6ekw - Revision history

OCA at 08:12, 3 April 2019

OCA — Wed, 03 Apr 2019 08:12:31 GMT

←Older revision		Revision as of 08:12, 3 April 2019
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	==Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita, in complex with naphthalene==		==Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita, in complex with naphthalene==
-	<StructureSection load='6ekw' size='340' side='right' caption='[[6ekw]], [[Resolution\|resolution]] 1.43Å' scene=''>	+	<StructureSection load='6ekw' size='340' side='right'caption='[[6ekw]], [[Resolution\|resolution]] 1.43Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6ekw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrae Agrae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EKW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EKW FirstGlance]. <br>		<table><tr><td colspan='2'>[[6ekw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrae Agrae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EKW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EKW FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Agrae]]		[[Category: Agrae]]
		+	[[Category: Large Structures]]
	[[Category: Unspecific peroxygenase]]		[[Category: Unspecific peroxygenase]]
	[[Category: Ramirez-Escudero, M]]		[[Category: Ramirez-Escudero, M]]

OCA at 08:53, 19 December 2018

OCA — Wed, 19 Dec 2018 08:53:09 GMT

←Older revision		Revision as of 08:53, 19 December 2018
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	<StructureSection load='6ekw' size='340' side='right' caption='[[6ekw]], [[Resolution\|resolution]] 1.43Å' scene=''>		<StructureSection load='6ekw' size='340' side='right' caption='[[6ekw]], [[Resolution\|resolution]] 1.43Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ekw]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EKW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EKW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ekw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrae Agrae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EKW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EKW FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MOH:METHANOL'>MOH</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NPY:NAPHTHALENE'>NPY</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MOH:METHANOL'>MOH</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NPY:NAPHTHALENE'>NPY</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2yor\|2yor]], [[2yp1\|2yp1]], [[5oxu\|5oxu]], [[5oxt\|5oxt]], [[5oy1\|5oy1]], [[5yo2\|5yo2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2yor\|2yor]], [[2yp1\|2yp1]], [[5oxu\|5oxu]], [[5oxt\|5oxt]], [[5oy1\|5oy1]], [[5yo2\|5yo2]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APO1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5400 AGRAE])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Unspecific_peroxygenase Unspecific peroxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.2.1 1.11.2.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Unspecific_peroxygenase Unspecific peroxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.2.1 1.11.2.1] </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=6ekw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ekw OCA], [http://pdbe.org/6ekw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ekw RCSB], [http://www.ebi.ac.uk/pdbsum/6ekw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ekw 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=6ekw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ekw OCA], [http://pdbe.org/6ekw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ekw RCSB], [http://www.ebi.ac.uk/pdbsum/6ekw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ekw ProSAT]</span></td></tr>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/APO1_AGRAE APO1_AGRAE]] Aromatic peroxidase that oxidizes aryl alcohols into the corresponding aldehydes and then into the corresponding benzoic acids. Oxidizes toluene and naphthalene. Catalyzes the regioselective peroxide-dependent hydroxylation of propranolol and diclofenac to 5-hydroxypropranolol and 4'-hydroxydiclofenac. Catalyzes the regioselective peroxide-dependent hydroxylation of naphthalene to 1-naphthol or 2-naphthol via a naphthalene 1,2-oxide intermediate. Catalyzes the regioselective peroxide-dependent oxidation of pyridine to pyridine N-oxide. Halogenates monochlorodimedone and phenol. Oxidizes the sulfer-containing heterocycle dibenzothiophene to yield ring-hydroxylation products and to a lesser extent sulfoxidation products.<ref>PMID:15294788</ref> <ref>PMID:16253244</ref> <ref>PMID:17410351</ref> <ref>PMID:19022254</ref> <ref>PMID:19039585</ref> <ref>PMID:18815784</ref> <ref>PMID:19394224</ref>		[[http://www.uniprot.org/uniprot/APO1_AGRAE APO1_AGRAE]] Aromatic peroxidase that oxidizes aryl alcohols into the corresponding aldehydes and then into the corresponding benzoic acids. Oxidizes toluene and naphthalene. Catalyzes the regioselective peroxide-dependent hydroxylation of propranolol and diclofenac to 5-hydroxypropranolol and 4'-hydroxydiclofenac. Catalyzes the regioselective peroxide-dependent hydroxylation of naphthalene to 1-naphthol or 2-naphthol via a naphthalene 1,2-oxide intermediate. Catalyzes the regioselective peroxide-dependent oxidation of pyridine to pyridine N-oxide. Halogenates monochlorodimedone and phenol. Oxidizes the sulfer-containing heterocycle dibenzothiophene to yield ring-hydroxylation products and to a lesser extent sulfoxidation products.<ref>PMID:15294788</ref> <ref>PMID:16253244</ref> <ref>PMID:17410351</ref> <ref>PMID:19022254</ref> <ref>PMID:19039585</ref> <ref>PMID:18815784</ref> <ref>PMID:19394224</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Because of their minimal requirements, substrate promiscuity and product selectivity, fungal peroxygenases are now considered to be the jewel in the crown of C-H oxyfunctionalization biocatalysts. In this work, the crystal structure of the first laboratory-evolved peroxygenase expressed by yeast was determined at a resolution of 1.5 A. Notable differences were detected between the evolved and native peroxygenase from Agrocybe aegerita, including the presence of a full N-terminus and a broader heme access channel due to the mutations that accumulated through directed evolution. Further mutagenesis and soaking experiments with a palette of peroxygenative and peroxidative substrates suggested dynamic trafficking through the heme channel as the main driving force for the exceptional substrate promiscuity of peroxygenase. Accordingly, this study provides the first structural evidence at an atomic level regarding the mode of substrate binding for this versatile biocatalyst, which is discussed within a biological and chemical context.
		+
		+	Structural Insights into the Substrate Promiscuity of a Laboratory-Evolved Peroxygenase.,Ramirez-Escudero M, Molina-Espeja P, Gomez de Santos P, Hofrichter M, Sanz-Aparicio J, Alcalde M ACS Chem Biol. 2018 Nov 16. doi: 10.1021/acschembio.8b00500. PMID:30376293<ref>PMID:30376293</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ekw" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Agrae]]
	[[Category: Unspecific peroxygenase]]		[[Category: Unspecific peroxygenase]]
	[[Category: Ramirez-Escudero, M]]		[[Category: Ramirez-Escudero, M]]

