5jox - Revision history

OCA at 07:24, 1 May 2024

OCA — Wed, 01 May 2024 07:24:34 GMT

←Older revision		Revision as of 07:24, 1 May 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/GH43A_BACO1 GH43A_BACO1] Alpha-L-arabinofuranosidase involved in xyloglucan degradation by mediating the cleavage of terminal non-reducing alpha-L-arabinofuranoside residues in xyloglucan branches, converting the 'S' units to 'X' units.<ref>PMID:24463512</ref>		[https://www.uniprot.org/uniprot/GH43A_BACO1 GH43A_BACO1] Alpha-L-arabinofuranosidase involved in xyloglucan degradation by mediating the cleavage of terminal non-reducing alpha-L-arabinofuranoside residues in xyloglucan branches, converting the 'S' units to 'X' units.<ref>PMID:24463512</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The human gastrointestinal tract harbours myriad bacterial species, collectively termed the microbiota, that strongly influence human health. Symbiotic members of our microbiota play a pivotal role in the digestion of complex carbohydrates that are otherwise recalcitrant to assimilation. Indeed, the intrinsic human polysaccharide-degrading enzyme repertoire is limited to various starch-based substrates; more complex polysaccharides demand microbial degradation. Select Bacteroidetes are responsible for the degradation of the ubiquitous vegetable xyloglucans (XyGs), through the concerted action of cohorts of enzymes and glycan-binding proteins encoded by specific xyloglucan utilization loci (XyGULs). Extending recent (meta)genomic, transcriptomic and biochemical analyses, significant questions remain regarding the structural biology of the molecular machinery required for XyG saccharification. Here, we reveal the three-dimensional structures of an alpha-xylosidase, a beta-glucosidase, and two alpha-l-arabinofuranosidases from the Bacteroides ovatus XyGUL. Aided by bespoke ligand synthesis, our analyses highlight key adaptations in these enzymes that confer individual specificity for xyloglucan side chains and dictate concerted, stepwise disassembly of xyloglucan oligosaccharides. In harness with our recent structural characterization of the vanguard endo-xyloglucanse and cell-surface glycan-binding proteins, the present analysis provides a near-complete structural view of xyloglucan recognition and catalysis by XyGUL proteins.
-
-	Structural dissection of a complex Bacteroides ovatus gene locus conferring xyloglucan metabolism in the human gut.,Hemsworth GR, Thompson AJ, Stepper J, Sobala LF, Coyle T, Larsbrink J, Spadiut O, Goddard-Borger ED, Stubbs KA, Brumer H, Davies GJ Open Biol. 2016 Jul;6(7). pii: 160142. doi: 10.1098/rsob.160142. PMID:27466444<ref>PMID:27466444</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5jox" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 19:01, 20 September 2023

OCA — Wed, 20 Sep 2023 19:01:23 GMT

←Older revision		Revision as of 19:01, 20 September 2023
Line 3:		Line 3:
	<StructureSection load='5jox' size='340' side='right'caption='[[5jox]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5jox' size='340' side='right'caption='[[5jox]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jox]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JOX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5JOX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jox]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_ovatus Bacteroides ovatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JOX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JOX FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDG:1~~,~~4-DIDEOXY-~~1~~,4-IMINO-L-ARABINITOL'>EDG</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='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Non~~-~~reducing_end_alpha~~-L-~~arabinofuranosidase Non-reducing end alpha~~-L-~~arabinofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.55 3.2.1.55]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDG:1,4-DIDEOXY-1,4-IMINO-L-ARABINITOL'>EDG</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5jox FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jox OCA], [~~http~~://pdbe.org/5jox PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jox RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jox PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jox 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=5jox FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jox OCA], [https://pdbe.org/5jox PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jox RCSB], [https://www.ebi.ac.uk/pdbsum/5jox PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jox ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GH43A_BACO1 GH43A_BACO1]] Alpha-L-arabinofuranosidase involved in xyloglucan degradation by mediating the cleavage of terminal non-reducing alpha-L-arabinofuranoside residues in xyloglucan branches, converting the 'S' units to 'X' units.<ref>PMID:24463512</ref>	+	[https://www.uniprot.org/uniprot/GH43A_BACO1 GH43A_BACO1] Alpha-L-arabinofuranosidase involved in xyloglucan degradation by mediating the cleavage of terminal non-reducing alpha-L-arabinofuranoside residues in xyloglucan branches, converting the 'S' units to 'X' units.<ref>PMID:24463512</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacteroides ovatus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Non-reducing end alpha-L-arabinofuranosidase]]~~	+	[[Category: Brumer H]]
-	[[Category: Brumer, H]]	+	[[Category: Coyle T]]
-	[[Category: Coyle, T]]	+	[[Category: Davies GJ]]
-	[[Category: Davies~~, G J~~]]	+	[[Category: Hemsworth GR]]
-	[[Category: Hemsworth~~, G R~~]]	+	[[Category: Larsbrink J]]
-	[[Category: Larsbrink, J]]	+	[[Category: Sobala LF]]
-	[[Category: Sobala~~, L F~~]]	+	[[Category: Spadiut O]]
-	[[Category: Spadiut, O]]	+	[[Category: Stepper J]]
-	[[Category: Stepper, J]]	+	[[Category: Stubbs KA]]
-	[[Category: Stubbs~~, K A~~]]	+	[[Category: Thompson AJ]]
-	[[Category: Thompson~~, A J]]~~	+
-	~~[[Category: Gh43]]~~	+
-	~~[[Category: Glycoside hydrolase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 11:32, 17 June 2020

