6lja - Revision history

OCA at 10:46, 27 March 2024

2024-03-27T10:46:27Z

←Older revision		Revision as of 10:46, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='6lja' size='340' side='right'caption='[[6lja]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='6lja' size='340' side='right'caption='[[6lja]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6lja]] 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=6LJA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LJA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6lja]] 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=6LJA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LJA 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=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]] 1.978Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=UAP:4-DEOXY-2-O-SULFO-ALPHA-L-THREO-HEX-4-ENOPYRANURONIC+ACID'>UAP</scene>~~</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=PRD_900026:HEPARIN+DISACCHARIDE+I-S,'>PRD_900026</scene>, <scene name='pdbligand=SGN:N,O6-DISULFO-GLUCOSAMINE'>SGN</scene>, <scene name='pdbligand=UAP:4-DEOXY-2-O-SULFO-ALPHA-L-THREO-HEX-4-ENOPYRANURONIC+ACID'>UAP</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=6lja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lja OCA], [https://pdbe.org/6lja PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lja RCSB], [https://www.ebi.ac.uk/pdbsum/6lja PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lja 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=6lja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lja OCA], [https://pdbe.org/6lja PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lja RCSB], [https://www.ebi.ac.uk/pdbsum/6lja PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lja ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/B3C5J6_9BACE B3C5J6_9BACE]
-	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 6lja" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__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: Heparan sulfate]]~~	+
-	~~[[Category: Heparin]]~~	+
-	~~[[Category: Heparinase]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 10:05, 7 July 2021

2021-07-07T10:05:42Z

←Older revision		Revision as of 10:05, 7 July 2021
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	==Crystal Structure of exoHep from Bacteroides intestinalis DSM 17393 complexed with disaccharide product==		==Crystal Structure of exoHep from Bacteroides intestinalis DSM 17393 complexed with disaccharide product==
-	<StructureSection load='6lja' size='340' side='right'caption='[[6lja]]' scene=''>	+	<StructureSection load='6lja' size='340' side='right'caption='[[6lja]], [[Resolution\|resolution]] 1.98Å' 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=6LJA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6LJA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6lja]] 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=6LJA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LJA 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=6lja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lja OCA], [~~http~~://pdbe.org/6lja PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6lja RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6lja PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6lja 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=SGN:N,O6-DISULFO-GLUCOSAMINE'>SGN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UAP:4-DEOXY-2-O-SULFO-ALPHA-L-THREO-HEX-4-ENOPYRANURONIC+ACID'>UAP</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=6lja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lja OCA], [https://pdbe.org/6lja PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lja RCSB], [https://www.ebi.ac.uk/pdbsum/6lja PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lja 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 6lja" 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: Heparan sulfate]]
		+	[[Category: Heparin]]
		+	[[Category: Heparinase]]
		+	[[Category: Lyase]]

OCA at 10:26, 24 December 2020

2020-12-24T10:26:13Z

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

-	~~The entry~~ 6lja is ~~ON HOLD until Paper Publication~~	+	==Crystal Structure of exoHep from Bacteroides intestinalis DSM 17393 complexed with disaccharide product==
-		+	<StructureSection load='6lja' size='340' side='right'caption='[[6lja]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LJA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LJA FirstGlance]. <br>
-	~~Description~~:	+	</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=6lja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lja OCA], [http://pdbe.org/6lja PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lja RCSB], [http://www.ebi.ac.uk/pdbsum/6lja PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lja ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Cao HY]]
		+	[[Category: Li FC]]
		+	[[Category: Wei L]]
		+	[[Category: Zhang QD]]
		+	[[Category: Zhang YZ]]

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

2019-12-25T07:05:16Z

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

←Older revision

Revision as of 07:05, 25 December 2019

OCA: New page: '''Unreleased structure''' The entry 6lja is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2019-12-25T07:05:14Z

New page: '''Unreleased structure''' The entry 6lja is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6lja is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]