5niw - Revision history

OCA at 13:01, 15 November 2023

OCA — Wed, 15 Nov 2023 13:01:03 GMT

←Older revision		Revision as of 13:01, 15 November 2023
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	<StructureSection load='5niw' size='340' side='right'caption='[[5niw]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5niw' size='340' side='right'caption='[[5niw]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5niw]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~A._niger A.~~ niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NIW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5NIW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5niw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_niger Aspergillus niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NIW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NIW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=P4C:O-ACETALDEHYDYL-HEXAETHYLENE+GLYCOL'>P4C</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.8Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gox ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5061 A. niger])</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=P4C:O-ACETALDEHYDYL-HEXAETHYLENE+GLYCOL'>P4C</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucose_oxidase Glucose oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.4 1.1.3.4] </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=5niw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5niw OCA], [https://pdbe.org/5niw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5niw RCSB], [https://www.ebi.ac.uk/pdbsum/5niw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5niw 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=5niw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5niw OCA], [~~http~~://pdbe.org/5niw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5niw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5niw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5niw ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/GOX_ASPNG GOX_ASPNG]
	<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: A. niger]]	+	[[Category: Aspergillus niger]]
-	~~[[Category: Glucose oxidase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Frank, D]]	+	[[Category: Frank D]]
-	[[Category: Hoffmann, K]]	+	[[Category: Hoffmann K]]
-	~~[[Category: His516 conformation]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Oxygen activation~~]]	+

OCA at 06:45, 16 October 2019

OCA — Wed, 16 Oct 2019 06:45:18 GMT

←Older revision		Revision as of 06:45, 16 October 2019
Line 1:		Line 1:

	==Glucose oxydase mutant A2==		==Glucose oxydase mutant A2==
-	<StructureSection load='5niw' size='340' side='right' caption='[[5niw]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5niw' size='340' side='right'caption='[[5niw]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5niw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/A._niger A. niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NIW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NIW FirstGlance]. <br>		<table><tr><td colspan='2'>[[5niw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/A._niger A. niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NIW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NIW FirstGlance]. <br>
Line 24:		Line 24:
	[[Category: A. niger]]		[[Category: A. niger]]
	[[Category: Glucose oxidase]]		[[Category: Glucose oxidase]]
		+	[[Category: Large Structures]]
	[[Category: Frank, D]]		[[Category: Frank, D]]
	[[Category: Hoffmann, K]]		[[Category: Hoffmann, K]]

OCA at 08:38, 10 January 2018

OCA — Wed, 10 Jan 2018 08:38:07 GMT

←Older revision		Revision as of 08:38, 10 January 2018
Line 3:		Line 3:
	<StructureSection load='5niw' size='340' side='right' caption='[[5niw]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5niw' size='340' side='right' caption='[[5niw]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5niw]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NIW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NIW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5niw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/A._niger A. niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NIW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NIW FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=P4C:O-ACETALDEHYDYL-HEXAETHYLENE+GLYCOL'>P4C</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=P4C:O-ACETALDEHYDYL-HEXAETHYLENE+GLYCOL'>P4C</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gox ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5061 A. niger])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucose_oxidase Glucose oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.4 1.1.3.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucose_oxidase Glucose oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.4 1.1.3.4] </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=5niw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5niw OCA], [http://pdbe.org/5niw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5niw RCSB], [http://www.ebi.ac.uk/pdbsum/5niw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5niw 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=5niw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5niw OCA], [http://pdbe.org/5niw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5niw RCSB], [http://www.ebi.ac.uk/pdbsum/5niw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5niw ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Glucose oxidase has wide applications in the pharmaceutical, chemical, and food industries. Many recent studies have enhanced key properties of this enzyme using directed evolution, yet without being able to reveal why these mutations are actually beneficial. This work presents a synergistic combination of experimental and computational methods, indicating how mutations, even when distant from the active site, positively affect glucose oxidase catalysis. We have determined the crystal structures of glucose oxidase mutants containing molecular oxygen in the active site. The catalytically important His516 residue has been previously shown to be flexible in the wild-type enzyme. The molecular dynamics simulations performed in this work allow us to quantify this floppiness, revealing that His516 exists in two states: catalytic and noncatalytic. The relative populations of these two substates are almost identical in the wild-type enzyme, with His516 readily shuffling between them. In the glucose oxidase mutants, on the other hand, the mutations enrich the catalytic His516 conformation and reduce the flexibility of this residue, leading to an enhancement in their catalytic efficiency. This study stresses the benefit of active site preorganization with respect to enzyme conversion rates by reducing molecular reorientation needs. We further suggest that the computational approach based on Hamiltonian replica exchange molecular dynamics, used in this study, may be a general approach to screening in silico for improved enzyme variants involving flexible catalytic residues.
		+
		+	Shuffling Active Site Substate Populations Affects Catalytic Activity: The Case of Glucose Oxidase.,Petrovic D, Frank D, Kamerlin SCL, Hoffmann K, Strodel B ACS Catal. 2017 Sep 1;7(9):6188-6197. doi: 10.1021/acscatal.7b01575. Epub 2017, Aug 1. PMID:29291138<ref>PMID:29291138</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5niw" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: A. niger]]
	[[Category: Glucose oxidase]]		[[Category: Glucose oxidase]]
	[[Category: Frank, D]]		[[Category: Frank, D]]

OCA at 07:27, 15 November 2017

OCA — Wed, 15 Nov 2017 07:27:29 GMT

←Older revision		Revision as of 07:27, 15 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5niw is ~~ON HOLD~~	+	==Glucose oxydase mutant A2==
-		+	<StructureSection load='5niw' size='340' side='right' caption='[[5niw]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~Authors~~: ~~Hoffmann~~, K., ~~Frank~~, D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5niw]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NIW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NIW FirstGlance]. <br>
-	~~Description~~: Glucose ~~oxydase mutant A2~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=P4C:O-ACETALDEHYDYL-HEXAETHYLENE+GLYCOL'>P4C</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucose_oxidase Glucose oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.4 1.1.3.4] </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=5niw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5niw OCA], [http://pdbe.org/5niw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5niw RCSB], [http://www.ebi.ac.uk/pdbsum/5niw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5niw ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Glucose oxidase]]
		+	[[Category: Frank, D]]
	[[Category: Hoffmann, K]]		[[Category: Hoffmann, K]]
-	[[Category: ~~Frank, D~~]]	+	[[Category: His516 conformation]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Oxygen activation]]

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

OCA — Wed, 05 Apr 2017 10:11:58 GMT

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

←Older revision

Revision as of 10:11, 5 April 2017

OCA: New page: '''Unreleased structure''' The entry 5niw is ON HOLD Authors: Hoffmann, K., Frank, D. Description: Glucose oxydase mutant A2 Category: Unreleased Structures [[Category: Hoffmann, K...

OCA — Wed, 05 Apr 2017 10:11:57 GMT

New page: '''Unreleased structure''' The entry 5niw is ON HOLD Authors: Hoffmann, K., Frank, D. Description: Glucose oxydase mutant A2 Category: Unreleased Structures [[Category: Hoffmann, K...

New page

'''Unreleased structure'''

The entry 5niw is ON HOLD

Authors: Hoffmann, K., Frank, D.

Description: Glucose oxydase mutant A2
[[Category: Unreleased Structures]]
[[Category: Hoffmann, K]]
[[Category: Frank, D]]