7nwf - Revision history

OCA at 12:40, 1 February 2024

OCA — Thu, 01 Feb 2024 12:40:38 GMT

←Older revision		Revision as of 12:40, 1 February 2024
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	<StructureSection load='7nwf' size='340' side='right'caption='[[7nwf]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='7nwf' size='340' side='right'caption='[[7nwf]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7nwf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bactn Bactn~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NWF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NWF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7nwf]] 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=7NWF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NWF FirstGlance]. <br>
-	</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=~~GOL~~:~~GLYCEROL~~'>~~GOL~~</scene>, <scene name='pdbligand=~~GAL~~:~~BETA-D-GALACTOSE~~'>~~GAL~~</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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BT_3987 ([https://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=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=7nwf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nwf OCA], [https://pdbe.org/7nwf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nwf RCSB], [https://www.ebi.ac.uk/pdbsum/7nwf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nwf 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=7nwf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nwf OCA], [https://pdbe.org/7nwf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nwf RCSB], [https://www.ebi.ac.uk/pdbsum/7nwf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nwf 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: ~~Bactn~~]]	+	[[Category: Bacteroides thetaiotaomicron VPI-5482]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Du~~, J J~~]]	+	[[Category: Du JJ]]
-	[[Category: Garcia-Alija, M]]	+	[[Category: Garcia-Alija M]]
-	[[Category: Guerin~~, M E~~]]	+	[[Category: Guerin ME]]
-	[[Category: Sundberg~~, E J~~]]	+	[[Category: Sundberg EJ]]
-	[[Category: Trastoy, B]]	+	[[Category: Trastoy B]]
-	~~[[Category: Bt3987]]~~	+
-	~~[[Category: Endo-b-n-acetylglucosaminidase]]~~	+
-	~~[[Category: Endobt-3987]]~~	+
-	~~[[Category: Glycoside hydrolase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:03, 22 September 2021

OCA — Wed, 22 Sep 2021 07:03:03 GMT

←Older revision		Revision as of 07:03, 22 September 2021
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	==Crystal structure of Bacteroides thetaiotamicron EndoBT-3987 in complex with hybrid-type glycan (GalGlcNAcMan5GlcNAc) product==		==Crystal structure of Bacteroides thetaiotamicron EndoBT-3987 in complex with hybrid-type glycan (GalGlcNAcMan5GlcNAc) product==
-	<StructureSection load='7nwf' size='340' side='right'caption='[[7nwf]]' scene=''>	+	<StructureSection load='7nwf' size='340' side='right'caption='[[7nwf]], [[Resolution\|resolution]] 2.00Å' 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=7NWF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NWF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7nwf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bactn Bactn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NWF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NWF 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=7nwf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nwf OCA], [https://pdbe.org/7nwf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nwf RCSB], [https://www.ebi.ac.uk/pdbsum/7nwf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nwf 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=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BT_3987 ([https://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'>[https://proteopedia.org/fgij/fg.htm?mol=7nwf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nwf OCA], [https://pdbe.org/7nwf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nwf RCSB], [https://www.ebi.ac.uk/pdbsum/7nwf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nwf ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	N-glycosylation is one of the most abundant posttranslational modifications of proteins, essential for many physiological processes, including protein folding, protein stability, oligomerization and aggregation, and molecular recognition events. Defects in the N-glycosylation pathway cause diseases that are classified as congenital disorders of glycosylation. The ability to manipulate protein N-glycosylation is critical not only to our fundamental understanding of biology but also for the development of new drugs for a wide range of human diseases. Chemoenzymatic synthesis using engineered endo-beta-N-acetylglucosaminidases (ENGases) has been used extensively to modulate the chemistry of N-glycosylated proteins. However, defining the molecular mechanisms by which ENGases specifically recognize and process N-glycans remains a major challenge. Here we present the X-ray crystal structure of the ENGase EndoBT-3987 from Bacteroides thetaiotaomicron in complex with a hybrid-type glycan product. In combination with alanine scanning mutagenesis, molecular docking calculations and enzymatic activity measurements conducted on a chemically engineered monoclonal antibody substrate unveil two mechanisms for hybrid-type recognition and processing by paradigmatic ENGases. Altogether, the experimental data provide pivotal insight into the molecular mechanism of substrate recognition and specificity for GH18 ENGases and further advance our understanding of chemoenzymatic synthesis and remodeling of homogeneous N-glycan glycoproteins.
		+
		+	GH18 endo-beta-N-acetylglucosaminidases use distinct mechanisms to process hybrid-type N-linked glycans.,Trastoy B, Du JJ, Li C, Garcia-Alija M, Klontz EH, Roberts BR, Donahue TC, Wang LX, Sundberg EJ, Guerin ME J Biol Chem. 2021 Aug;297(2):101011. doi: 10.1016/j.jbc.2021.101011. Epub 2021, Jul 26. PMID:34324829<ref>PMID:34324829</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7nwf" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bactn]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Du JJ]]	+	[[Category: Du, J J]]
-	[[Category: Garcia-Alija M]]	+	[[Category: Garcia-Alija, M]]
-	[[Category: Guerin ME]]	+	[[Category: Guerin, M E]]
-	[[Category: Sundberg EJ]]	+	[[Category: Sundberg, E J]]
-	[[Category: Trastoy B]]	+	[[Category: Trastoy, B]]
		+	[[Category: Bt3987]]
		+	[[Category: Endo-b-n-acetylglucosaminidase]]
		+	[[Category: Endobt-3987]]
		+	[[Category: Glycoside hydrolase]]
		+	[[Category: Hydrolase]]

OCA at 10:20, 4 August 2021

OCA — Wed, 04 Aug 2021 10:20:51 GMT

←Older revision		Revision as of 10:20, 4 August 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7nwf is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of Bacteroides thetaiotamicron EndoBT-3987 in complex with hybrid-type glycan (GalGlcNAcMan5GlcNAc) product==
-		+	<StructureSection load='7nwf' size='340' side='right'caption='[[7nwf]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NWF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NWF FirstGlance]. <br>
-	~~Description~~:	+	</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=7nwf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nwf OCA], [https://pdbe.org/7nwf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nwf RCSB], [https://www.ebi.ac.uk/pdbsum/7nwf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nwf ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Du JJ]]
		+	[[Category: Garcia-Alija M]]
		+	[[Category: Guerin ME]]
		+	[[Category: Sundberg EJ]]
		+	[[Category: Trastoy B]]

OCA at 05:47, 14 April 2021

OCA — Wed, 14 Apr 2021 05:47:17 GMT

←Older revision		Revision as of 05:47, 14 April 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 24 Mar 2021 05:41:30 GMT

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

←Older revision

Revision as of 05:41, 24 March 2021

OCA: New page: '''Unreleased structure''' The entry 7nwf is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 24 Mar 2021 05:41:29 GMT

New page: '''Unreleased structure''' The entry 7nwf is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7nwf is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]