4w7n - Revision history

OCA at 10:41, 10 January 2024

OCA — Wed, 10 Jan 2024 10:41:04 GMT

←Older revision		Revision as of 10:41, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4w7n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Auricularia_auricula-judae Auricularia auricula-judae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W7N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4W7N FirstGlance]. <br>		<table><tr><td colspan='2'>[[4w7n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Auricularia_auricula-judae Auricularia auricula-judae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W7N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4W7N FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.401Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=4w7n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w7n OCA], [https://pdbe.org/4w7n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4w7n RCSB], [https://www.ebi.ac.uk/pdbsum/4w7n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4w7n 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=4w7n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w7n OCA], [https://pdbe.org/4w7n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4w7n RCSB], [https://www.ebi.ac.uk/pdbsum/4w7n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4w7n ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:56, 7 April 2023

OCA — Fri, 07 Apr 2023 06:56:17 GMT

←Older revision		Revision as of 06:56, 7 April 2023
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	<StructureSection load='4w7n' size='340' side='right'caption='[[4w7n]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='4w7n' size='340' side='right'caption='[[4w7n]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4w7n]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Auraj Auraj~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W7N OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4W7N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4w7n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Auricularia_auricula-judae Auricularia auricula-judae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W7N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4W7N FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dye_decolorizing_peroxidase Dye decolorizing peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.19 1.11.1.19] </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=4w7n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w7n OCA], [https://pdbe.org/4w7n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4w7n RCSB], [https://www.ebi.ac.uk/pdbsum/4w7n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4w7n ProSAT]</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=4w7n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w7n OCA], [~~http~~://pdbe.org/4w7n PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4w7n RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4w7n PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4w7n ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DYP_AURAJ DYP_AURAJ] Manganese-independent peroxidase that is able to convert a large number of compounds, but its physiological substrate is not known. In addition to classic peroxidase substrates (e.g. 2,6-dimethoxyphenol), oxidizes dyes such as Reactive Blue 5 and Reactive Black 5.<ref>PMID:19756587</ref> <ref>PMID:23111597</ref> <ref>PMID:25153532</ref> <ref>PMID:25495127</ref> <ref>PMID:25542606</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Auraj]]~~	+	[[Category: Auricularia auricula-judae]]
-	~~[[Category: Dye decolorizing peroxidase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Medrano~~, F J~~]]	+	[[Category: Medrano FJ]]
-	[[Category: Romero, A]]	+	[[Category: Romero A]]
-	~~[[Category: Glycoprotein]]~~	+
-	~~[[Category: Heme]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 08:12, 23 May 2019

OCA — Thu, 23 May 2019 08:12:20 GMT

←Older revision		Revision as of 08:12, 23 May 2019
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	==CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICULARIA AURICULA-JUDAE. Y147S AND W377S DOUBLE MUTANT==		==CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICULARIA AURICULA-JUDAE. Y147S AND W377S DOUBLE MUTANT==
-	<StructureSection load='4w7n' size='340' side='right' caption='[[4w7n]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='4w7n' size='340' side='right'caption='[[4w7n]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4w7n]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W7N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4W7N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4w7n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Auraj Auraj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W7N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4W7N FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dye_decolorizing_peroxidase Dye decolorizing peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.19 1.11.1.19] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dye_decolorizing_peroxidase Dye decolorizing peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.19 1.11.1.19] </span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Auraj]]
	[[Category: Dye decolorizing peroxidase]]		[[Category: Dye decolorizing peroxidase]]
		+	[[Category: Large Structures]]
	[[Category: Medrano, F J]]		[[Category: Medrano, F J]]
	[[Category: Romero, A]]		[[Category: Romero, A]]

OCA at 01:17, 19 January 2017

OCA — Thu, 19 Jan 2017 01:17:34 GMT

←Older revision		Revision as of 01:17, 19 January 2017
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICULARIA AURICULA-JUDAE. Y147S AND W377S DOUBLE MUTANT==		==CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICULARIA AURICULA-JUDAE. Y147S AND W377S DOUBLE MUTANT==
	<StructureSection load='4w7n' size='340' side='right' caption='[[4w7n]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='4w7n' size='340' side='right' caption='[[4w7n]], [[Resolution\|resolution]] 1.40Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dye_decolorizing_peroxidase Dye decolorizing peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.19 1.11.1.19] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dye_decolorizing_peroxidase Dye decolorizing peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.19 1.11.1.19] </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=4w7n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w7n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4w7n RCSB], [http://www.ebi.ac.uk/pdbsum/4w7n 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=4w7n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w7n OCA], [http://pdbe.org/4w7n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4w7n RCSB], [http://www.ebi.ac.uk/pdbsum/4w7n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4w7n ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 4w7n" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:45, 11 March 2015

