4pwb - Revision history

OCA at 17:23, 20 September 2023

OCA — Wed, 20 Sep 2023 17:23:31 GMT

←Older revision		Revision as of 17:23, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4pwb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Phleum_pratense Phleum pratense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PWB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PWB FirstGlance]. <br>		<table><tr><td colspan='2'>[[4pwb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Phleum_pratense Phleum pratense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PWB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PWB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=XE:XENON'>XE</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]] 1.9Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=XE:XENON'>XE</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=4pwb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pwb OCA], [https://pdbe.org/4pwb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pwb RCSB], [https://www.ebi.ac.uk/pdbsum/4pwb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pwb 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=4pwb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pwb OCA], [https://pdbe.org/4pwb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pwb RCSB], [https://www.ebi.ac.uk/pdbsum/4pwb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pwb ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:34, 8 February 2023

OCA — Wed, 08 Feb 2023 07:34:41 GMT

←Older revision		Revision as of 07:34, 8 February 2023
Line 1:		Line 1:
		+
	==Phl p 4 I153V variant, a glucose oxidase, pressurized with Xenon==		==Phl p 4 I153V variant, a glucose oxidase, pressurized with Xenon==
-	<StructureSection load='4pwb' size='340' side='right' caption='[[4pwb]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='4pwb' size='340' side='right'caption='[[4pwb]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4pwb]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Common_timothy Common timothy~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PWB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4PWB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4pwb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Phleum_pratense Phleum pratense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PWB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PWB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=XE:XENON'>XE</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=XE:XENON'>XE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pve\|4pve]], [[4pvh\|4pvh]], [[4pvj\|4pvj]], [[4pvk\|4pvk]], [[4pzf\|4pzf]], [[4pwc\|4pwc]]</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=4pwb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pwb OCA], [https://pdbe.org/4pwb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pwb RCSB], [https://www.ebi.ac.uk/pdbsum/4pwb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pwb ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phlp4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=15957 Common timothy])~~</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=4pwb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pwb OCA], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4pwb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4pwb PDBsum]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B2ZWE9_PHLPR B2ZWE9_PHLPR]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 16:		Line 17:
	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 4pwb" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Common timothy~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Keller, W~~]]	+	[[Category: Phleum pratense]]
-	[[Category: ~~Macheroux, P~~]]	+	[[Category: Keller W]]
-	[[Category: ~~Zafred, D~~]]	+	[[Category: Macheroux P]]
-	[[Category: ~~Allergen]]~~	+	[[Category: Zafred D]]
-	~~[[Category: Bi-covalent flavinylation]]~~	+
-	~~[[Category: Flavoprotein]]~~	+
-	~~[[Category: Glucose oxidase]]~~	+
-	~~[[Category: Grass pollen]]~~	+
-	~~[[Category: High oxygen reactivity]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 06:46, 22 April 2015

OCA — Wed, 22 Apr 2015 06:46:13 GMT

←Older revision		Revision as of 06:46, 22 April 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[4pwb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Common_timothy Common timothy]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PWB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PWB FirstGlance]. <br>		<table><tr><td colspan='2'>[[4pwb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Common_timothy Common timothy]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PWB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PWB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=XE:XENON'>XE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=XE:XENON'>XE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pve\|4pve]], [[4pvh\|4pvh]], [[4pvj\|4pvj]], [[4pvk\|4pvk]], [[4pwc\|4pwc]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pve\|4pve]], [[4pvh\|4pvh]], [[4pvj\|4pvj]], [[4pvk\|4pvk]], [[4pzf\|4pzf]], [[4pwc\|4pwc]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phlp4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=15957 Common timothy])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phlp4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=15957 Common timothy])</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=4pwb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pwb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4pwb RCSB], [http://www.ebi.ac.uk/pdbsum/4pwb 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=4pwb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pwb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4pwb RCSB], [http://www.ebi.ac.uk/pdbsum/4pwb PDBsum]</span></td></tr>

OCA at 07:19, 1 April 2015

OCA — Wed, 01 Apr 2015 07:19:15 GMT

←Older revision		Revision as of 07:19, 1 April 2015
Line 1:		Line 1:
-	==~~Engineered~~ oxidase ~~reveals steric control of oxygen reduction~~==	+	==Phl p 4 I153V variant, a glucose oxidase, pressurized with Xenon==
	<StructureSection load='4pwb' size='340' side='right' caption='[[4pwb]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='4pwb' size='340' side='right' caption='[[4pwb]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==

