5xj9 - Revision history

OCA at 10:18, 27 March 2024

2024-03-27T10:18:50Z

←Older revision		Revision as of 10:18, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5xj9' size='340' side='right'caption='[[5xj9]], [[Resolution\|resolution]] 1.83Å' scene=''>		<StructureSection load='5xj9' size='340' side='right'caption='[[5xj9]], [[Resolution\|resolution]] 1.83Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xj9]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XJ9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5XJ9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xj9]] 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=5XJ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XJ9 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=78M:(2S)~~-2,~~3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE'>78M</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.83Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~FME~~:N-~~FORMYLMETHIONINE~~'>~~FME~~</scene><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=78M:(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE'>78M</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<~~tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[5xj5\|5xj5]], [[5xj6\|5xj6]], [[5xj7\|5xj7]], [[5xj8\|5xj8]]~~</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=5xj9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xj9 OCA], [https://pdbe.org/5xj9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xj9 RCSB], [https://www.ebi.ac.uk/pdbsum/5xj9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xj9 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=5xj9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xj9 OCA], [~~http~~://pdbe.org/5xj9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xj9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xj9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xj9 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PLSY_AQUAE PLSY_AQUAE]] Catalyzes the transfer of an acyl group from acyl-phosphate (acyl-PO(4)) to glycerol-3-phosphate (G3P) to form lysophosphatidic acid (LPA). This enzyme utilizes acyl-phosphate as fatty acyl donor, but not acyl-CoA or acyl-ACP.	+	[https://www.uniprot.org/uniprot/PLSY_AQUAE PLSY_AQUAE] Catalyzes the transfer of an acyl group from acyl-phosphate (acyl-PO(4)) to glycerol-3-phosphate (G3P) to form lysophosphatidic acid (LPA). This enzyme utilizes acyl-phosphate as fatty acyl donor, but not acyl-CoA or acyl-ACP.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The membrane-integral glycerol 3-phosphate (G3P) acyltransferase PlsY catalyses the committed and essential step in bacterial phospholipid biosynthesis by acylation of G3P, forming lysophosphatidic acid. It contains no known acyltransferase motifs, lacks eukaryotic homologs, and uses the unusual acyl-phosphate as acyl donor, as opposed to acyl-CoA or acyl-carrier protein for other acyltransferases. Previous studies have identified several PlsY inhibitors as potential antimicrobials. Here we determine the crystal structure of PlsY at 1.48 A resolution, revealing a seven-transmembrane helix fold. Four additional substrate- and product-bound structures uncover the atomic details of its relatively inflexible active site. Structure and mutagenesis suggest a different acylation mechanism of 'substrate-assisted catalysis' that, unlike other acyltransferases, does not require a proteinaceous catalytic base to complete. The structure data and a high-throughput enzymatic assay developed in this work should prove useful for virtual and experimental screening of inhibitors against this vital bacterial enzyme.	+
-		+
-	Structural insights into the committed step of bacterial phospholipid biosynthesis.,Li Z, Tang Y, Wu Y, Zhao S, Bao J, Luo Y, Li D Nat Commun. 2017 Nov 22;8(1):1691. doi: 10.1038/s41467-017-01821-9. PMID:29167463<ref>PMID:29167463</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5xj9" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aquifex aeolicus VF5]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Li, D]]	+	[[Category: Li D]]
-	[[Category: Li, Z]]	+	[[Category: Li Z]]
-	[[Category: Tang, Y]]	+	[[Category: Tang Y]]
-	~~[[Category: Glycerylphosphate acyltransferase]]~~	+
-	~~[[Category: Gpat]]~~	+
-	~~[[Category: In meso]]~~	+
-	~~[[Category: Lipid cubic phase]]~~	+
-	~~[[Category: Lipid metabolism]]~~	+
-	~~[[Category: Lipidic cubic phase]]~~	+
-	~~[[Category: Monoacylglycerol]]~~	+
-	~~[[Category: Phosphate]]~~	+
-	~~[[Category: Phospholipid biosynthesis]]~~	+
-	~~[[Category: Plsy]]~~	+
-	~~[[Category: Product]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Ygih~~]]	+

OCA at 06:51, 14 October 2020

2020-10-14T06:51:36Z

←Older revision		Revision as of 06:51, 14 October 2020
Line 1:		Line 1:

	==Crystal structure of PlsY (YgiH), an integral membrane glycerol 3-phosphate acyltransferase - the orthophosphate form==		==Crystal structure of PlsY (YgiH), an integral membrane glycerol 3-phosphate acyltransferase - the orthophosphate form==
-	<StructureSection load='5xj9' size='340' side='right' caption='[[5xj9]], [[Resolution\|resolution]] 1.83Å' scene=''>	+	<StructureSection load='5xj9' size='340' side='right'caption='[[5xj9]], [[Resolution\|resolution]] 1.83Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xj9]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XJ9 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XJ9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xj9]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XJ9 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XJ9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=78M:(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE'>78M</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=78M:(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE'>78M</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xj5\|5xj5]], [[5xj6\|5xj6]], [[5xj7\|5xj7]], [[5xj8\|5xj8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xj5\|5xj5]], [[5xj6\|5xj6]], [[5xj7\|5xj7]], [[5xj8\|5xj8]]</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=5xj9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xj9 OCA], [http://pdbe.org/5xj9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xj9 RCSB], [http://www.ebi.ac.uk/pdbsum/5xj9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xj9 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=5xj9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xj9 OCA], [http://pdbe.org/5xj9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xj9 RCSB], [http://www.ebi.ac.uk/pdbsum/5xj9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xj9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Li, D]]		[[Category: Li, D]]
	[[Category: Li, Z]]		[[Category: Li, Z]]

