7kv5 - Revision history

OCA at 14:58, 6 March 2024

OCA — Wed, 06 Mar 2024 14:58:00 GMT

←Older revision		Revision as of 14:58, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='7kv5' size='340' side='right'caption='[[7kv5]], [[Resolution\|resolution]] 1.82Å' scene=''>		<StructureSection load='7kv5' size='340' side='right'caption='[[7kv5]], [[Resolution\|resolution]] 1.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7kv5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bacteroides_fluxus_dsm_22534~~ Bacteroides fluxus ~~dsm 22534~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KV5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KV5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7kv5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_fluxus_YIT_12057 Bacteroides fluxus YIT 12057]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KV5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KV5 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GAI:GUANIDINE'>GAI</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]] 1.82Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~HMPREF9446_00613 ([https~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=763034 Bacteroides fluxus DSM 22534]~~)</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GAI:GUANIDINE'>GAI</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=7kv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kv5 OCA], [https://pdbe.org/7kv5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kv5 RCSB], [https://www.ebi.ac.uk/pdbsum/7kv5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kv5 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=7kv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kv5 OCA], [https://pdbe.org/7kv5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kv5 RCSB], [https://www.ebi.ac.uk/pdbsum/7kv5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kv5 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/F3PPH3_9BACE F3PPH3_9BACE]
-	Complex glycans that evade our digestive system are major nutrients that feed the human gut microbiota (HGM). The prevalence of Bacteroidetes in the HGM of populations worldwide is engendered by the evolution of Polysaccharide Utilization Locus (PUL), which encode concerted protein systems to utilize the myriad complex glycans in our diets. Despite their crucial roles in glycan recognition and transport, cell-surface glycan-binding proteins (SGBPs) remained understudied cogs in the PUL machinery. Here, we report the structural and biochemical characterization of a suite of SGBP-A and SGBP-B structures from three syntenic beta(1,3)-glucan utilization loci (1,3GULs) from Bacteroides thetaiotaomicron (Bt), B. uniformis (Bu), and B. fluxus (Bf), which have varying specificities for distinct beta-glucans. Ligand complexes provide definitive insight into beta(1,3)-glucan selectivity in the HGM, including structural features enabling dual beta(1,3)-glucan/mixed-linkage beta(1,3)/beta(1,4)-glucan binding capability in some orthologs. The tertiary structural conservation of SusD-like SGBPs-A is juxtaposed with the diverse architectures and binding modes of the SGBPs-B. Specifically, the structures of the tri-modular BtSGBP-B and BuSGBP-B revealed a tandem repeat of Carbohydrate-Binding Module-Like domains connected by long linkers. In contrast, BfSGBP-B comprises a bi-modular architecture with a distinct beta-barrel domain at the C-terminus that bears a shallow binding canyon. The molecular insights obtained here contribute to our fundamental understanding of HGM function, which in turn may inform tailored microbial intervention therapies.	+
-		+
-	~~Distinct protein architectures mediate species-specific beta-glucan binding and metabolism in the human gut microbiota.,Tamura K, Dejean G, Van Petegem F, Brumer H J Biol Chem. 2021 Feb 12~~:~~100415. doi: 10.1016~~/~~j.jbc.2021.100415. PMID:33587952<ref>PMID:33587952<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 7kv5" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacteroides fluxus ~~dsm 22534~~]]	+	[[Category: Bacteroides fluxus YIT 12057]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Brumer, H]]	+	[[Category: Brumer H]]
-	~~[[Category: Petegem, F Van~~]]	+	[[Category: Tamura K]]
-	[[Category: Tamura, K]]	+	[[Category: Van Petegem F]]
-	[[Category: ~~Cbm]]~~	+
-	~~[[Category: Lectin]]~~	+
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 15:04, 3 March 2021

OCA — Wed, 03 Mar 2021 15:04:22 GMT

←Older revision		Revision as of 15:04, 3 March 2021
Line 1:		Line 1:

	==Surface glycan-binding protein B from Bacteroides fluxus==		==Surface glycan-binding protein B from Bacteroides fluxus==
-	<StructureSection load='7kv5' size='340' side='right'caption='[[7kv5]]' scene=''>	+	<StructureSection load='7kv5' size='340' side='right'caption='[[7kv5]], [[Resolution\|resolution]] 1.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KV5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KV5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7kv5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_fluxus_dsm_22534 Bacteroides fluxus dsm 22534]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KV5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KV5 FirstGlance]. <br>
-	</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=7kv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kv5 OCA], [https://pdbe.org/7kv5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kv5 RCSB], [https://www.ebi.ac.uk/pdbsum/7kv5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kv5 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GAI:GUANIDINE'>GAI</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">HMPREF9446_00613 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=763034 Bacteroides fluxus DSM 22534])</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=7kv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kv5 OCA], [https://pdbe.org/7kv5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kv5 RCSB], [https://www.ebi.ac.uk/pdbsum/7kv5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kv5 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Complex glycans that evade our digestive system are major nutrients that feed the human gut microbiota (HGM). The prevalence of Bacteroidetes in the HGM of populations worldwide is engendered by the evolution of Polysaccharide Utilization Locus (PUL), which encode concerted protein systems to utilize the myriad complex glycans in our diets. Despite their crucial roles in glycan recognition and transport, cell-surface glycan-binding proteins (SGBPs) remained understudied cogs in the PUL machinery. Here, we report the structural and biochemical characterization of a suite of SGBP-A and SGBP-B structures from three syntenic beta(1,3)-glucan utilization loci (1,3GULs) from Bacteroides thetaiotaomicron (Bt), B. uniformis (Bu), and B. fluxus (Bf), which have varying specificities for distinct beta-glucans. Ligand complexes provide definitive insight into beta(1,3)-glucan selectivity in the HGM, including structural features enabling dual beta(1,3)-glucan/mixed-linkage beta(1,3)/beta(1,4)-glucan binding capability in some orthologs. The tertiary structural conservation of SusD-like SGBPs-A is juxtaposed with the diverse architectures and binding modes of the SGBPs-B. Specifically, the structures of the tri-modular BtSGBP-B and BuSGBP-B revealed a tandem repeat of Carbohydrate-Binding Module-Like domains connected by long linkers. In contrast, BfSGBP-B comprises a bi-modular architecture with a distinct beta-barrel domain at the C-terminus that bears a shallow binding canyon. The molecular insights obtained here contribute to our fundamental understanding of HGM function, which in turn may inform tailored microbial intervention therapies.
		+
		+	Distinct protein architectures mediate species-specific beta-glucan binding and metabolism in the human gut microbiota.,Tamura K, Dejean G, Van Petegem F, Brumer H J Biol Chem. 2021 Feb 12:100415. doi: 10.1016/j.jbc.2021.100415. PMID:33587952<ref>PMID:33587952</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7kv5" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacteroides fluxus dsm 22534]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Brumer H]]	+	[[Category: Brumer, H]]
-	[[Category: Tamura K]]	+	[[Category: Petegem, F Van]]
-	[[Category: ~~Van Petegem F~~]]	+	[[Category: Tamura, K]]
		+	[[Category: Cbm]]
		+	[[Category: Lectin]]
		+	[[Category: Sugar binding protein]]

OCA at 10:02, 17 February 2021

OCA — Wed, 17 Feb 2021 10:02:27 GMT

←Older revision		Revision as of 10:02, 17 February 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7kv5 ~~is ON HOLD until Paper Publication~~	+	==Surface glycan-binding protein B from Bacteroides fluxus==
-		+	<StructureSection load='7kv5' size='340' side='right'caption='[[7kv5]]' scene=''>
-	~~Authors~~: ~~Tamura~~, K., ~~Brumer~~, H., ~~Van Petegem~~, F.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KV5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KV5 FirstGlance]. <br>
-	~~Description: Surface glycan-binding protein B from Bacteroides fluxus~~	+	</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=7kv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kv5 OCA], [https://pdbe.org/7kv5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kv5 RCSB], [https://www.ebi.ac.uk/pdbsum/7kv5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kv5 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Brumer, H]]	+	__TOC__
-	[[Category: ~~Van Petegem, F~~]]	+	</StructureSection>
-	[[Category: ~~Tamura, K~~]]	+	[[Category: Large Structures]]
		+	[[Category: Brumer H]]
		+	[[Category: Tamura K]]
		+	[[Category: Van Petegem F]]

OCA at 11:12, 16 December 2020

OCA — Wed, 16 Dec 2020 11:12:54 GMT

←Older revision		Revision as of 11:12, 16 December 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7kv5 is ON HOLD	+	The entry 7kv5 is ON HOLD until Paper Publication

	Authors: Tamura, K., Brumer, H., Van Petegem, F.		Authors: Tamura, K., Brumer, H., Van Petegem, F.

OCA: Protected "7kv5" [edit=sysop:move=sysop]

OCA — Wed, 02 Dec 2020 05:56:30 GMT

Protected "7kv5" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:56, 2 December 2020

OCA: New page: '''Unreleased structure''' The entry 7kv5 is ON HOLD Authors: Tamura, K., Brumer, H., Van Petegem, F. Description: Surface glycan-binding protein B from Bacteroides fluxus [[Category: ...

OCA — Wed, 02 Dec 2020 05:56:29 GMT

New page: '''Unreleased structure''' The entry 7kv5 is ON HOLD Authors: Tamura, K., Brumer, H., Van Petegem, F. Description: Surface glycan-binding protein B from Bacteroides fluxus [[Category: ...

New page

'''Unreleased structure'''

The entry 7kv5 is ON HOLD

Authors: Tamura, K., Brumer, H., Van Petegem, F.

Description: Surface glycan-binding protein B from Bacteroides fluxus
[[Category: Unreleased Structures]]
[[Category: Brumer, H]]
[[Category: Van Petegem, F]]
[[Category: Tamura, K]]