6q8m - Revision history

OCA at 11:55, 24 January 2024

OCA — Wed, 24 Jan 2024 11:55:22 GMT

←Older revision		Revision as of 11:55, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6q8m' size='340' side='right'caption='[[6q8m]], [[Resolution\|resolution]] 1.42Å' scene=''>		<StructureSection load='6q8m' size='340' side='right'caption='[[6q8m]], [[Resolution\|resolution]] 1.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6q8m]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Aspergillus_aculeatus_atcc_16872~~ Aspergillus aculeatus ~~atcc~~ 16872]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q8M OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6Q8M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6q8m]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_aculeatus_ATCC_16872 Aspergillus aculeatus ATCC 16872]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q8M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Q8M FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=EDO:1,2~~-~~ETHANEDIOL'>EDO</scene>~~, ~~<scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 1.42Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~ASPACDRAFT_127619 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=690307 Aspergillus aculeatus ATCC 16872])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Endo~~-~~1,4~~-~~beta~~-~~xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8]~~ </~~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=6q8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q8m OCA], [https://pdbe.org/6q8m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6q8m RCSB], [https://www.ebi.ac.uk/pdbsum/6q8m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6q8m 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=6q8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q8m OCA], [~~http~~://pdbe.org/6q8m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6q8m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6q8m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6q8m ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A1L9WG58_ASPA1 A0A1L9WG58_ASPA1] Endo-1,4-mannanase, a crucial enzyme for depolymerization of seed galactomannans and wood galactoglucomannans.[ARBA:ARBA00002993]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Aspergillus aculeatus ~~atcc~~ 16872]]	+	[[Category: Aspergillus aculeatus ATCC 16872]]
-	~~[[Category: Endo-1,4-beta-xylanase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Blagova, E]]	+	[[Category: Blagova E]]
-	[[Category: Davies~~, G J~~]]	+	[[Category: Davies GJ]]
-	[[Category: Moroz, O]]	+	[[Category: Moroz O]]
-	[[Category: Rowland~~, R J~~]]	+	[[Category: Rowland RJ]]
-	[[Category: Wu, L]]	+	[[Category: Wu L]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 12:43, 17 July 2019

OCA — Wed, 17 Jul 2019 12:43:38 GMT

←Older revision		Revision as of 12:43, 17 July 2019
Line 3:		Line 3:
	<StructureSection load='6q8m' size='340' side='right'caption='[[6q8m]], [[Resolution\|resolution]] 1.42Å' scene=''>		<StructureSection load='6q8m' size='340' side='right'caption='[[6q8m]], [[Resolution\|resolution]] 1.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6q8m]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q8M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6Q8M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6q8m]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_aculeatus_atcc_16872 Aspergillus aculeatus atcc 16872]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q8M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6Q8M FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ASPACDRAFT_127619 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=690307 Aspergillus aculeatus ATCC 16872])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=6q8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q8m OCA], [http://pdbe.org/6q8m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6q8m RCSB], [http://www.ebi.ac.uk/pdbsum/6q8m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6q8m 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=6q8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q8m OCA], [http://pdbe.org/6q8m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6q8m RCSB], [http://www.ebi.ac.uk/pdbsum/6q8m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6q8m ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Plant polysaccharides represent a virtually unlimited feedstock for the generation of biofuels and other commodities. However, the extraordinary recalcitrance of plant polysaccharides toward breakdown necessitates a continued search for enzymes that degrade these materials efficiently under defined conditions. Activity-based protein profiling provides a route for the functional discovery of such enzymes in complex mixtures and under industrially relevant conditions. Here, we show the detection and identification of beta-xylosidases and endo-beta-1,4-xylanases in the secretomes of Aspergillus niger, by the use of chemical probes inspired by the beta-glucosidase inhibitor cyclophellitol. Furthermore, we demonstrate the use of these activity-based probes (ABPs) to assess enzyme-substrate specificities, thermal stabilities, and other biotechnologically relevant parameters. Our experiments highlight the utility of ABPs as promising tools for the discovery of relevant enzymes useful for biomass breakdown.
		+
		+	Dynamic and Functional Profiling of Xylan-Degrading Enzymes in Aspergillus Secretomes Using Activity-Based Probes.,Schroder SP, de Boer C, McGregor NGS, Rowland RJ, Moroz O, Blagova E, Reijngoud J, Arentshorst M, Osborn D, Morant MD, Abbate E, Stringer MA, Krogh KBRM, Raich L, Rovira C, Berrin JG, van Wezel GP, Ram AFJ, Florea BI, van der Marel GA, Codee JDC, Wilson KS, Wu L, Davies GJ, Overkleeft HS ACS Cent Sci. 2019 Jun 26;5(6):1067-1078. doi: 10.1021/acscentsci.9b00221. Epub, 2019 May 24. PMID:31263766<ref>PMID:31263766</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6q8m" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aspergillus aculeatus atcc 16872]]
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 22:53, 5 June 2019

