6ebu - Revision history

OCA at 14:40, 13 March 2024

OCA — Wed, 13 Mar 2024 14:40:34 GMT

←Older revision		Revision as of 14:40, 13 March 2024
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	<StructureSection load='6ebu' size='340' side='right'caption='[[6ebu]], [[Resolution\|resolution]] 2.37Å' scene=''>		<StructureSection load='6ebu' size='340' side='right'caption='[[6ebu]], [[Resolution\|resolution]] 2.37Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ebu]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Aquae Aquae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EBU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6EBU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ebu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus_VF5 Aquifex aeolicus VF5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EBU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6EBU FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BOG:B~~-~~OCTYLGLUCOSIDE'>BOG</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.372Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~aq_1706 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=224324 AQUAE])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=6ebu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ebu OCA], [~~http~~://pdbe.org/6ebu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ebu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ebu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ebu 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=6ebu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ebu OCA], [https://pdbe.org/6ebu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ebu RCSB], [https://www.ebi.ac.uk/pdbsum/6ebu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ebu ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/O67603_AQUAE O67603_AQUAE]
-	Although distinct lipid phosphatases are thought to be required for processing lipid A (component of the outer leaflet of the outer membrane), glycerophospholipid (component of the inner membrane and the inner leaflet of the outer membrane), and undecaprenyl pyrophosphate (C55-PP; precursors of peptidoglycan and O antigens of lipopolysaccharide) in Gram-negative bacteria, we report that the lipid A 1-phosphatases, LpxEs, functionally connect multiple layers of cell envelope biogenesis in Gram-negative bacteria. We found that Aquifex aeolicus LpxE structurally resembles YodM in Bacillus subtilis, a phosphatase for phosphatidylglycerol phosphate (PGP) with a weak in vitro activity on C55-PP, and rescues Escherichia coli deficient in PGP and C55-PP phosphatase activities; deletion of lpxE in Francisella novicida reduces the MIC value of bacitracin, indicating a significant contribution of LpxE to the native bacterial C55-PP phosphatase activity. Suppression of plasmid-borne lpxE in F. novicida deficient in chromosomally encoded C55-PP phosphatase activities results in cell enlargement, loss of O-antigen repeats of lipopolysaccharide, and ultimately cell death. These discoveries implicate LpxE as the first example of a multifunctional regulatory enzyme that orchestrates lipid A modification, O-antigen production, and peptidoglycan biogenesis to remodel multiple layers of the Gram-negative bacterial envelope.IMPORTANCE Dephosphorylation of the lipid A 1-phosphate by LpxE in Gram-negative bacteria plays important roles in antibiotic resistance, bacterial virulence, and modulation of the host immune system. Our results demonstrate that in addition to removing the 1-phosphate from lipid A, LpxEs also dephosphorylate undecaprenyl pyrophosphate, an important metabolite for the synthesis of the essential envelope components, peptidoglycan and O-antigen. Therefore, LpxEs participate in multiple layers of biogenesis of the Gram-negative bacterial envelope and increase antibiotic resistance. This discovery marks an important step toward understanding the regulation and biogenesis of the Gram-negative bacterial envelope.	+
-		+
-	The Lipid A 1-Phosphatase, LpxE, Functionally Connects Multiple Layers of Bacterial Envelope Biogenesis.,Zhao J, An J, Hwang D, Wu Q, Wang S, Gillespie RA, Yang EG, Guan Z, Zhou P, Chung HS MBio. 2019 Jun 18;10(3). pii: ~~mBio.00886-19. doi: 10.1128~~/~~mBio.00886-19. PMID:31213552<ref>PMID:31213552<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6ebu" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aquae~~]]	+	[[Category: Aquifex aeolicus VF5]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Wang, S]]	+	[[Category: Wang S]]
-	[[Category: Wu, Q]]	+	[[Category: Wu Q]]
-	[[Category: Zhou, P]]	+	[[Category: Zhou P]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Lipid a 1-phosphatase]]~~	+
-	~~[[Category: Lpxe]]~~	+
-	~~[[Category: Uppp~~]]	+

