6eui - Revision history

OCA at 07:31, 1 May 2024

2024-05-01T07:31:49Z

←Older revision		Revision as of 07:31, 1 May 2024
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	<StructureSection load='6eui' size='340' side='right'caption='[[6eui]], [[Resolution\|resolution]] 1.76Å' scene=''>		<StructureSection load='6eui' size='340' side='right'caption='[[6eui]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6eui]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bactn Bactn~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EUI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6EUI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6eui]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron_VPI-5482 Bacteroides thetaiotaomicron VPI-5482]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EUI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6EUI FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CA:CALCIUM+ION'>CA</scene~~>, ~~<scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</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]] 1.76Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~BT_3683 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=226186 BACTN])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene></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=6eui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eui OCA], [~~http~~://pdbe.org/6eui PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6eui RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6eui PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6eui 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=6eui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eui OCA], [https://pdbe.org/6eui PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6eui RCSB], [https://www.ebi.ac.uk/pdbsum/6eui PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6eui ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q8A1H8_BACTN Q8A1H8_BACTN]
-	Glycans are major nutrients for the human gut microbiota (HGM). Arabinogalactan proteins (AGPs) comprise a heterogenous group of plant glycans in which a beta1,3-galactan backbone and beta1,6-galactan side chains are conserved. Diversity is provided by the variable nature of the sugars that decorate the galactans. The mechanisms by which nutritionally relevant AGPs are degraded in the HGM are poorly understood. Here we explore how the HGM organism Bacteroides thetaiotaomicron metabolizes AGPs. We propose a sequential degradative model in which exo-acting glycoside hydrolase (GH) family 43 beta1,3-galactanases release the side chains. These oligosaccharide side chains are depolymerized by the synergistic action of exo-acting enzymes in which catalytic interactions are dependent on whether degradation is initiated by a lyase or GH. We identified two GHs that establish two previously undiscovered GH families. The crystal structures of the exo-beta1,3-galactanases identified a key specificity determinant and departure from the canonical catalytic apparatus of GH43 enzymes. Growth studies of Bacteroidetes spp. on complex AGP revealed 3 keystone organisms that facilitated utilization of the glycan by 17 recipient bacteria, which included B. thetaiotaomicron. A surface endo-beta1,3-galactanase, when engineered into B. thetaiotaomicron, enabled the bacterium to utilize complex AGPs and act as a keystone organism.	+
-		+
-	A surface endogalactanase in Bacteroides thetaiotaomicron confers keystone status for arabinogalactan degradation.,Cartmell A, Munoz-Munoz J, Briggs JA, Ndeh DA, Lowe EC, Basle A, Terrapon N, Stott K, Heunis T, Gray J, Yu L, Dupree P, Fernandes PZ, Shah S, Williams SJ, Labourel A, Trost M, Henrissat B, Gilbert HJ Nat Microbiol. 2018 Nov;3(11):~~1314-1326. doi: 10.1038~~/~~s41564-018-0258-8. Epub, 2018 Oct 22. PMID:30349080<ref>PMID:30349080<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6eui" style="background-color:#fffaf0;"><~~/~~div>~~	+

	==See Also==		==See Also==
		+	*[[Galactosidase 3D structures\|Galactosidase 3D structures]]
	*[[Glucanase 3D structures\|Glucanase 3D structures]]		*[[Glucanase 3D structures\|Glucanase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bactn~~]]	+	[[Category: Bacteroides thetaiotaomicron VPI-5482]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cartmell, A]]	+	[[Category: Cartmell A]]
-	[[Category: Gilbert~~, H J]]~~	+	[[Category: Gilbert HJ]]
-	~~[[Category: Galactosidase]]~~	+
-	~~[[Category: Arabiogalactan]]~~	+
-	~~[[Category: Beta 1]]~~	+
-	~~[[Category: Gh43]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:11, 16 October 2019

2019-10-16T07:11:12Z

←Older revision		Revision as of 07:11, 16 October 2019
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 6eui" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6eui" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Glucanase 3D structures\|Glucanase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:10, 1 May 2019

2019-05-01T09:10:49Z

←Older revision		Revision as of 09:10, 1 May 2019
Line 1:		Line 1:

	==The GH43, Beta 1,3 Galactosidase, BT3683 with galactose==		==The GH43, Beta 1,3 Galactosidase, BT3683 with galactose==
-	<StructureSection load='6eui' size='340' side='right' caption='[[6eui]], [[Resolution\|resolution]] 1.76Å' scene=''>	+	<StructureSection load='6eui' size='340' side='right'caption='[[6eui]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6eui]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EUI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EUI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6eui]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bactn Bactn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EUI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EUI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BT_3683 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226186 BACTN])</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=6eui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eui OCA], [http://pdbe.org/6eui PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6eui RCSB], [http://www.ebi.ac.uk/pdbsum/6eui PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6eui 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=6eui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eui OCA], [http://pdbe.org/6eui PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6eui RCSB], [http://www.ebi.ac.uk/pdbsum/6eui PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6eui ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Glycans are major nutrients for the human gut microbiota (HGM). Arabinogalactan proteins (AGPs) comprise a heterogenous group of plant glycans in which a beta1,3-galactan backbone and beta1,6-galactan side chains are conserved. Diversity is provided by the variable nature of the sugars that decorate the galactans. The mechanisms by which nutritionally relevant AGPs are degraded in the HGM are poorly understood. Here we explore how the HGM organism Bacteroides thetaiotaomicron metabolizes AGPs. We propose a sequential degradative model in which exo-acting glycoside hydrolase (GH) family 43 beta1,3-galactanases release the side chains. These oligosaccharide side chains are depolymerized by the synergistic action of exo-acting enzymes in which catalytic interactions are dependent on whether degradation is initiated by a lyase or GH. We identified two GHs that establish two previously undiscovered GH families. The crystal structures of the exo-beta1,3-galactanases identified a key specificity determinant and departure from the canonical catalytic apparatus of GH43 enzymes. Growth studies of Bacteroidetes spp. on complex AGP revealed 3 keystone organisms that facilitated utilization of the glycan by 17 recipient bacteria, which included B. thetaiotaomicron. A surface endo-beta1,3-galactanase, when engineered into B. thetaiotaomicron, enabled the bacterium to utilize complex AGPs and act as a keystone organism.
		+
		+	A surface endogalactanase in Bacteroides thetaiotaomicron confers keystone status for arabinogalactan degradation.,Cartmell A, Munoz-Munoz J, Briggs JA, Ndeh DA, Lowe EC, Basle A, Terrapon N, Stott K, Heunis T, Gray J, Yu L, Dupree P, Fernandes PZ, Shah S, Williams SJ, Labourel A, Trost M, Henrissat B, Gilbert HJ Nat Microbiol. 2018 Nov;3(11):1314-1326. doi: 10.1038/s41564-018-0258-8. Epub, 2018 Oct 22. PMID:30349080<ref>PMID:30349080</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6eui" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bactn]]
		+	[[Category: Large Structures]]
	[[Category: Cartmell, A]]		[[Category: Cartmell, A]]
	[[Category: Gilbert, H J]]		[[Category: Gilbert, H J]]

OCA at 08:04, 17 October 2018

2018-10-17T08:04:17Z

←Older revision		Revision as of 08:04, 17 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 6eui ~~is ON HOLD~~	+	==The GH43, Beta 1,3 Galactosidase, BT3683 with galactose==
-		+	<StructureSection load='6eui' size='340' side='right' caption='[[6eui]], [[Resolution\|resolution]] 1.76Å' scene=''>
-	~~Authors~~: ~~Cartmell, A~~.~~, Gilbert, H~~.J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6eui]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EUI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EUI FirstGlance]. <br>
-	~~Description~~: ~~The GH43~~, ~~Beta 1~~,~~3 Glacatosidase~~, ~~BT3683 with galactose~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=6eui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eui OCA], [http://pdbe.org/6eui PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6eui RCSB], [http://www.ebi.ac.uk/pdbsum/6eui PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6eui ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Cartmell, A]]		[[Category: Cartmell, A]]
-	[[Category: Gilbert, H.J]]	+	[[Category: Gilbert, H J]]
		+	[[Category: Galactosidase]]
		+	[[Category: Arabiogalactan]]
		+	[[Category: Beta 1]]
		+	[[Category: Gh43]]
		+	[[Category: Hydrolase]]

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

2017-11-08T06:42:52Z

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

←Older revision

Revision as of 06:42, 8 November 2017

OCA: New page: '''Unreleased structure''' The entry 6eui is ON HOLD Authors: Cartmell, A., Gilbert, H.J. Description: The GH43, Beta 1,3 Glacatosidase, BT3683 with galactose [[Category: Unreleased St...

2017-11-08T06:42:51Z

New page: '''Unreleased structure''' The entry 6eui is ON HOLD Authors: Cartmell, A., Gilbert, H.J. Description: The GH43, Beta 1,3 Glacatosidase, BT3683 with galactose [[Category: Unreleased St...

New page

'''Unreleased structure'''

The entry 6eui is ON HOLD

Authors: Cartmell, A., Gilbert, H.J.

Description: The GH43, Beta 1,3 Glacatosidase, BT3683 with galactose
[[Category: Unreleased Structures]]
[[Category: Cartmell, A]]
[[Category: Gilbert, H.J]]