OCA — Wed, 05 Jun 2019 22:53:38 GMT

←Older revision		Revision as of 22:53, 5 June 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6q8m ~~is ON HOLD until Paper Publication~~	+	==GH10 endo-xylanase==
-		+	<StructureSection load='6q8m' size='340' side='right'caption='[[6q8m]], [[Resolution\|resolution]] 1.42Å' scene=''>
-	~~Authors~~: ~~Davies, G~~.J.~~, Rowland, R~~.J.~~, Wu, L~~., ~~Moroz~~, O., ~~Blagova~~, E.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6q8m]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q8M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6Q8M FirstGlance]. <br>
-	~~Description~~: ~~GH10 endo~~-~~xylanase~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>
-	[[Category: Wu, L]]	+	<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=6q8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q8m OCA], [http://pdbe.org/6q8m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6q8m RCSB], [http://www.ebi.ac.uk/pdbsum/6q8m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6q8m ProSAT]</span></td></tr>
-	[[Category: ~~Rowland, R.J~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Endo-1,4-beta-xylanase]]
		+	[[Category: Large Structures]]
	[[Category: Blagova, E]]		[[Category: Blagova, E]]
		+	[[Category: Davies, G J]]
	[[Category: Moroz, O]]		[[Category: Moroz, O]]
-	[[Category: ~~Davies~~, G.J]]	+	[[Category: Rowland, R J]]
		+	[[Category: Wu, L]]
		+	[[Category: Hydrolase]]

OCA at 06:52, 30 January 2019

OCA — Wed, 30 Jan 2019 06:52:03 GMT

←Older revision		Revision as of 06:52, 30 January 2019
Line 3:		Line 3:
	The entry 6q8m is ON HOLD until Paper Publication		The entry 6q8m is ON HOLD until Paper Publication

-	Authors: Davies, G.J., Rowland, R.J., Wu, L.	+	Authors: Davies, G.J., Rowland, R.J., Wu, L., Moroz, O., Blagova, E.

	Description: GH10 endo-xylanase		Description: GH10 endo-xylanase
Line 9:		Line 9:
	[[Category: Wu, L]]		[[Category: Wu, L]]
	[[Category: Rowland, R.J]]		[[Category: Rowland, R.J]]
		+	[[Category: Blagova, E]]
		+	[[Category: Moroz, O]]
	[[Category: Davies, G.J]]		[[Category: Davies, G.J]]

OCA: Protected "6q8m" [edit=sysop:move=sysop]

OCA — Wed, 26 Dec 2018 06:57:47 GMT

Protected "6q8m" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:57, 26 December 2018

OCA: New page: '''Unreleased structure''' The entry 6q8m is ON HOLD until Paper Publication Authors: Davies, G.J., Rowland, R.J., Wu, L. Description: GH10 endo-xylanase [[Category: Unreleased Structu...

OCA — Wed, 26 Dec 2018 06:57:45 GMT

New page: '''Unreleased structure''' The entry 6q8m is ON HOLD until Paper Publication Authors: Davies, G.J., Rowland, R.J., Wu, L. Description: GH10 endo-xylanase [[Category: Unreleased Structu...

New page

'''Unreleased structure'''

The entry 6q8m is ON HOLD until Paper Publication

Authors: Davies, G.J., Rowland, R.J., Wu, L.

Description: GH10 endo-xylanase
[[Category: Unreleased Structures]]
[[Category: Wu, L]]
[[Category: Rowland, R.J]]
[[Category: Davies, G.J]]