5oxu - Revision history

OCA at 01:27, 28 December 2023

2023-12-28T01:27:59Z

←Older revision		Revision as of 01:27, 28 December 2023
Line 3:		Line 3:
	<StructureSection load='5oxu' size='340' side='right'caption='[[5oxu]], [[Resolution\|resolution]] 1.47Å' scene=''>		<StructureSection load='5oxu' size='340' side='right'caption='[[5oxu]], [[Resolution\|resolution]] 1.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5oxu]] 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=5OXU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OXU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5oxu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cyclocybe_aegerita Cyclocybe aegerita]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OXU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OXU 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=PO4:PHOSPHATE+ION'>PO4</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]] 1.47Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2yor\|2yor]], [[2yp1\|2yp1]], [[5oxt\|5oxt]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=PO4:PHOSPHATE+ION'>PO4</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5oxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oxu OCA], [https://pdbe.org/5oxu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5oxu RCSB], [https://www.ebi.ac.uk/pdbsum/5oxu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5oxu 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/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=5oxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oxu OCA], [~~http~~://pdbe.org/5oxu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5oxu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5oxu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5oxu ProSAT]</span></td></tr>	+
	</table>		</table>
	== 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>	+	[https://www.uniprot.org/uniprot/APO1_CYCAE APO1_CYCAE] 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 sulfur-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:18815784</ref> <ref>PMID:19022254</ref> <ref>PMID:19039585</ref> <ref>PMID:19394224</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Agrae~~]]	+	[[Category: Cyclocybe aegerita]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Unspecific peroxygenase]]~~	+	[[Category: Ramirez-Escudero M]]
-	[[Category: Ramirez-Escudero, M]]	+	[[Category: Sanz-Aparicio J]]
-	[[Category: Sanz-Aparicio, J]]	+
-	~~[[Category: Agrocybe aegerita]]~~	+
-	~~[[Category: Directed evolution]]~~	+
-	~~[[Category: Heme-thiolate peroxidase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Padai]]~~	+
-	~~[[Category: Upo~~]]	+

OCA at 08:02, 3 April 2019

2019-04-03T08:02:23Z

←Older revision		Revision as of 08:02, 3 April 2019
Line 1:		Line 1:

	==Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita==		==Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita==
-	<StructureSection load='5oxu' size='340' side='right' caption='[[5oxu]], [[Resolution\|resolution]] 1.47Å' scene=''>	+	<StructureSection load='5oxu' size='340' side='right'caption='[[5oxu]], [[Resolution\|resolution]] 1.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5oxu]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OXU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OXU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5oxu]] 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=5OXU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OXU 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=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=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]], [[5oxt\|5oxt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2yor\|2yor]], [[2yp1\|2yp1]], [[5oxt\|5oxt]]</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=5oxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oxu OCA], [http://pdbe.org/5oxu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oxu RCSB], [http://www.ebi.ac.uk/pdbsum/5oxu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oxu 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=5oxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oxu OCA], [http://pdbe.org/5oxu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oxu RCSB], [http://www.ebi.ac.uk/pdbsum/5oxu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oxu ProSAT]</span></td></tr>
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Agrae]]
		+	[[Category: Large Structures]]
	[[Category: Unspecific peroxygenase]]		[[Category: Unspecific peroxygenase]]
	[[Category: Ramirez-Escudero, M]]		[[Category: Ramirez-Escudero, M]]

OCA at 08:10, 26 December 2018

2018-12-26T08:10:52Z

←Older revision		Revision as of 08:10, 26 December 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5oxu is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita==
		+	<StructureSection load='5oxu' size='340' side='right' caption='[[5oxu]], [[Resolution\|resolution]] 1.47Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5oxu]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OXU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OXU 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=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]], [[5oxt\|5oxt]]</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=5oxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oxu OCA], [http://pdbe.org/5oxu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oxu RCSB], [http://www.ebi.ac.uk/pdbsum/5oxu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oxu 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>
		+	<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.

-	~~Authors~~:	+	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>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5oxu" style="background-color:#fffaf0;"></div>
		+	== 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: Oxidoreductase]]
		+	[[Category: Padai]]
		+	[[Category: Upo]]

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

2017-09-27T12:58:55Z

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

←Older revision

Revision as of 12:58, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5oxu is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2017-09-27T12:58:54Z

New page: '''Unreleased structure''' The entry 5oxu is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5oxu is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]