 Feb 2009 19:32:07 GMT

←Older revision		Revision as of 19:32, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2P5Q is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Populus_trichocarpa_x_populus_deltoides Populus trichocarpa x populus deltoides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P5Q OCA].	+	2P5Q is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Populus_trichocarpa_x_populus_deltoides Populus trichocarpa x populus deltoides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P5Q OCA].

	==Reference==		==Reference==
-	Crystal structures of a poplar thioredoxin peroxidase that exhibits the structure of glutathione peroxidases: insights into redox-driven conformational changes., Koh CS, Didierjean C, Navrot N, Panjikar S, Mulliert G, Rouhier N, Jacquot JP, Aubry A, Shawkataly O, Corbier C, J Mol Biol. 2007 Jul 13;370(3):512-29. Epub 2007 Apr 19. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17531267 17531267]~~	+	<ref group="xtra">PMID:17531267</ref><references group="xtra"/>
	[[Category: Populus trichocarpa x populus deltoides]]		[[Category: Populus trichocarpa x populus deltoides]]
-	[[Category: Single protein]]
	[[Category: Aubry, A.]]		[[Category: Aubry, A.]]
	[[Category: Corbier, C.]]		[[Category: Corbier, C.]]
Line 38:		Line 37:
	[[Category: Thioredoxin fold]]		[[Category: Thioredoxin fold]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 05~~:39:~~09 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 21:32:05 2009''