OCA at 06:56, 29 April 2020

OCA — Wed, 29 Apr 2020 06:56:12 GMT

←Older revision		Revision as of 06:56, 29 April 2020
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	<StructureSection load='6ebu' size='340' side='right'caption='[[6ebu]], [[Resolution\|resolution]] 2.37Å' scene=''>		<StructureSection load='6ebu' size='340' side='right'caption='[[6ebu]], [[Resolution\|resolution]] 2.37Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ebu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquae Aquae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EBU OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6EBU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ebu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquae Aquae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EBU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6EBU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aq_1706 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aq_1706 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</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=6ebu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ebu OCA], [http://pdbe.org/6ebu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ebu RCSB], [http://www.ebi.ac.uk/pdbsum/6ebu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ebu ProSAT]</span></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=6ebu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ebu OCA], [http://pdbe.org/6ebu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ebu RCSB], [http://www.ebi.ac.uk/pdbsum/6ebu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ebu ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 25:		Line 25:
	[[Category: Wang, S]]		[[Category: Wang, S]]
	[[Category: Wu, Q]]		[[Category: Wu, Q]]
		+	[[Category: Zhou, P]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Lipid a 1-phosphatase]]		[[Category: Lipid a 1-phosphatase]]
	[[Category: Lpxe]]		[[Category: Lpxe]]
	[[Category: Uppp]]		[[Category: Uppp]]

OCA at 11:13, 1 January 2020

OCA — Wed, 01 Jan 2020 11:13:22 GMT

←Older revision		Revision as of 11:13, 1 January 2020
Line 3:		Line 3:
	<StructureSection load='6ebu' size='340' side='right'caption='[[6ebu]], [[Resolution\|resolution]] 2.37Å' scene=''>		<StructureSection load='6ebu' size='340' side='right'caption='[[6ebu]], [[Resolution\|resolution]] 2.37Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ebu]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EBU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EBU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ebu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquae Aquae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EBU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EBU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aq_1706 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</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=6ebu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ebu OCA], [http://pdbe.org/6ebu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ebu RCSB], [http://www.ebi.ac.uk/pdbsum/6ebu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ebu 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=6ebu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ebu OCA], [http://pdbe.org/6ebu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ebu RCSB], [http://www.ebi.ac.uk/pdbsum/6ebu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ebu ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aquae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Wang, S]]		[[Category: Wang, S]]