OCA — Wed, 11 Mar 2015 11:45:00 GMT

←Older revision		Revision as of 11:45, 11 March 2015
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-	'''~~Unreleased~~ structure'''	+	==CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICULARIA AURICULA-JUDAE. Y147S AND W377S DOUBLE MUTANT==
		+	<StructureSection load='4w7n' size='340' side='right' caption='[[4w7n]], [[Resolution\|resolution]] 1.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4w7n]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W7N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4W7N FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dye_decolorizing_peroxidase Dye decolorizing peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.19 1.11.1.19] </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=4w7n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w7n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4w7n RCSB], [http://www.ebi.ac.uk/pdbsum/4w7n PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Dye-decolorizing peroxidase (DyP) of Auricularia auricula-judae has been expressed in Escherichia coli as a representative of a new DyP family, and subjected to mutagenic, spectroscopic, crystallographic and computational studies. The crystal structure of DyP shows a buried haem cofactor, and surface tryptophan and tyrosine residues potentially involved in long-range electron transfer from bulky dyes. Simulations using PELE (Protein Energy Landscape Exploration) software provided several binding-energy optima for the anthraquinone-type RB19 (Reactive Blue 19) near the above aromatic residues and the haem access-channel. Subsequent QM/MM (quantum mechanics/molecular mechanics) calculations showed a higher tendency of Trp-377 than other exposed haem-neighbouring residues to harbour a catalytic protein radical, and identified the electron-transfer pathway. The existence of such a radical in H2O2-activated DyP was shown by low-temperature EPR, being identified as a mixed tryptophanyl/tyrosyl radical in multifrequency experiments. The signal was dominated by the Trp-377 neutral radical contribution, which disappeared in the W377S variant, and included a tyrosyl contribution assigned to Tyr-337 after analysing the W377S spectra. Kinetics of substrate oxidation by DyP suggests the existence of high- and low-turnover sites. The high-turnover site for oxidation of RB19 (kcat> 200 s-1) and other DyP substrates was assigned to Trp-377 since it was absent from the W377S variant. The low-turnover site/s (RB19 kcat ~20 s-1) could correspond to the haem access-channel, since activity was decreased when the haem channel was occluded by the G169L mutation. If a tyrosine residue is also involved, it will be different from Tyr-337 since all activities are largely unaffected in the Y337S variant.

-	~~The entry 4w7n is ON HOLD until Paper Publication~~	+	Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study.,Linde D, Pogni R, Canellas M, Lucas F, Guallar V, Baratto MC, Sinicropi A, Saez-Jimenez V, Coscolin C, Romero A, Medrano FJ, Ruiz-Duenas FJ, Martinez AT Biochem J. 2015 Mar 1;466(2):253-62. doi: 10.1042/BJ20141211. PMID:25495127<ref>PMID:25495127</ref>

-	~~Authors: Medrano~~, F.J.~~, Romero, A~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICULARIA AURICULA-JUDAE. Y147S AND W377S DOUBLE MUTANT~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dye decolorizing peroxidase]]
		+	[[Category: Medrano, F J]]
	[[Category: Romero, A]]		[[Category: Romero, A]]
-	[[Category: ~~Medrano, F.J~~]]	+	[[Category: Glycoprotein]]
		+	[[Category: Heme]]
		+	[[Category: Oxidoreductase]]

OCA at 19:11, 24 December 2014

OCA — Wed, 24 Dec 2014 19:11:09 GMT

←Older revision		Revision as of 19:11, 24 December 2014
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	Description: CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICULARIA AURICULA-JUDAE. Y147S AND W377S DOUBLE MUTANT		Description: CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICULARIA AURICULA-JUDAE. Y147S AND W377S DOUBLE MUTANT
		+	[[Category: Unreleased Structures]]
		+	[[Category: Romero, A]]
		+	[[Category: Medrano, F.J]]

OCA at 04:46, 4 September 2014

OCA — Thu, 04 Sep 2014 04:46:36 GMT

←Older revision		Revision as of 04:46, 4 September 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4w7n is ON HOLD	+	The entry 4w7n is ON HOLD until Paper Publication

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

	Description: CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICULARIA AURICULA-JUDAE. Y147S AND W377S DOUBLE MUTANT		Description: CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICULARIA AURICULA-JUDAE. Y147S AND W377S DOUBLE MUTANT

OCA: Protected "4w7n" [edit=sysop:move=sysop]

OCA — Wed, 27 Aug 2014 07:32:47 GMT

Protected "4w7n" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:32, 27 August 2014

OCA: New page: '''Unreleased structure''' The entry 4w7n is ON HOLD Authors: Medrano, F.J., Romero, A. Description: CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICULARIA AURICULA-JUDA...

OCA — Wed, 27 Aug 2014 07:32:45 GMT

New page: '''Unreleased structure''' The entry 4w7n is ON HOLD Authors: Medrano, F.J., Romero, A. Description: CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICULARIA AURICULA-JUDA...

New page

'''Unreleased structure'''

The entry 4w7n is ON HOLD

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

Description: CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICULARIA AURICULA-JUDAE. Y147S AND W377S DOUBLE MUTANT