5w8n - Revision history

OCA at 14:14, 13 March 2024

OCA — Wed, 13 Mar 2024 14:14:43 GMT

←Older revision		Revision as of 14:14, 13 March 2024
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	<StructureSection load='5w8n' size='340' side='right'caption='[[5w8n]], [[Resolution\|resolution]] 2.02Å' scene=''>		<StructureSection load='5w8n' size='340' side='right'caption='[[5w8n]], [[Resolution\|resolution]] 2.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w8n]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecobd Ecobd~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W8N OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5W8N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w8n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5W8N FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5w8s\|5w8s]], [[5w8x\|5w8x]]</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]] 2.02Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">lpxB, ECBD_3437 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=469008 ECOBD])</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=5w8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w8n OCA], [https://pdbe.org/5w8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5w8n RCSB], [https://www.ebi.ac.uk/pdbsum/5w8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5w8n ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lipid-A-disaccharide_synthase Lipid-A-disaccharide synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.182 2.4.1.182] </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=5w8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w8n OCA], [~~http~~://pdbe.org/5w8n PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5w8n RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5w8n PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5w8n ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~A0A140NAT1_ECOBD A0A140NAT1_ECOBD]~~] Condensation of UDP-2,3-diacylglucosamine and 2,3-diacylglucosamine-1-phosphate to form lipid A disaccharide, a precursor of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell.~~[HAMAP-Rule:MF_00392][SAAS:SAAS00702254]~~	+	[https://www.uniprot.org/uniprot/LPXB_ECOLI LPXB_ECOLI] Condensation of UDP-2,3-diacylglucosamine and 2,3-diacylglucosamine-1-phosphate to form lipid A disaccharide, a precursor of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Most Gram-negative bacteria are surrounded by a glycolipid called lipopolysaccharide (LPS), which forms a barrier to hydrophobic toxins and, in pathogenic bacteria, is a virulence factor. During LPS biosynthesis, a membrane-associated glycosyltransferase (LpxB) forms a tetra-acylated disaccharide that is further acylated to form the membrane anchor moiety of LPS. Here we solve the structure of a soluble and catalytically competent LpxB by X-ray crystallography. The structure reveals that LpxB has a glycosyltransferase-B family fold but with a highly intertwined, C-terminally swapped dimer comprising four domains. We identify key catalytic residues with a product, UDP, bound in the active site, as well as clusters of hydrophobic residues that likely mediate productive membrane association or capture of lipidic substrates. These studies provide the basis for rational design of antibiotics targeting a crucial step in LPS biosynthesis.	+
-		+
-	Crystal structure of lipid A disaccharide synthase LpxB from Escherichia coli.,Bohl TE, Shi K, Lee JK, Aihara H Nat Commun. 2018 Jan 25;9(1):377. doi: 10.1038/s41467-017-02712-9. PMID:29371662<ref>PMID:29371662</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5w8n" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Ecobd]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Lipid-A-disaccharide synthase]]~~	+	[[Category: Aihara H]]
-	[[Category: Aihara, H]]	+	[[Category: Bohl TE]]
-	[[Category: Bohl~~, T E~~]]	+	[[Category: Lee JK]]
-	[[Category: Lee~~, J K~~]]	+	[[Category: Shi K]]
-	[[Category: Shi, K]]	+
-	~~[[Category: C-terminal swap]]~~	+
-	~~[[Category: Dimer]]~~	+
-	~~[[Category: Glycosyltransferase b]]~~	+
-	~~[[Category: Lipid a disaccharide synthase]]~~	+
-	~~[[Category: Lipid a synthesis pathway]]~~	+
-	~~[[Category: Lipiopolysaccharide synthesis]]~~	+
-	~~[[Category: Raetz pathway]]~~	+
-	~~[[Category: Rossmann-like]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:47, 1 January 2020

OCA — Wed, 01 Jan 2020 09:47:19 GMT

←Older revision		Revision as of 09:47, 1 January 2020
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	==Lipid A Disaccharide Synthase (LpxB)-6 solubilizing mutations==		==Lipid A Disaccharide Synthase (LpxB)-6 solubilizing mutations==
-	<StructureSection load='5w8n' size='340' side='right' caption='[[5w8n]], [[Resolution\|resolution]] 2.02Å' scene=''>	+	<StructureSection load='5w8n' size='340' side='right'caption='[[5w8n]], [[Resolution\|resolution]] 2.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5w8n]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecobd Ecobd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W8N FirstGlance]. <br>		<table><tr><td colspan='2'>[[5w8n]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecobd Ecobd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W8N FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Ecobd]]		[[Category: Ecobd]]
		+	[[Category: Large Structures]]
	[[Category: Lipid-A-disaccharide synthase]]		[[Category: Lipid-A-disaccharide synthase]]
	[[Category: Aihara, H]]		[[Category: Aihara, H]]