OCA at 06:45, 3 July 2019

OCA — Wed, 03 Jul 2019 06:45:15 GMT

←Older revision		Revision as of 06:45, 3 July 2019
Line 7:		Line 7:
	<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=6ebu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ebu OCA], [http://pdbe.org/6ebu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ebu RCSB], [http://www.ebi.ac.uk/pdbsum/6ebu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ebu 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=6ebu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ebu OCA], [http://pdbe.org/6ebu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ebu RCSB], [http://www.ebi.ac.uk/pdbsum/6ebu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ebu ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Although distinct lipid phosphatases are thought to be required for processing lipid A (component of the outer leaflet of the outer membrane), glycerophospholipid (component of the inner membrane and the inner leaflet of the outer membrane), and undecaprenyl pyrophosphate (C55-PP; precursors of peptidoglycan and O antigens of lipopolysaccharide) in Gram-negative bacteria, we report that the lipid A 1-phosphatases, LpxEs, functionally connect multiple layers of cell envelope biogenesis in Gram-negative bacteria. We found that Aquifex aeolicus LpxE structurally resembles YodM in Bacillus subtilis, a phosphatase for phosphatidylglycerol phosphate (PGP) with a weak in vitro activity on C55-PP, and rescues Escherichia coli deficient in PGP and C55-PP phosphatase activities; deletion of lpxE in Francisella novicida reduces the MIC value of bacitracin, indicating a significant contribution of LpxE to the native bacterial C55-PP phosphatase activity. Suppression of plasmid-borne lpxE in F. novicida deficient in chromosomally encoded C55-PP phosphatase activities results in cell enlargement, loss of O-antigen repeats of lipopolysaccharide, and ultimately cell death. These discoveries implicate LpxE as the first example of a multifunctional regulatory enzyme that orchestrates lipid A modification, O-antigen production, and peptidoglycan biogenesis to remodel multiple layers of the Gram-negative bacterial envelope.IMPORTANCE Dephosphorylation of the lipid A 1-phosphate by LpxE in Gram-negative bacteria plays important roles in antibiotic resistance, bacterial virulence, and modulation of the host immune system. Our results demonstrate that in addition to removing the 1-phosphate from lipid A, LpxEs also dephosphorylate undecaprenyl pyrophosphate, an important metabolite for the synthesis of the essential envelope components, peptidoglycan and O-antigen. Therefore, LpxEs participate in multiple layers of biogenesis of the Gram-negative bacterial envelope and increase antibiotic resistance. This discovery marks an important step toward understanding the regulation and biogenesis of the Gram-negative bacterial envelope.
		+
		+	The Lipid A 1-Phosphatase, LpxE, Functionally Connects Multiple Layers of Bacterial Envelope Biogenesis.,Zhao J, An J, Hwang D, Wu Q, Wang S, Gillespie RA, Yang EG, Guan Z, Zhou P, Chung HS MBio. 2019 Jun 18;10(3). pii: mBio.00886-19. doi: 10.1128/mBio.00886-19. PMID:31213552<ref>PMID:31213552</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ebu" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:44, 26 June 2019

OCA — Wed, 26 Jun 2019 06:44:44 GMT

←Older revision		Revision as of 06:44, 26 June 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ebu is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of Aquifex aeolicus LpxE==
-		+	<StructureSection load='6ebu' size='340' side='right'caption='[[6ebu]], [[Resolution\|resolution]] 2.37Å' scene=''>
-	~~Authors~~: Wu, Q., ~~Wang~~, S.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6ebu]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EBU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EBU FirstGlance]. <br>
-	~~Description: Crystal structure of Aquifex aeolicus LpxE~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6ebu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ebu OCA], [http://pdbe.org/6ebu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ebu RCSB], [http://www.ebi.ac.uk/pdbsum/6ebu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ebu ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Wang, S]]
	[[Category: Wu, Q]]		[[Category: Wu, Q]]
-	[[Category: ~~Wang, S~~]]	+	[[Category: Hydrolase]]
		+	[[Category: Lipid a 1-phosphatase]]
		+	[[Category: Lpxe]]
		+	[[Category: Uppp]]

OCA at 04:42, 22 August 2018

OCA — Wed, 22 Aug 2018 04:42:07 GMT

←Older revision		Revision as of 04:42, 22 August 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6ebu is ON HOLD	+	The entry 6ebu is ON HOLD until Paper Publication

	Authors: Wu, Q., Wang, S.		Authors: Wu, Q., Wang, S.

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

OCA — Wed, 15 Aug 2018 14:51:20 GMT

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

←Older revision

Revision as of 14:51, 15 August 2018

OCA: New page: '''Unreleased structure''' The entry 6ebu is ON HOLD Authors: Wu, Q., Wang, S. Description: Crystal structure of Aquifex aeolicus LpxE Category: Unreleased Structures [[Category: W...

OCA — Wed, 15 Aug 2018 14:51:18 GMT

New page: '''Unreleased structure''' The entry 6ebu is ON HOLD Authors: Wu, Q., Wang, S. Description: Crystal structure of Aquifex aeolicus LpxE Category: Unreleased Structures [[Category: W...

New page

'''Unreleased structure'''

The entry 6ebu is ON HOLD

Authors: Wu, Q., Wang, S.

Description: Crystal structure of Aquifex aeolicus LpxE
[[Category: Unreleased Structures]]
[[Category: Wu, Q]]
[[Category: Wang, S]]