5abn - Revision history

OCA at 11:06, 10 January 2024

2024-01-10T11:06:55Z

←Older revision		Revision as of 11:06, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5abn]] 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=5ABN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ABN FirstGlance]. <br>		<table><tr><td colspan='2'>[[5abn]] 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=5ABN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ABN 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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.194Å</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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5abn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5abn OCA], [https://pdbe.org/5abn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5abn RCSB], [https://www.ebi.ac.uk/pdbsum/5abn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5abn 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=5abn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5abn OCA], [https://pdbe.org/5abn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5abn RCSB], [https://www.ebi.ac.uk/pdbsum/5abn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5abn ProSAT]</span></td></tr>
	</table>		</table>

OCA at 04:49, 25 May 2023

2023-05-25T04:49:52Z

←Older revision		Revision as of 04:49, 25 May 2023
Line 3:		Line 3:
	<StructureSection load='5abn' size='340' side='right'caption='[[5abn]], [[Resolution\|resolution]] 2.19Å' scene=''>		<StructureSection load='5abn' size='340' side='right'caption='[[5abn]], [[Resolution\|resolution]] 2.19Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5abn]] 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=5ABN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ABN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5abn]] 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=5ABN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ABN 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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5abo\|5abo]], [[5abq\|5abq]]</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=5abn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5abn OCA], [https://pdbe.org/5abn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5abn RCSB], [https://www.ebi.ac.uk/pdbsum/5abn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5abn ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/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=5abn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5abn OCA], [~~http~~://pdbe.org/5abn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5abn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5abn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5abn 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>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Boletus of the steppes]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Versatile peroxidase~~]]	+	[[Category: Pleurotus eryngii]]
-	[[Category: Medrano~~, F J~~]]	+	[[Category: Medrano FJ]]
-	[[Category: Romero, A]]	+	[[Category: Romero A]]
-	~~[[Category: Electron transfer]]~~	+
-	~~[[Category: Heme]]~~	+
-	~~[[Category: Hydrogen peroxide]]~~	+
-	~~[[Category: Iron]]~~	+
-	~~[[Category: Lignin degradation]]~~	+
-	~~[[Category: Lignin peroxidase]]~~	+
-	~~[[Category: Manganese]]~~	+
-	~~[[Category: Manganese peroxidase]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Mn-independent oxidation phenolic non-phenolic aromatic]]~~	+
-	~~[[Category: Mnii oxidation]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Peroxidase]]~~	+
-	~~[[Category: Polyvalent peroxidase]]~~	+
-	~~[[Category: Protoporphyrin ix]]~~	+
-	~~[[Category: Secreted]]~~	+
-	~~[[Category: Zymogen~~]]	+

OCA at 07:51, 3 July 2019

2019-07-03T07:51:06Z

←Older revision		Revision as of 07:51, 3 July 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 5abn is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==CRYSTAL STRUCTURE ANALYSIS OF FUNGAL VERSATILE PEROXIDASE FROM PLEUROTUS ERYNGII. MUTANT VPi. MUTATED RESIDUES D69S, T70D, S86E, D146T, Q202L, H232E, Q239R AND S301K.==
		+	<StructureSection load='5abn' size='340' side='right'caption='[[5abn]], [[Resolution\|resolution]] 2.19Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5abn]] 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=5ABN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ABN 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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5abo\|5abo]], [[5abq\|5abq]]</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=5abn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5abn OCA], [http://pdbe.org/5abn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5abn RCSB], [http://www.ebi.ac.uk/pdbsum/5abn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5abn ProSAT]</span></td></tr>
		+	</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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Versatile peroxidase (VP) from the white-rot fungus Pleurotus eryngii is a high redox potential peroxidase of biotechnological interest able to oxidize a wide range of recalcitrant substrates including lignin, phenolic and non-phenolic aromatic compounds and dyes. However, the relatively low stability towards pH of this and other fungal peroxidases is a drawback for their industrial application. A strategy based on the comparative analysis of the crystal structures of VP and the highly pH-stable manganese peroxidase (MnP4) from Pleurotus ostreatus was followed to improve the VP pH stability. Several interactions, including hydrogen bonds and salt bridges, and charged residues exposed to the solvent were identified as putatively contributing to the pH stability of MnP4. The eight amino acid residues responsible for these interactions and seven surface basic residues were introduced into VP by directed mutagenesis. Furthermore, two cysteines were also included to explore the effect of an extra disulfide bond stabilizing the distal Ca2+ region. Three of the four designed variants were crystallized and new interactions were confirmed, being correlated with the observed improvement in pH stability. The extra hydrogen bonds and salt bridges stabilized the heme pocket at acidic and neutral pH as revealed by UV-visible spectroscopy. They led to a VP variant that retained a significant percentage of the initial activity at both pH 3.5 (61% after 24 h) and pH 7 (55% after 120 h) compared with the native enzyme, which was almost completely inactivated. The introduction of extra solvent-exposed basic residues and an additional disulfide bond into the above variant further improved the stability at acidic pH (85% residual activity at pH 3.5 after 24 h when introduced separately, and 64% at pH 3 when introduced together). The analysis of the results provides a rational explanation to the pH stability improvement achieved.