OCA at 07:20, 6 December 2017

2017-12-06T07:20:45Z

←Older revision		Revision as of 07:20, 6 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xj9 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of PlsY (YgiH), an integral membrane glycerol 3-phosphate acyltransferase - the orthophosphate form==
		+	<StructureSection load='5xj9' size='340' side='right' caption='[[5xj9]], [[Resolution\|resolution]] 1.83Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5xj9]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XJ9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XJ9 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=78M:(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE'>78M</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xj5\|5xj5]], [[5xj6\|5xj6]], [[5xj7\|5xj7]], [[5xj8\|5xj8]]</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=5xj9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xj9 OCA], [http://pdbe.org/5xj9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xj9 RCSB], [http://www.ebi.ac.uk/pdbsum/5xj9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xj9 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PLSY_AQUAE PLSY_AQUAE]] Catalyzes the transfer of an acyl group from acyl-phosphate (acyl-PO(4)) to glycerol-3-phosphate (G3P) to form lysophosphatidic acid (LPA). This enzyme utilizes acyl-phosphate as fatty acyl donor, but not acyl-CoA or acyl-ACP.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The membrane-integral glycerol 3-phosphate (G3P) acyltransferase PlsY catalyses the committed and essential step in bacterial phospholipid biosynthesis by acylation of G3P, forming lysophosphatidic acid. It contains no known acyltransferase motifs, lacks eukaryotic homologs, and uses the unusual acyl-phosphate as acyl donor, as opposed to acyl-CoA or acyl-carrier protein for other acyltransferases. Previous studies have identified several PlsY inhibitors as potential antimicrobials. Here we determine the crystal structure of PlsY at 1.48 A resolution, revealing a seven-transmembrane helix fold. Four additional substrate- and product-bound structures uncover the atomic details of its relatively inflexible active site. Structure and mutagenesis suggest a different acylation mechanism of 'substrate-assisted catalysis' that, unlike other acyltransferases, does not require a proteinaceous catalytic base to complete. The structure data and a high-throughput enzymatic assay developed in this work should prove useful for virtual and experimental screening of inhibitors against this vital bacterial enzyme.

-	~~Authors: Li~~, Z., Tang, Y., Li, D.	+	Structural insights into the committed step of bacterial phospholipid biosynthesis.,Li Z, Tang Y, Wu Y, Zhao S, Bao J, Luo Y, Li D Nat Commun. 2017 Nov 22;8(1):1691. doi: 10.1038/s41467-017-01821-9. PMID:29167463<ref>PMID:29167463</ref>

-	~~Description: Crystal structure of~~ a ~~membrane protein with ligand P~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5xj9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Li, D]]		[[Category: Li, D]]
-	[[Category: Tang, Y]]
	[[Category: Li, Z]]		[[Category: Li, Z]]
		+	[[Category: Tang, Y]]
		+	[[Category: Glycerylphosphate acyltransferase]]
		+	[[Category: Gpat]]
		+	[[Category: In meso]]
		+	[[Category: Lipid cubic phase]]
		+	[[Category: Lipid metabolism]]
		+	[[Category: Lipidic cubic phase]]
		+	[[Category: Monoacylglycerol]]
		+	[[Category: Phosphate]]
		+	[[Category: Phospholipid biosynthesis]]
		+	[[Category: Plsy]]
		+	[[Category: Product]]
		+	[[Category: Transferase]]
		+	[[Category: Ygih]]

OCA at 15:30, 27 September 2017

2017-09-27T15:30:54Z

←Older revision		Revision as of 15:30, 27 September 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5xj9 is ON HOLD	+	The entry 5xj9 is ON HOLD until Paper Publication

	Authors: Li, Z., Tang, Y., Li, D.		Authors: Li, Z., Tang, Y., Li, D.

OCA: Protected "5xj9" [edit=sysop:move=sysop]

2017-05-10T12:01:12Z

Protected "5xj9" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:01, 10 May 2017

OCA: New page: '''Unreleased structure''' The entry 5xj9 is ON HOLD Authors: Li, Z., Tang, Y., Li, D. Description: Crystal structure of a membrane protein with ligand P [[Category: Unreleased Structu...

2017-05-10T12:01:11Z

New page: '''Unreleased structure''' The entry 5xj9 is ON HOLD Authors: Li, Z., Tang, Y., Li, D. Description: Crystal structure of a membrane protein with ligand P [[Category: Unreleased Structu...

New page

'''Unreleased structure'''

The entry 5xj9 is ON HOLD

Authors: Li, Z., Tang, Y., Li, D.

Description: Crystal structure of a membrane protein with ligand P
[[Category: Unreleased Structures]]
[[Category: Li, D]]
[[Category: Tang, Y]]
[[Category: Li, Z]]