5e7h - Revision history

OCA at 06:15, 5 July 2023

2023-07-05T06:15:42Z

←Older revision		Revision as of 06:15, 5 July 2023
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	<StructureSection load='5e7h' size='340' side='right'caption='[[5e7h]], [[Resolution\|resolution]] 1.57Å' scene=''>		<StructureSection load='5e7h' size='340' side='right'caption='[[5e7h]], [[Resolution\|resolution]] 1.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5e7h]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Baco1 Baco1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E7H OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5E7H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5e7h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_ovatus_ATCC_8483 Bacteroides ovatus ATCC 8483]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E7H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5E7H FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>~~, ~~<scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.57Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5e75\|5e75]], [[5e76\|5e76]], [[5e7g\|5e7g]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<~~tr id~~='~~gene~~'><~~td class="sblockLbl"~~><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">BACOVA_02650 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=411476 BACO1])~~</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=5e7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e7h OCA], [https://pdbe.org/5e7h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5e7h RCSB], [https://www.ebi.ac.uk/pdbsum/5e7h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5e7h 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=5e7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e7h OCA], [~~http~~://pdbe.org/5e7h PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5e7h RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5e7h PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5e7h ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/Y2650_BACO1 Y2650_BACO1]] Polysaccharide-binding protein present at the surface of the cell. Probably mediates xyloglucan-binding before xyloglucan transport in the periplasm for degradation.<ref>PMID:24463512</ref>	+	[https://www.uniprot.org/uniprot/Y2650_BACO1 Y2650_BACO1] Polysaccharide-binding protein present at the surface of the cell. Probably mediates xyloglucan-binding before xyloglucan transport in the periplasm for degradation.<ref>PMID:24463512</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Baco1~~]]	+	[[Category: Bacteroides ovatus ATCC 8483]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Koropatkin~~, N M]]~~	+	[[Category: Koropatkin NM]]
-	~~[[Category: Carbohydrate-binding protein]]~~	+
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 06:46, 22 April 2020

2020-04-22T06:46:22Z

←Older revision		Revision as of 06:46, 22 April 2020
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	==Crystal structure of domains CD (residues 230-489) of Bacova_02650==		==Crystal structure of domains CD (residues 230-489) of Bacova_02650==
-	<StructureSection load='5e7h' size='340' side='right' caption='[[5e7h]], [[Resolution\|resolution]] 1.57Å' scene=''>	+	<StructureSection load='5e7h' size='340' side='right'caption='[[5e7h]], [[Resolution\|resolution]] 1.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5e7h]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E7H OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5E7H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5e7h]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Baco1 Baco1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E7H OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5E7H FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5e75\|5e75]], [[5e76\|5e76]], [[5e7g\|5e7g]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5e75\|5e75]], [[5e76\|5e76]], [[5e7g\|5e7g]]</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=5e7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e7h OCA], [http://pdbe.org/5e7h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e7h RCSB], [http://www.ebi.ac.uk/pdbsum/5e7h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5e7h ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BACOVA_02650 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=411476 BACO1])</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=5e7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e7h OCA], [http://pdbe.org/5e7h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e7h RCSB], [http://www.ebi.ac.uk/pdbsum/5e7h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5e7h ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baco1]]
		+	[[Category: Large Structures]]
	[[Category: Koropatkin, N M]]		[[Category: Koropatkin, N M]]
	[[Category: Carbohydrate-binding protein]]		[[Category: Carbohydrate-binding protein]]
	[[Category: Sugar binding protein]]		[[Category: Sugar binding protein]]

OCA at 05:37, 9 September 2016

2016-09-09T05:37:05Z

←Older revision		Revision as of 05:37, 9 September 2016
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5e75\|5e75]], [[5e76\|5e76]], [[5e7g\|5e7g]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5e75\|5e75]], [[5e76\|5e76]], [[5e7g\|5e7g]]</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=5e7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e7h OCA], [http://pdbe.org/5e7h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e7h RCSB], [http://www.ebi.ac.uk/pdbsum/5e7h 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=5e7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e7h OCA], [http://pdbe.org/5e7h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e7h RCSB], [http://www.ebi.ac.uk/pdbsum/5e7h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5e7h ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 08:36, 1 June 2016