OCA at 06:44, 7 February 2018

OCA — Wed, 07 Feb 2018 06:44:11 GMT

←Older revision		Revision as of 06:44, 7 February 2018
Line 3:		Line 3:
	<StructureSection load='5w8n' size='340' side='right' caption='[[5w8n]], [[Resolution\|resolution]] 2.02Å' scene=''>		<StructureSection load='5w8n' size='340' side='right' caption='[[5w8n]], [[Resolution\|resolution]] 2.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w8n]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W8N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w8n]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecobd Ecobd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W8N FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5w8s\|5w8s]], [[5w8x\|5w8x]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5w8s\|5w8s]], [[5w8x\|5w8x]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lpxB, ECBD_3437 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=469008 ECOBD])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lipid-A-disaccharide_synthase Lipid-A-disaccharide synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.182 2.4.1.182] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lipid-A-disaccharide_synthase Lipid-A-disaccharide synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.182 2.4.1.182] </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=5w8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w8n OCA], [http://pdbe.org/5w8n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w8n RCSB], [http://www.ebi.ac.uk/pdbsum/5w8n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w8n 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=5w8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w8n OCA], [http://pdbe.org/5w8n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w8n RCSB], [http://www.ebi.ac.uk/pdbsum/5w8n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w8n ProSAT]</span></td></tr>
Line 10:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/A0A140NAT1_ECOBD A0A140NAT1_ECOBD]] Condensation of UDP-2,3-diacylglucosamine and 2,3-diacylglucosamine-1-phosphate to form lipid A disaccharide, a precursor of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell.[HAMAP-Rule:MF_00392][SAAS:SAAS00702254]		[[http://www.uniprot.org/uniprot/A0A140NAT1_ECOBD A0A140NAT1_ECOBD]] Condensation of UDP-2,3-diacylglucosamine and 2,3-diacylglucosamine-1-phosphate to form lipid A disaccharide, a precursor of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell.[HAMAP-Rule:MF_00392][SAAS:SAAS00702254]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Most Gram-negative bacteria are surrounded by a glycolipid called lipopolysaccharide (LPS), which forms a barrier to hydrophobic toxins and, in pathogenic bacteria, is a virulence factor. During LPS biosynthesis, a membrane-associated glycosyltransferase (LpxB) forms a tetra-acylated disaccharide that is further acylated to form the membrane anchor moiety of LPS. Here we solve the structure of a soluble and catalytically competent LpxB by X-ray crystallography. The structure reveals that LpxB has a glycosyltransferase-B family fold but with a highly intertwined, C-terminally swapped dimer comprising four domains. We identify key catalytic residues with a product, UDP, bound in the active site, as well as clusters of hydrophobic residues that likely mediate productive membrane association or capture of lipidic substrates. These studies provide the basis for rational design of antibiotics targeting a crucial step in LPS biosynthesis.
		+
		+	Crystal structure of lipid A disaccharide synthase LpxB from Escherichia coli.,Bohl TE, Shi K, Lee JK, Aihara H Nat Commun. 2018 Jan 25;9(1):377. doi: 10.1038/s41467-017-02712-9. PMID:29371662<ref>PMID:29371662</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5w8n" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecobd]]
	[[Category: Lipid-A-disaccharide synthase]]		[[Category: Lipid-A-disaccharide synthase]]
	[[Category: Aihara, H]]		[[Category: Aihara, H]]

OCA at 05:52, 31 January 2018

OCA — Wed, 31 Jan 2018 05:52:18 GMT

←Older revision		Revision as of 05:52, 31 January 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5w8n is ~~ON HOLD until Paper Publication~~	+	==Lipid A Disaccharide Synthase (LpxB)-6 solubilizing mutations==
-		+	<StructureSection load='5w8n' size='340' side='right' caption='[[5w8n]], [[Resolution\|resolution]] 2.02Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5w8n]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W8N FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5w8s\|5w8s]], [[5w8x\|5w8x]]</td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lipid-A-disaccharide_synthase Lipid-A-disaccharide synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.182 2.4.1.182] </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=5w8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w8n OCA], [http://pdbe.org/5w8n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w8n RCSB], [http://www.ebi.ac.uk/pdbsum/5w8n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w8n ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0A140NAT1_ECOBD A0A140NAT1_ECOBD]] Condensation of UDP-2,3-diacylglucosamine and 2,3-diacylglucosamine-1-phosphate to form lipid A disaccharide, a precursor of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell.[HAMAP-Rule:MF_00392][SAAS:SAAS00702254]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Lipid-A-disaccharide synthase]]
		+	[[Category: Aihara, H]]
		+	[[Category: Bohl, T E]]
		+	[[Category: Lee, J K]]
		+	[[Category: Shi, K]]
		+	[[Category: C-terminal swap]]
		+	[[Category: Dimer]]
		+	[[Category: Glycosyltransferase b]]
		+	[[Category: Lipid a disaccharide synthase]]
		+	[[Category: Lipid a synthesis pathway]]
		+	[[Category: Lipiopolysaccharide synthesis]]
		+	[[Category: Raetz pathway]]
		+	[[Category: Rossmann-like]]
		+	[[Category: Transferase]]

OCA: Protected "5w8n" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 14:34:40 GMT

Protected "5w8n" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:34, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5w8n is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 14:34:38 GMT

New page: '''Unreleased structure''' The entry 5w8n is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5w8n is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]