OCA — Wed, 17 Jun 2020 11:32:14 GMT

←Older revision		Revision as of 11:32, 17 June 2020
Line 1:		Line 1:

	==Bacteroides ovatus Xyloglucan PUL GH43A in complex with AraDNJ==		==Bacteroides ovatus Xyloglucan PUL GH43A in complex with AraDNJ==
-	<StructureSection load='5jox' size='340' side='right' caption='[[5jox]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5jox' size='340' side='right'caption='[[5jox]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jox]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JOX OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JOX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jox]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JOX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JOX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDG:1,4-DIDEOXY-1,4-IMINO-L-ARABINITOL'>EDG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDG:1,4-DIDEOXY-1,4-IMINO-L-ARABINITOL'>EDG</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-reducing_end_alpha-L-arabinofuranosidase Non-reducing end alpha-L-arabinofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.55 3.2.1.55] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-reducing_end_alpha-L-arabinofuranosidase Non-reducing end alpha-L-arabinofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.55 3.2.1.55] </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=5jox FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jox OCA], [http://pdbe.org/5jox PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jox RCSB], [http://www.ebi.ac.uk/pdbsum/5jox PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jox ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5jox FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jox OCA], [http://pdbe.org/5jox PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jox RCSB], [http://www.ebi.ac.uk/pdbsum/5jox PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jox ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Non-reducing end alpha-L-arabinofuranosidase]]		[[Category: Non-reducing end alpha-L-arabinofuranosidase]]
	[[Category: Brumer, H]]		[[Category: Brumer, H]]

OCA at 16:11, 10 August 2016

OCA — Wed, 10 Aug 2016 16:11:35 GMT

←Older revision		Revision as of 16:11, 10 August 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jox is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Bacteroides ovatus Xyloglucan PUL GH43A in complex with AraDNJ==
		+	<StructureSection load='5jox' size='340' side='right' caption='[[5jox]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5jox]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JOX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JOX FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDG:1,4-DIDEOXY-1,4-IMINO-L-ARABINITOL'>EDG</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-reducing_end_alpha-L-arabinofuranosidase Non-reducing end alpha-L-arabinofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.55 3.2.1.55] </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=5jox FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jox OCA], [http://pdbe.org/5jox PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jox RCSB], [http://www.ebi.ac.uk/pdbsum/5jox PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jox ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GH43A_BACO1 GH43A_BACO1]] Alpha-L-arabinofuranosidase involved in xyloglucan degradation by mediating the cleavage of terminal non-reducing alpha-L-arabinofuranoside residues in xyloglucan branches, converting the 'S' units to 'X' units.<ref>PMID:24463512</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The human gastrointestinal tract harbours myriad bacterial species, collectively termed the microbiota, that strongly influence human health. Symbiotic members of our microbiota play a pivotal role in the digestion of complex carbohydrates that are otherwise recalcitrant to assimilation. Indeed, the intrinsic human polysaccharide-degrading enzyme repertoire is limited to various starch-based substrates; more complex polysaccharides demand microbial degradation. Select Bacteroidetes are responsible for the degradation of the ubiquitous vegetable xyloglucans (XyGs), through the concerted action of cohorts of enzymes and glycan-binding proteins encoded by specific xyloglucan utilization loci (XyGULs). Extending recent (meta)genomic, transcriptomic and biochemical analyses, significant questions remain regarding the structural biology of the molecular machinery required for XyG saccharification. Here, we reveal the three-dimensional structures of an alpha-xylosidase, a beta-glucosidase, and two alpha-l-arabinofuranosidases from the Bacteroides ovatus XyGUL. Aided by bespoke ligand synthesis, our analyses highlight key adaptations in these enzymes that confer individual specificity for xyloglucan side chains and dictate concerted, stepwise disassembly of xyloglucan oligosaccharides. In harness with our recent structural characterization of the vanguard endo-xyloglucanse and cell-surface glycan-binding proteins, the present analysis provides a near-complete structural view of xyloglucan recognition and catalysis by XyGUL proteins.

-	~~Authors~~:	+	Structural dissection of a complex Bacteroides ovatus gene locus conferring xyloglucan metabolism in the human gut.,Hemsworth GR, Thompson AJ, Stepper J, Sobala LF, Coyle T, Larsbrink J, Spadiut O, Goddard-Borger ED, Stubbs KA, Brumer H, Davies GJ Open Biol. 2016 Jul;6(7). pii: 160142. doi: 10.1098/rsob.160142. PMID:27466444<ref>PMID:27466444</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5jox" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Non-reducing end alpha-L-arabinofuranosidase]]
		+	[[Category: Brumer, H]]
		+	[[Category: Coyle, T]]
		+	[[Category: Davies, G J]]
		+	[[Category: Hemsworth, G R]]
		+	[[Category: Larsbrink, J]]
		+	[[Category: Sobala, L F]]
		+	[[Category: Spadiut, O]]
		+	[[Category: Stepper, J]]
		+	[[Category: Stubbs, K A]]
		+	[[Category: Thompson, A J]]
		+	[[Category: Gh43]]
		+	[[Category: Glycoside hydrolase]]
		+	[[Category: Hydrolase]]

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

OCA — Sun, 15 May 2016 15:41:08 GMT

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

←Older revision

Revision as of 15:41, 15 May 2016

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

OCA — Sun, 15 May 2016 15:41:07 GMT

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

New page

'''Unreleased structure'''

The entry 5jox is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]