2016-06-01T08:36:51Z

←Older revision		Revision as of 08:36, 1 June 2016
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/Y2650_BACO1 Y2650_BACO1]] Polysaccharide-binding protein present at the surface of the cell. Probably mediates xyloglucan-binding before xyloglucan transport in the periplasm for degradation.<ref>PMID:24463512</ref>		[[http://www.uniprot.org/uniprot/Y2650_BACO1 Y2650_BACO1]] Polysaccharide-binding protein present at the surface of the cell. Probably mediates xyloglucan-binding before xyloglucan transport in the periplasm for degradation.<ref>PMID:24463512</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Polysaccharide utilization loci (PUL) within the genomes of resident human gut Bacteroidetes are central to the metabolism of the otherwise indigestible complex carbohydrates known as "dietary fiber." However, functional characterization of PUL lags significantly behind sequencing efforts, which limits physiological understanding of the human-bacterial symbiosis. In particular, the molecular basis of complex polysaccharide recognition, an essential prerequisite to hydrolysis by cell surface glycosidases and subsequent metabolism, is generally poorly understood. Here, we present the biochemical, structural, and reverse genetic characterization of two unique cell surface glycan-binding proteins (SGBPs) encoded by a xyloglucan utilization locus (XyGUL) from Bacteroides ovatus, which are integral to growth on this key dietary vegetable polysaccharide. Biochemical analysis reveals that these outer membrane-anchored proteins are in fact exquisitely specific for the highly branched xyloglucan (XyG) polysaccharide. The crystal structure of SGBP-A, a SusD homolog, with a bound XyG tetradecasaccharide reveals an extended carbohydrate-binding platform that primarily relies on recognition of the beta-glucan backbone. The unique, tetra-modular structure of SGBP-B is comprised of tandem Ig-like folds, with XyG binding mediated at the distal C-terminal domain. Despite displaying similar affinities for XyG, reverse-genetic analysis reveals that SGBP-B is only required for the efficient capture of smaller oligosaccharides, whereas the presence of SGBP-A is more critical than its carbohydrate-binding ability for growth on XyG. Together, these data demonstrate that SGBP-A and SGBP-B play complementary, specialized roles in carbohydrate capture by B. ovatus and elaborate a model of how vegetable xyloglucans are accessed by the Bacteroidetes IMPORTANCE: The Bacteroidetes are dominant bacteria in the human gut that are responsible for the digestion of the complex polysaccharides that constitute "dietary fiber." Although this symbiotic relationship has been appreciated for decades, little is currently known about how Bacteroidetes seek out and bind plant cell wall polysaccharides as a necessary first step in their metabolism. Here, we provide the first biochemical, crystallographic, and genetic insight into how two surface glycan-binding proteins from the complex Bacteroides ovatus xyloglucan utilization locus (XyGUL) enable recognition and uptake of this ubiquitous vegetable polysaccharide. Our combined analysis illuminates new fundamental aspects of complex polysaccharide recognition, cleavage, and import at the Bacteroidetes cell surface that may facilitate the development of prebiotics to target this phylum of gut bacteria.
		+
		+	Molecular Dissection of Xyloglucan Recognition in a Prominent Human Gut Symbiont.,Tauzin AS, Kwiatkowski KJ, Orlovsky NI, Smith CJ, Creagh AL, Haynes CA, Wawrzak Z, Brumer H, Koropatkin NM MBio. 2016 Apr 26;7(2). pii: e02134-15. doi: 10.1128/mBio.02134-15. PMID:27118585<ref>PMID:27118585</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5e7h" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 19:41, 13 May 2016

2016-05-13T19:41:51Z

←Older revision		Revision as of 19:41, 13 May 2016
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-	'''Unreleased structure'''

-	~~The entry 5e7h is ON HOLD until Paper Publication~~	+	==Crystal structure of domains CD (residues 230-489) of Bacova_02650==
-		+	<StructureSection load='5e7h' size='340' side='right' caption='[[5e7h]], [[Resolution\|resolution]] 1.57Å' scene=''>
-	~~Authors: Koropatkin, N.M.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5e7h]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E7H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5E7H FirstGlance]. <br>
-	~~Description:~~ Crystal structure of domains CD (residues 230-489) of Bacova_02650	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5e75\|5e75]], [[5e76\|5e76]], [[5e7g\|5e7g]]</td></tr>
-	[[Category: Koropatkin, N.M]]	+	<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=5e7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e7h OCA], [http://pdbe.org/5e7h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e7h RCSB], [http://www.ebi.ac.uk/pdbsum/5e7h PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Y2650_BACO1 Y2650_BACO1]] Polysaccharide-binding protein present at the surface of the cell. Probably mediates xyloglucan-binding before xyloglucan transport in the periplasm for degradation.<ref>PMID:24463512</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Koropatkin, N M]]
		+	[[Category: Carbohydrate-binding protein]]
		+	[[Category: Sugar binding protein]]

OCA at 02:29, 1 December 2015

2015-12-01T02:29:27Z

←Older revision		Revision as of 02:29, 1 December 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5e7h is ON HOLD	+	The entry 5e7h is ON HOLD until Paper Publication

	Authors: Koropatkin, N.M.		Authors: Koropatkin, N.M.

OCA: Protected "5e7h" [edit=sysop:move=sysop]

2015-10-22T04:27:30Z

Protected "5e7h" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:27, 22 October 2015

OCA: New page: '''Unreleased structure''' The entry 5e7h is ON HOLD Authors: Koropatkin, N.M. Description: Crystal structure of domains CD (residues 230-489) of Bacova_02650 [[Category: Unreleased St...

2015-10-22T04:27:28Z

New page: '''Unreleased structure''' The entry 5e7h is ON HOLD Authors: Koropatkin, N.M. Description: Crystal structure of domains CD (residues 230-489) of Bacova_02650 [[Category: Unreleased St...

New page

'''Unreleased structure'''

The entry 5e7h is ON HOLD

Authors: Koropatkin, N.M.

Description: Crystal structure of domains CD (residues 230-489) of Bacova_02650
[[Category: Unreleased Structures]]
[[Category: Koropatkin, N.M]]