OCA at 11:25, 4 March 2015

OCA — Wed, 04 Mar 2015 11:25:53 GMT

←Older revision		Revision as of 11:25, 4 March 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4pwb\| PDB=4pwb \| SCENE= }}~~	+	==Engineered oxidase reveals steric control of oxygen reduction==
-	===Engineered oxidase reveals steric control of oxygen reduction===	+	<StructureSection load='4pwb' size='340' side='right' caption='[[4pwb]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4pwb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Common_timothy Common timothy]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PWB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PWB FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=XE:XENON'>XE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pve\|4pve]], [[4pvh\|4pvh]], [[4pvj\|4pvj]], [[4pvk\|4pvk]], [[4pwc\|4pwc]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phlp4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=15957 Common timothy])</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=4pwb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pwb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4pwb RCSB], [http://www.ebi.ac.uk/pdbsum/4pwb PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The ability of flavoenzymes to reduce dioxygen varies greatly, and is controlled by the protein environment, which may cause either a rapid reaction (oxidases) or a sluggish reaction (dehydrogenases). Previously, a 'gatekeeper' amino acid residue was identified that controls the reactivity to dioxygen in proteins from the vanillyl alcohol oxidase superfamily of flavoenzymes. We have identified an alternative gatekeeper residue that similarly controls dioxygen reactivity in the grass pollen allergen Phl p 4, a member of this superfamily that has glucose dehydrogenase activity and the highest redox potential measured in a flavoenzyme. A substitution at the alternative gatekeeper site (I153V) transformed the enzyme into an efficient oxidase by increasing dioxygen reactivity by a factor of 60 000. An inverse exchange (V169I) in the structurally related berberine bridge enzyme (BBE) decreased its dioxygen reactivity by a factor of 500. Structural and biochemical characterization of these and additional variants showed that our model enzymes possess a cavity that binds an anion and resembles the 'oxyanion hole' in the proximity of the flavin ring. We showed also that steric control of access to this site is the most important parameter affecting dioxygen reactivity in BBE-like enzymes. Analysis of flavin-dependent oxidases from other superfamilies revealed similar structural features, suggesting that dioxygen reactivity may be governed by a common mechanistic principle. DATABASE: Structural data are available in PDB database under the accession numbers 4PVE, 4PVH, 4PVJ, 4PVK, 4PWB, 4PWC and 4PZF .

-	~~==About this Structure==~~	+	Rationally engineered flavin-dependent oxidase reveals steric control of dioxygen reduction.,Zafred D, Steiner B, Teufelberger AR, Hromic A, Karplus PA, Schofield CJ, Wallner S, Macheroux P FEBS J. 2015 Jan 24. doi: 10.1111/febs.13212. PMID:25619330<ref>PMID:25619330</ref>
-	~~[[4pwb]] is a 1 chain structure~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.~~il/oca-bin~~/~~ocashort?id~~=~~4PWB OCA~~].	+
-	[[Category: Keller, W.]]	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: Macheroux, P.]]	+	</div>
-	[[Category: Zafred, D.]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Common timothy]]
		+	[[Category: Keller, W]]
		+	[[Category: Macheroux, P]]
		+	[[Category: Zafred, D]]
	[[Category: Allergen]]		[[Category: Allergen]]
	[[Category: Bi-covalent flavinylation]]		[[Category: Bi-covalent flavinylation]]

OCA at 09:41, 2 April 2014

OCA — Wed, 02 Apr 2014 09:41:59 GMT

←Older revision		Revision as of 09:41, 2 April 2014
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4pwb\| PDB=4pwb \| SCENE= }}
		+	===Engineered oxidase reveals steric control of oxygen reduction===

-	~~The entry~~ 4pwb is ~~ON HOLD~~	+	==About this Structure==
-		+	[[4pwb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PWB OCA].
-	~~Authors~~: ~~Zafred, D~~., Keller, W., Macheroux, P.	+	[[Category: Keller, W.]]
-		+	[[Category: Macheroux, P.]]
-	~~Description~~: ~~Engineered~~ oxidase ~~reveals steric control of~~ oxygen ~~reduction~~	+	[[Category: Zafred, D.]]
		+	[[Category: Allergen]]
		+	[[Category: Bi-covalent flavinylation]]
		+	[[Category: Flavoprotein]]
		+	[[Category: Glucose oxidase]]
		+	[[Category: Grass pollen]]
		+	[[Category: High oxygen reactivity]]
		+	[[Category: Oxidoreductase]]

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

OCA — Wed, 26 Mar 2014 08:53:40 GMT

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

←Older revision

Revision as of 08:53, 26 March 2014

OCA: New page: '''Unreleased structure''' The entry 4pwb is ON HOLD Authors: Zafred, D., Keller, W., Macheroux, P. Description: Engineered oxidase reveals steric control of oxygen reduction

OCA — Wed, 26 Mar 2014 08:53:39 GMT

New page: '''Unreleased structure''' The entry 4pwb is ON HOLD Authors: Zafred, D., Keller, W., Macheroux, P. Description: Engineered oxidase reveals steric control of oxygen reduction

New page

'''Unreleased structure'''

The entry 4pwb is ON HOLD

Authors: Zafred, D., Keller, W., Macheroux, P.

Description: Engineered oxidase reveals steric control of oxygen reduction