6ljl - Revision history

OCA at 11:02, 22 November 2023

OCA — Wed, 22 Nov 2023 11:02:09 GMT

←Older revision		Revision as of 11:02, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='6ljl' size='340' side='right'caption='[[6ljl]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='6ljl' size='340' side='right'caption='[[6ljl]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ljl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bacteroides_intestinalis_341~~ Bacteroides intestinalis ~~341~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LJL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LJL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ljl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_intestinalis_DSM_17393 Bacteroides intestinalis DSM 17393]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LJL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LJL FirstGlance]. <br>
-	</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=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=IDS:2-O-SULFO-ALPHA-L-IDOPYRANURONIC+ACID'>IDS</scene>, <scene name='pdbligand=SGN:N,O6-DISULFO-GLUCOSAMINE'>SGN</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]] 1.73Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BACINT_00178 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=471870 Bacteroides intestinalis 341])</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=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=IDS:2-O-SULFO-ALPHA-L-IDOPYRANURONIC+ACID'>IDS</scene>, <scene name='pdbligand=SGN:N,O6-DISULFO-GLUCOSAMINE'>SGN</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=6ljl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ljl OCA], [https://pdbe.org/6ljl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ljl RCSB], [https://www.ebi.ac.uk/pdbsum/6ljl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ljl 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=6ljl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ljl OCA], [https://pdbe.org/6ljl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ljl RCSB], [https://www.ebi.ac.uk/pdbsum/6ljl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ljl ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B3C5J6_9BACE B3C5J6_9BACE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacteroides intestinalis ~~341~~]]	+	[[Category: Bacteroides intestinalis DSM 17393]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cao~~, H Y~~]]	+	[[Category: Cao HY]]
-	[[Category: Li~~, F C~~]]	+	[[Category: Li FC]]
-	[[Category: Wei, L]]	+	[[Category: Wei L]]
-	[[Category: Zhang~~, Q D~~]]	+	[[Category: Zhang QD]]
-	[[Category: Zhang~~, Y Z]]~~	+	[[Category: Zhang YZ]]
-	~~[[Category: Crystall]]~~	+
-	~~[[Category: Heparan sulfate]]~~	+
-	~~[[Category: Heparin]]~~	+
-	~~[[Category: Heparinase]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 10:05, 7 July 2021

OCA — Wed, 07 Jul 2021 10:05:50 GMT

←Older revision		Revision as of 10:05, 7 July 2021
Line 1:		Line 1:

	==Crystal Structure of exoHep-Y390A/H555A complexed with a tetrasaccharide substrate==		==Crystal Structure of exoHep-Y390A/H555A complexed with a tetrasaccharide substrate==
-	<StructureSection load='6ljl' size='340' side='right'caption='[[6ljl]]' scene=''>	+	<StructureSection load='6ljl' size='340' side='right'caption='[[6ljl]], [[Resolution\|resolution]] 1.73Å' 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=6LJL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6LJL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ljl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_intestinalis_341 Bacteroides intestinalis 341]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LJL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LJL FirstGlance]. <br>
-	</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=6ljl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ljl OCA], [~~http~~://pdbe.org/6ljl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ljl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ljl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ljl 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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=IDS:2-O-SULFO-ALPHA-L-IDOPYRANURONIC+ACID'>IDS</scene>, <scene name='pdbligand=SGN:N,O6-DISULFO-GLUCOSAMINE'>SGN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BACINT_00178 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=471870 Bacteroides intestinalis 341])</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=6ljl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ljl OCA], [https://pdbe.org/6ljl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ljl RCSB], [https://www.ebi.ac.uk/pdbsum/6ljl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ljl ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Heparinases (Hepases) are critical tools for the studies of highly heterogeneous heparin (HP)/heparan sulfate (HS). However, exolytic heparinases urgently needed for the sequencing of HP/HS chains remain undiscovered. Herein, a type of exolytic heparinases (exoHepases) is identified from the genomes of different bacteria. These exoHepases share almost no homology with known Hepases and prefer to digest HP rather than HS chains by sequentially releasing unsaturated disaccharides from their reducing ends. The structural study of an exoHepase (BIexoHep) shows that an N-terminal conserved DUF4962 superfamily domain is essential to the enzyme activities of these exoHepases, which is involved in the formation of a unique L-shaped catalytic cavity controlling the sequential digestion of substrates through electrostatic interactions. Further, several HP octasaccharides have been preliminarily sequenced by using BIexoHep. Overall, this study fills the research gap of exoHepases and provides urgently needed tools for the structural and functional studies of HP/HS chains.
		+
		+	Discovery of exolytic heparinases and their catalytic mechanism and potential application.,Zhang Q, Cao HY, Wei L, Lu D, Du M, Yuan M, Shi D, Chen X, Wang P, Chen XL, Chi L, Zhang YZ, Li F Nat Commun. 2021 Feb 24;12(1):1263. doi: 10.1038/s41467-021-21441-8. PMID:33627653<ref>PMID:33627653</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ljl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacteroides intestinalis 341]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cao HY]]	+	[[Category: Cao, H Y]]
-	[[Category: Li FC]]	+	[[Category: Li, F C]]
-	[[Category: Wei L]]	+	[[Category: Wei, L]]
-	[[Category: Zhang QD]]	+	[[Category: Zhang, Q D]]
-	[[Category: Zhang YZ]]	+	[[Category: Zhang, Y Z]]
		+	[[Category: Crystall]]
		+	[[Category: Heparan sulfate]]
		+	[[Category: Heparin]]
		+	[[Category: Heparinase]]
		+	[[Category: Lyase]]

