2vka - Revision history

OCA at 15:22, 13 December 2023

OCA — Wed, 13 Dec 2023 15:22:50 GMT

←Older revision		Revision as of 15:22, 13 December 2023
Line 3:		Line 3:
	<StructureSection load='2vka' size='340' side='right'caption='[[2vka]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2vka' size='340' side='right'caption='[[2vka]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vka]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Boletus_of_the_steppes Boletus of the steppes~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VKA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vka]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pleurotus_eryngii Pleurotus eryngii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VKA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 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;'>[[2boq\|2boq]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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'>[https://en.wikipedia.org/wiki/Versatile_peroxidase Versatile peroxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.16 1.11.1.16] </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=2vka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vka OCA], [https://pdbe.org/2vka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vka RCSB], [https://www.ebi.ac.uk/pdbsum/2vka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vka 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=2vka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vka OCA], [https://pdbe.org/2vka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vka RCSB], [https://www.ebi.ac.uk/pdbsum/2vka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vka ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/VPL2_PLEER VPL2_PLEER]] A versatile ligninolytic peroxidase that combines the substrate specificity characteristics of the two other ligninolytic peroxidases, manganese peroxidase and lignin peroxidase.<ref>PMID:9987124</ref>	+	[https://www.uniprot.org/uniprot/VPL2_PLEER VPL2_PLEER] A versatile ligninolytic peroxidase that combines the substrate specificity characteristics of the two other ligninolytic peroxidases, manganese peroxidase and lignin peroxidase.<ref>PMID:9987124</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Boletus of the steppes]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Versatile peroxidase~~]]	+	[[Category: Pleurotus eryngii]]
-	[[Category: Martinez~~, A T~~]]	+	[[Category: Martinez AT]]
-	[[Category: Martinez~~, M J~~]]	+	[[Category: Martinez MJ]]
-	[[Category: Mate~~, M J~~]]	+	[[Category: Mate MJ]]
-	[[Category: Morales, M]]	+	[[Category: Morales M]]
-	[[Category: Romero, A]]	+	[[Category: Romero A]]
-	[[Category: Ruiz-Duenas~~, F J~~]]	+	[[Category: Ruiz-Duenas FJ]]
-	[[Category: Smith, A]]	+	[[Category: Smith A]]
-	~~[[Category: Aromatic-substrate binding]]~~	+
-	~~[[Category: Lignin degradation]]~~	+
-	~~[[Category: Lignin peroxidase]]~~	+
-	~~[[Category: Manganese peroxidase]]~~	+
-	~~[[Category: Mn-independent oxidation]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Polyvalent peroxidase~~]]	+

OCA at 11:38, 30 March 2022

OCA — Wed, 30 Mar 2022 11:38:52 GMT

←Older revision		Revision as of 11:38, 30 March 2022
Line 3:		Line 3:
	<StructureSection load='2vka' size='340' side='right'caption='[[2vka]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2vka' size='340' side='right'caption='[[2vka]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vka]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Boletus_of_the_steppes Boletus of the steppes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2VKA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vka]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Boletus_of_the_steppes Boletus of the steppes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VKA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2boq\|2boq]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2boq\|2boq]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Versatile_peroxidase Versatile peroxidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.16 1.11.1.16] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Versatile_peroxidase Versatile peroxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.16 1.11.1.16] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=2vka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vka OCA], [~~http~~://pdbe.org/2vka PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2vka RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2vka PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2vka 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=2vka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vka OCA], [https://pdbe.org/2vka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vka RCSB], [https://www.ebi.ac.uk/pdbsum/2vka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vka ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/VPL2_PLEER VPL2_PLEER]] A versatile ligninolytic peroxidase that combines the substrate specificity characteristics of the two other ligninolytic peroxidases, manganese peroxidase and lignin peroxidase.<ref>PMID:9987124</ref>	+	[[https://www.uniprot.org/uniprot/VPL2_PLEER VPL2_PLEER]] A versatile ligninolytic peroxidase that combines the substrate specificity characteristics of the two other ligninolytic peroxidases, manganese peroxidase and lignin peroxidase.<ref>PMID:9987124</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:03, 25 June 2020

OCA — Thu, 25 Jun 2020 08:03:16 GMT

←Older revision		Revision as of 08:03, 25 June 2020
Line 1:		Line 1:

	==Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus eryngii Versatile Peroxidase==		==Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus eryngii Versatile Peroxidase==
-	<StructureSection load='2vka' size='340' side='right' caption='[[2vka]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='2vka' size='340' side='right'caption='[[2vka]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vka]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Boletus_of_the_steppes Boletus of the steppes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKA OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2VKA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vka]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Boletus_of_the_steppes Boletus of the steppes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2VKA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2boq\|2boq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2boq\|2boq]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Versatile_peroxidase Versatile peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.16 1.11.1.16] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Versatile_peroxidase Versatile peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.16 1.11.1.16] </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=2vka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vka OCA], [http://pdbe.org/2vka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vka RCSB], [http://www.ebi.ac.uk/pdbsum/2vka PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vka ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2vka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vka OCA], [http://pdbe.org/2vka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vka RCSB], [http://www.ebi.ac.uk/pdbsum/2vka PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vka ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Boletus of the steppes]]		[[Category: Boletus of the steppes]]
		+	[[Category: Large Structures]]
	[[Category: Versatile peroxidase]]		[[Category: Versatile peroxidase]]
	[[Category: Martinez, A T]]		[[Category: Martinez, A T]]

OCA at 21:04, 19 September 2018

OCA — Wed, 19 Sep 2018 21:04:12 GMT

←Older revision		Revision as of 21:04, 19 September 2018
Line 1:		Line 1:
-	==~~SITE~~-~~DIRECTED MUTAGENESIS OF THE CATALYTIC TRYPTOPHAN ENVIRONMENT IN PLEUROTUS ERYNGII VERSATILE PEROXIDASE~~==	+
		+	==Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus eryngii Versatile Peroxidase==
	<StructureSection load='2vka' size='340' side='right' caption='[[2vka]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2vka' size='340' side='right' caption='[[2vka]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2boq\|2boq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2boq\|2boq]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Versatile_peroxidase Versatile peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.16 1.11.1.16] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Versatile_peroxidase Versatile peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.16 1.11.1.16] </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=2vka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vka OCA], [http://pdbe.org/2vka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vka RCSB], [http://www.ebi.ac.uk/pdbsum/2vka 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=2vka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vka OCA], [http://pdbe.org/2vka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vka RCSB], [http://www.ebi.ac.uk/pdbsum/2vka PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vka ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vk/2vka_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vk/2vka_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>

OCA at 03:03, 9 February 2016

OCA — Tue, 09 Feb 2016 03:03:55 GMT

←Older revision		Revision as of 03:03, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='2vka' size='340' side='right' caption='[[2vka]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2vka' size='340' side='right' caption='[[2vka]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vka]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pleurotus_eryngii Pleurotus eryngii~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VKA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vka]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Boletus_of_the_steppes Boletus of the steppes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VKA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2boq\|2boq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2boq\|2boq]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Versatile_peroxidase Versatile peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.16 1.11.1.16] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Versatile_peroxidase Versatile peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.16 1.11.1.16] </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=2vka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vka OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vka RCSB], [http://www.ebi.ac.uk/pdbsum/2vka 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=2vka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vka OCA], [http://pdbe.org/2vka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vka RCSB], [http://www.ebi.ac.uk/pdbsum/2vka PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	<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=2vka ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 28:
	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 2vka" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pleurotus eryngii~~]]	+	[[Category: Boletus of the steppes]]
	[[Category: Versatile peroxidase]]		[[Category: Versatile peroxidase]]
	[[Category: Martinez, A T]]		[[Category: Martinez, A T]]