-	~~Authors:~~ Medrano, F.J., ~~Romero, A~~.	+	Improving the pH-stability of Versatile Peroxidase by Comparative Structural Analysis with a Naturally-Stable Manganese Peroxidase.,Saez-Jimenez V, Fernandez-Fueyo E, Medrano FJ, Romero A, Martinez AT, Ruiz-Duenas FJ PLoS One. 2015 Oct 23;10(10):e0140984. doi: 10.1371/journal.pone.0140984., eCollection 2015. PMID:26496708<ref>PMID:26496708</ref>

-	~~Description: CRYSTAL STRUCTURE ANALYSIS OF FUNGAL VERSATILE PEROXIDASE FROM PLEUROTUS ERYNGII~~. ~~MUTANT VPi~~. ~~MUTATED RESIDUES D69S, T70D, S86E, D146T, Q202L, H232E, Q239R AND S301K~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 5abn" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Boletus of the steppes]]
		+	[[Category: Large Structures]]
		+	[[Category: Versatile peroxidase]]
		+	[[Category: Medrano, F J]]
	[[Category: Romero, A]]		[[Category: Romero, A]]
-	[[Category: ~~Medrano, F.J~~]]	+	[[Category: Electron transfer]]
		+	[[Category: Heme]]
		+	[[Category: Hydrogen peroxide]]
		+	[[Category: Iron]]
		+	[[Category: Lignin degradation]]
		+	[[Category: Lignin peroxidase]]
		+	[[Category: Manganese]]
		+	[[Category: Manganese peroxidase]]
		+	[[Category: Metal-binding]]
		+	[[Category: Mn-independent oxidation phenolic non-phenolic aromatic]]
		+	[[Category: Mnii oxidation]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Peroxidase]]
		+	[[Category: Polyvalent peroxidase]]
		+	[[Category: Protoporphyrin ix]]
		+	[[Category: Secreted]]
		+	[[Category: Zymogen]]

OCA at 10:53, 26 August 2015

2015-08-26T10:53:48Z

←Older revision		Revision as of 10:53, 26 August 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Medrano, F.J., Romero, A.		Authors: Medrano, F.J., Romero, A.

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

2015-08-20T09:53:21Z

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

←Older revision

Revision as of 09:53, 20 August 2015

OCA: New page: '''Unreleased structure''' The entry 5abn is ON HOLD Authors: Medrano, F.J., Romero, A. Description: CRYSTAL STRUCTURE ANALYSIS OF FUNGAL VERSATILE PEROXIDASE FROM PLEUROTUS ERYNGII. M...

2015-08-20T09:53:19Z

New page: '''Unreleased structure''' The entry 5abn is ON HOLD Authors: Medrano, F.J., Romero, A. Description: CRYSTAL STRUCTURE ANALYSIS OF FUNGAL VERSATILE PEROXIDASE FROM PLEUROTUS ERYNGII. M...

New page

'''Unreleased structure'''

The entry 5abn is ON HOLD

Authors: Medrano, F.J., Romero, A.

Description: CRYSTAL STRUCTURE ANALYSIS OF FUNGAL VERSATILE PEROXIDASE FROM PLEUROTUS ERYNGII. MUTANT VPi. MUTATED RESIDUES D69S, T70D, S86E, D146T, Q202L, H232E, Q239R AND S301K.
[[Category: Unreleased Structures]]
[[Category: Romero, A]]
[[Category: Medrano, F.J]]