OCA at 10:26, 24 December 2020

OCA — Thu, 24 Dec 2020 10:26:14 GMT

←Older revision		Revision as of 10:26, 24 December 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ljl ~~is ON HOLD until Paper Publication~~	+	==Crystal Structure of exoHep-Y390A/H555A complexed with a tetrasaccharide substrate==
-		+	<StructureSection load='6ljl' size='340' side='right'caption='[[6ljl]]' scene=''>
-	~~Authors~~: ~~Zhang, Q~~.D., ~~Cao, H~~.Y., ~~Wei~~, L., ~~Li, F~~.C., ~~Zhang, Y~~.Z.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LJL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LJL FirstGlance]. <br>
-	~~Description: Crystal Structure of exoHep-Y390A~~/~~H555A complexed with a tetrasaccharide substrate~~	+	</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=6ljl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ljl OCA], [http://pdbe.org/6ljl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ljl RCSB], [http://www.ebi.ac.uk/pdbsum/6ljl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ljl ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Li, F.C~~]]	+	__TOC__
-	[[Category: ~~Cao, H.Y~~]]	+	</StructureSection>
-	[[Category: ~~Zhang, Y.Z~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Wei, L~~]]	+	[[Category: Cao HY]]
-	[[Category: Zhang~~, Q.D~~]]	+	[[Category: Li FC]]
		+	[[Category: Wei L]]
		+	[[Category: Zhang QD]]
		+	[[Category: Zhang YZ]]

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

OCA — Wed, 25 Dec 2019 07:06:15 GMT

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

←Older revision

Revision as of 07:06, 25 December 2019

OCA: New page: '''Unreleased structure''' The entry 6ljl is ON HOLD until Paper Publication Authors: Zhang, Q.D., Cao, H.Y., Wei, L., Li, F.C., Zhang, Y.Z. Description: Crystal Structure of exoHep-Y3...

OCA — Wed, 25 Dec 2019 07:06:13 GMT

New page: '''Unreleased structure''' The entry 6ljl is ON HOLD until Paper Publication Authors: Zhang, Q.D., Cao, H.Y., Wei, L., Li, F.C., Zhang, Y.Z. Description: Crystal Structure of exoHep-Y3...

New page

'''Unreleased structure'''

The entry 6ljl is ON HOLD until Paper Publication

Authors: Zhang, Q.D., Cao, H.Y., Wei, L., Li, F.C., Zhang, Y.Z.

Description: Crystal Structure of exoHep-Y390A/H555A complexed with a tetrasaccharide substrate
[[Category: Unreleased Structures]]
[[Category: Li, F.C]]
[[Category: Cao, H.Y]]
[[Category: Zhang, Y.Z]]
[[Category: Wei, L]]
[[Category: Zhang, Q.D]]