OCA at 06:46, 12 December 2018

OCA — Wed, 12 Dec 2018 06:46:14 GMT

←Older revision		Revision as of 06:46, 12 December 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ekw is ~~ON HOLD~~ ~~until Paper Publication~~	+	==Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita, in complex with naphthalene==
-		+	<StructureSection load='6ekw' size='340' side='right' caption='[[6ekw]], [[Resolution\|resolution]] 1.43Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6ekw]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EKW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EKW FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MOH:METHANOL'>MOH</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NPY:NAPHTHALENE'>NPY</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2yor\|2yor]], [[2yp1\|2yp1]], [[5oxu\|5oxu]], [[5oxt\|5oxt]], [[5oy1\|5oy1]], [[5yo2\|5yo2]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Unspecific_peroxygenase Unspecific peroxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.2.1 1.11.2.1] </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=6ekw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ekw OCA], [http://pdbe.org/6ekw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ekw RCSB], [http://www.ebi.ac.uk/pdbsum/6ekw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ekw ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/APO1_AGRAE APO1_AGRAE]] Aromatic peroxidase that oxidizes aryl alcohols into the corresponding aldehydes and then into the corresponding benzoic acids. Oxidizes toluene and naphthalene. Catalyzes the regioselective peroxide-dependent hydroxylation of propranolol and diclofenac to 5-hydroxypropranolol and 4'-hydroxydiclofenac. Catalyzes the regioselective peroxide-dependent hydroxylation of naphthalene to 1-naphthol or 2-naphthol via a naphthalene 1,2-oxide intermediate. Catalyzes the regioselective peroxide-dependent oxidation of pyridine to pyridine N-oxide. Halogenates monochlorodimedone and phenol. Oxidizes the sulfer-containing heterocycle dibenzothiophene to yield ring-hydroxylation products and to a lesser extent sulfoxidation products.<ref>PMID:15294788</ref> <ref>PMID:16253244</ref> <ref>PMID:17410351</ref> <ref>PMID:19022254</ref> <ref>PMID:19039585</ref> <ref>PMID:18815784</ref> <ref>PMID:19394224</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Unspecific peroxygenase]]
		+	[[Category: Ramirez-Escudero, M]]
		+	[[Category: Sanz-Aparicio, J]]
		+	[[Category: Agrocybe aegerita]]
		+	[[Category: Directed evolution]]
		+	[[Category: Heme-thiolate peroxidase]]
		+	[[Category: Naphthalene]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Padai]]
		+	[[Category: Upo]]

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

OCA — Wed, 04 Oct 2017 08:19:39 GMT

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

←Older revision

Revision as of 08:19, 4 October 2017

OCA: New page: '''Unreleased structure''' The entry 6ekw is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 04 Oct 2017 08:19:37 GMT

New page: '''Unreleased structure''' The entry 6ekw is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6ekw is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]