6t8k - Revision history

OCA at 12:56, 24 January 2024

OCA — Wed, 24 Jan 2024 12:56:59 GMT

←Older revision		Revision as of 12:56, 24 January 2024
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	<StructureSection load='6t8k' size='340' side='right'caption='[[6t8k]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6t8k' size='340' side='right'caption='[[6t8k]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6t8k]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T8K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6T8K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6t8k]] is a 2 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=6T8K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6T8K FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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='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=6t8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t8k OCA], [~~http~~://pdbe.org/6t8k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6t8k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6t8k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6t8k ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=6t8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t8k OCA], [https://pdbe.org/6t8k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6t8k RCSB], [https://www.ebi.ac.uk/pdbsum/6t8k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6t8k ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8A0N4_BACTN Q8A0N4_BACTN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacteroides thetaiotaomicron VPI-5482]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cifuente~~, J O~~]]	+	[[Category: Cifuente JO]]
-	[[Category: Du~~, J J~~]]	+	[[Category: Du JJ]]
-	[[Category: Guerin~~, M E~~]]	+	[[Category: Guerin ME]]
-	[[Category: Klontz~~, E H~~]]	+	[[Category: Klontz EH]]
-	[[Category: Sundberg~~, E J~~]]	+	[[Category: Sundberg EJ]]
-	[[Category: Trastoy, B]]	+	[[Category: Trastoy B]]
-	~~[[Category: Endo-b-n-acetylglucosaminidase]]~~	+
-	~~[[Category: Endobt]]~~	+
-	~~[[Category: Glycoside hydrolase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 09:24, 26 February 2020

OCA — Wed, 26 Feb 2020 09:24:31 GMT

←Older revision		Revision as of 09:24, 26 February 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6t8k is ~~ON HOLD~~	+	==Crystal structure of Bacteroides thetaiotamicron EndoBT-3987 in complex with Man9GlcNAc product in P1==
		+	<StructureSection load='6t8k' size='340' side='right'caption='[[6t8k]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6t8k]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T8K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6T8K FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=6t8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t8k OCA], [http://pdbe.org/6t8k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6t8k RCSB], [http://www.ebi.ac.uk/pdbsum/6t8k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6t8k ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The human gut microbiota plays a central role not only in regulating the metabolism of nutrients but also promoting immune homeostasis, immune responses and protection against pathogen colonization. The genome of the Gram-negative symbiont Bacteroides thetaiotaomicron, a dominant member of the human intestinal microbiota, encodes polysaccharide utilization loci PULs, the apparatus required to orchestrate the degradation of a specific glycan. EndoBT-3987 is a key endo-beta-N-acetylglucosaminidase (ENGase) that initiates the degradation/processing of mammalian high-mannose-type (HM-type) N-glycans in the intestine. Here, we provide structural snapshots of EndoBT-3987, including the unliganded form, the EndoBT-3987-Man9GlcNAc2Asn substrate complex, and two EndoBT-3987-Man9GlcNAc and EndoBT-3987-Man5GlcNAc product complexes. In combination with alanine scanning mutagenesis and activity measurements we unveil the molecular mechanism of HM-type recognition and specificity for EndoBT-3987 and an important group of the GH18 ENGases, including EndoH, an enzyme extensively used in biotechnology, and for which the mechanism of substrate recognition was largely unknown.

-	~~Authors~~:	+	Structural basis of mammalian high-mannose N-glycan processing by human gut Bacteroides.,Trastoy B, Du JJ, Klontz EH, Li C, Cifuente JO, Wang LX, Sundberg EJ, Guerin ME Nat Commun. 2020 Feb 14;11(1):899. doi: 10.1038/s41467-020-14754-7. PMID:32060313<ref>PMID:32060313</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6t8k" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Cifuente, J O]]
		+	[[Category: Du, J J]]
		+	[[Category: Guerin, M E]]
		+	[[Category: Klontz, E H]]
		+	[[Category: Sundberg, E J]]
		+	[[Category: Trastoy, B]]
		+	[[Category: Endo-b-n-acetylglucosaminidase]]
		+	[[Category: Endobt]]
		+	[[Category: Glycoside hydrolase]]
		+	[[Category: Hydrolase]]

OCA: Protected "6t8k" [edit=sysop:move=sysop]

OCA — Wed, 30 Oct 2019 07:33:12 GMT

Protected "6t8k" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:33, 30 October 2019

OCA: New page: '''Unreleased structure''' The entry 6t8k is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 30 Oct 2019 07:33:10 GMT

New page: '''Unreleased structure''' The entry 6t8k is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6t8k is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]