OCA at 03:58, 25 December 2014

OCA — Thu, 25 Dec 2014 03:58:05 GMT

←Older revision		Revision as of 03:58, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2vka]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pleurotus_eryngii Pleurotus eryngii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VKA FirstGlance]. <br>		<table><tr><td colspan='2'>[[2vka]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pleurotus_eryngii Pleurotus eryngii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VKA FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2boq\|2boq]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2boq\|2boq]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Versatile_peroxidase Versatile peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.16 1.11.1.16] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Versatile_peroxidase Versatile peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.16 1.11.1.16] </span></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=2vka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vka OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vka RCSB], [http://www.ebi.ac.uk/pdbsum/2vka 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=2vka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vka OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vka RCSB], [http://www.ebi.ac.uk/pdbsum/2vka PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VPL2_PLEER VPL2_PLEER]] A versatile ligninolytic peroxidase that combines the substrate specificity characteristics of the two other ligninolytic peroxidases, manganese peroxidase and lignin peroxidase.<ref>PMID:9987124</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	[[Category: Pleurotus eryngii]]		[[Category: Pleurotus eryngii]]
	[[Category: Versatile peroxidase]]		[[Category: Versatile peroxidase]]
-	[[Category: Martinez, A T.]]	+	[[Category: Martinez, A T]]
-	[[Category: Martinez, M J.]]	+	[[Category: Martinez, M J]]
-	[[Category: Mate, M J.]]	+	[[Category: Mate, M J]]
-	[[Category: Morales, M.]]	+	[[Category: Morales, M]]
-	[[Category: Romero, A.]]	+	[[Category: Romero, A]]
-	[[Category: Ruiz-Duenas, F J.]]	+	[[Category: Ruiz-Duenas, F J]]
-	[[Category: Smith, A.]]	+	[[Category: Smith, A]]
	[[Category: Aromatic-substrate binding]]		[[Category: Aromatic-substrate binding]]
	[[Category: Lignin degradation]]		[[Category: Lignin degradation]]

OCA at 01:33, 1 October 2014

OCA — Wed, 01 Oct 2014 01:33:50 GMT

←Older revision		Revision as of 01:33, 1 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2vka.~~png~~\|~~left~~\|200px]]	+	==SITE-DIRECTED MUTAGENESIS OF THE CATALYTIC TRYPTOPHAN ENVIRONMENT IN PLEUROTUS ERYNGII VERSATILE PEROXIDASE==
		+	<StructureSection load='2vka' size='340' side='right' caption='[[2vka]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2vka]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pleurotus_eryngii Pleurotus eryngii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VKA FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2boq\|2boq]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Versatile_peroxidase Versatile peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.16 1.11.1.16] </span></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=2vka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vka OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vka RCSB], [http://www.ebi.ac.uk/pdbsum/2vka 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/vk/2vka_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 ==
		+	Lignin degradation by fungal peroxidases is initiated by one-electron transfer to an exposed tryptophan radical, a reaction mediated by veratryl alcohol (VA) in lignin peroxidase (LiP). Versatile peroxidase (VP) differs not only in its oxidation of Mn2+ at a second catalytic site but also in its ability to directly oxidize different aromatic compounds. The catalytic tryptophan environment was compared in LiP and VP crystal structures, and six residues near VP Trp164 were modified by site-directed mutagenesis. Oxidation of Mn2+ was practically unaffected. However, several mutations modified the oxidation kinetics of the high-redox-potential substrates VA and Reactive Black 5 (RB5), demonstrating that other residues contribute to substrate oxidation by the Trp164 radical. Introducing acidic residues at the tryptophan environment did not increase the efficiency of VP oxidizing VA. On the contrary, all variants harboring the R257D mutation lost their activity on RB5. Interestingly, this activity was restored when VA was added as a mediator, revealing the LiP-type behavior of this variant. Moreover, combination of the A260F and R257A mutations strongly increased (20-50-fold) the apparent second-order rate constants for reduction of VP compounds I and II by VA to values similar to those found in LiP. Dissociation of the enzyme-product complex seemed to be the limiting step in the turnover of this improved variant. Nonexposed residues in the vicinity of Trp164 can also affect VP activity, as found with the M247F mutation. This was a direct effect since no modification of the surrounding residues was found in the crystal structure of this variant.

