6euh - Revision history

OCA at 12:21, 9 May 2024

2024-05-09T12:21:36Z

←Older revision		Revision as of 12:21, 9 May 2024
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	<StructureSection load='6euh' size='340' side='right'caption='[[6euh]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6euh' size='340' side='right'caption='[[6euh]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6euh]] is a 3 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=6EUH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6EUH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6euh]] is a 3 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=6EUH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6EUH 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=DGJ:(2R,3S,4R,5S)-2-(HYDROXYMETHYL)PIPERIDINE-3,4,5-TRIOL'>DGJ</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]] 2Å</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=DGJ:(2R,3S,4R,5S)-2-(HYDROXYMETHYL)PIPERIDINE-3,4,5-TRIOL'>DGJ</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=6euh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6euh OCA], [~~http~~://pdbe.org/6euh PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6euh RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6euh PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6euh 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=6euh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6euh OCA], [https://pdbe.org/6euh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6euh RCSB], [https://www.ebi.ac.uk/pdbsum/6euh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6euh ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8A1H8_BACTN Q8A1H8_BACTN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
		+	*[[Galactosidase 3D structures\|Galactosidase 3D structures]]
	*[[Glucanase 3D structures\|Glucanase 3D structures]]		*[[Glucanase 3D structures\|Glucanase 3D structures]]
	== References ==		== References ==
Line 24:		Line 27:
	__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: Hexasaccharide]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:10, 16 October 2019

2019-10-16T07:10:59Z

←Older revision		Revision as of 07:10, 16 October 2019
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	</div>		</div>
	<div class="pdbe-citations 6euh" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6euh" 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 galactodeoxynojirimycin==		==The GH43, Beta 1,3 Galactosidase, BT3683 with galactodeoxynojirimycin==
-	<StructureSection load='6euh' size='340' side='right' caption='[[6euh]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='6euh' size='340' side='right'caption='[[6euh]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6euh]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EUH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EUH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6euh]] is a 3 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=6EUH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EUH 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=DGJ:(2R,3S,4R,5S)-2-(HYDROXYMETHYL)PIPERIDINE-3,4,5-TRIOL'>DGJ</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=DGJ:(2R,3S,4R,5S)-2-(HYDROXYMETHYL)PIPERIDINE-3,4,5-TRIOL'>DGJ</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=6euh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6euh OCA], [http://pdbe.org/6euh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6euh RCSB], [http://www.ebi.ac.uk/pdbsum/6euh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6euh 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=6euh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6euh OCA], [http://pdbe.org/6euh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6euh RCSB], [http://www.ebi.ac.uk/pdbsum/6euh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6euh 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 6euh" 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

2018-10-17T08:04:08Z

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

-	The ~~entry~~ 6euh ~~is ON HOLD~~	+	==The GH43, Beta 1,3 Galactosidase, BT3683 with galactodeoxynojirimycin==
-		+	<StructureSection load='6euh' size='340' side='right' caption='[[6euh]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~Authors~~: ~~Cartmell, A~~.~~, Gilbert, H~~.J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6euh]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EUH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EUH FirstGlance]. <br>
-	~~Description~~: ~~The GH43~~, ~~Beta 1~~,3 ~~Glacatosidase~~, ~~BT3683 with galactodeoxynojirimycin~~	+	</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=DGJ:(2R,3S,4R,5S)-2-(HYDROXYMETHYL)PIPERIDINE-3,4,5-TRIOL'>DGJ</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=6euh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6euh OCA], [http://pdbe.org/6euh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6euh RCSB], [http://www.ebi.ac.uk/pdbsum/6euh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6euh 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: Hexasaccharide]]
		+	[[Category: Hydrolase]]

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

2017-11-08T06:42:49Z

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

←Older revision

Revision as of 06:42, 8 November 2017

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

2017-11-08T06:42:48Z

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

New page

'''Unreleased structure'''

The entry 6euh is ON HOLD

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

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