-	~~{{STRUCTURE_2vka\| PDB=2vka \| SCENE= }}~~	+	Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus eryngii Versatile Peroxidase(,).,Ruiz-Duenas FJ, Morales M, Mate MJ, Romero A, Martinez MJ, Smith AT, Martinez AT Biochemistry. 2008 Feb 12;47(6):1685-95. Epub 2008 Jan 18. PMID:18201105<ref>PMID:18201105</ref>

-	~~===SITE-DIRECTED MUTAGENESIS OF THE CATALYTIC TRYPTOPHAN ENVIRONMENT IN PLEUROTUS ERYNGII VERSATILE PEROXIDASE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18201105}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2vka]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pleurotus_eryngii Pleurotus eryngii]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2VKA OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018201105<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Pleurotus eryngii]]		[[Category: Pleurotus eryngii]]
	[[Category: Versatile peroxidase]]		[[Category: Versatile peroxidase]]

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

OCA — Mon, 07 Jan 2013 19:35:23 GMT

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

←Older revision

Revision as of 19:35, 7 January 2013

OCA at 19:35, 7 January 2013

OCA — Mon, 07 Jan 2013 19:35:21 GMT

←Older revision		Revision as of 19:35, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2vka.png\|left\|200px]]		[[Image:2vka.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2vka", 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_2vka\| PDB=2vka \| SCENE= }}		{{STRUCTURE_2vka\| PDB=2vka \| SCENE= }}

	===SITE-DIRECTED MUTAGENESIS OF THE CATALYTIC TRYPTOPHAN ENVIRONMENT IN PLEUROTUS ERYNGII VERSATILE PEROXIDASE===		===SITE-DIRECTED MUTAGENESIS OF THE CATALYTIC TRYPTOPHAN ENVIRONMENT IN PLEUROTUS ERYNGII VERSATILE PEROXIDASE===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18201105}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18201105 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18201105}}		{{ABSTRACT_PUBMED_18201105}}

	==About this Structure==		==About this Structure==
-	~~2VKA~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Pleurotus_eryngii Pleurotus eryngii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKA OCA].	+	[[2vka]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pleurotus_eryngii Pleurotus eryngii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKA OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18201105~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018201105</ref><references group="xtra"/>
	[[Category: Pleurotus eryngii]]		[[Category: Pleurotus eryngii]]
		+	[[Category: Versatile peroxidase]]
	[[Category: Martinez, A T.]]		[[Category: Martinez, A T.]]
	[[Category: Martinez, M J.]]		[[Category: Martinez, M J.]]
Line 32:		Line 21:
	[[Category: Ruiz-Duenas, F J.]]		[[Category: Ruiz-Duenas, F J.]]
	[[Category: Smith, A.]]		[[Category: Smith, A.]]
-	[[Category: Allelic variant]]
	[[Category: Aromatic-substrate binding]]		[[Category: Aromatic-substrate binding]]
-	[[Category: Electron transfer]]
-	[[Category: Homology modeling]]
	[[Category: Lignin degradation]]		[[Category: Lignin degradation]]
	[[Category: Lignin peroxidase]]		[[Category: Lignin peroxidase]]
	[[Category: Manganese peroxidase]]		[[Category: Manganese peroxidase]]
-	[[Category: Mn-independent ~~oxidation phenolic non-phenolic aromatic]]~~	+	[[Category: Mn-independent oxidation]]
-	~~[[Category: Mnii~~ oxidation]]	+
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-	[[Category: Peroxidase]]
	[[Category: Polyvalent peroxidase]]		[[Category: Polyvalent peroxidase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 05:57:04 2009''

OCA at 03:57, 17 February 2009

OCA — Tue, 17 Feb 2009 03:57:05 GMT

←Older revision		Revision as of 03:57, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2VKA is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Pleurotus_eryngii Pleurotus eryngii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKA OCA].	+	2VKA is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Pleurotus_eryngii Pleurotus eryngii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKA OCA].

	==Reference==		==Reference==
-	Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus eryngii Versatile Peroxidase(,)., Ruiz-Duenas FJ, Morales M, Mate MJ, Romero A, Martinez MJ, Smith AT, Martinez AT, Biochemistry. 2008 Feb 12;47(6):1685-95. Epub 2008 Jan 18. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18201105 18201105]~~	+	<ref group="xtra">PMID:18201105</ref><references group="xtra"/>
	[[Category: Pleurotus eryngii]]		[[Category: Pleurotus eryngii]]
-	[[Category: Single protein]]
	[[Category: Martinez, A T.]]		[[Category: Martinez, A T.]]
	[[Category: Martinez, M J.]]		[[Category: Martinez, M J.]]
Line 46:		Line 45:
	[[Category: Polyvalent peroxidase]]		[[Category: Polyvalent peroxidase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 09~~:24:~~24 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 05:57:04 2009''