6kz8 - Revision history

OCA at 10:44, 27 March 2024

OCA — Wed, 27 Mar 2024 10:44:56 GMT

←Older revision		Revision as of 10:44, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='6kz8' size='340' side='right'caption='[[6kz8]], [[Resolution\|resolution]] 2.29Å' scene=''>		<StructureSection load='6kz8' size='340' side='right'caption='[[6kz8]], [[Resolution\|resolution]] 2.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kz8]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Arath Arath~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KZ8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6KZ8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kz8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KZ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KZ8 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=PA8:1~~,2~~-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE'>PA8</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]] 2.291Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>PLDALPHA1, PLD1, At3g15730, MSJ11.13 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~3702 ARATH])</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=PA8:1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE'>PA8</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Phospholipase_D Phospholipase D]~~, ~~with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=~~3~~.1.4.4 3.1.4.4]~~ </~~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=6kz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kz8 OCA], [https://pdbe.org/6kz8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kz8 RCSB], [https://www.ebi.ac.uk/pdbsum/6kz8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kz8 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=6kz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kz8 OCA], [~~http~~://pdbe.org/6kz8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6kz8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6kz8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6kz8 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PLDA1_ARATH PLDA1_ARATH]] Hydrolyzes glycerol-phospholipids at the terminal phosphodiesteric bond to generate phosphatidic acids (PA). Plays an important role in various cellular processes, including phytohormone action and response to stress, characterized by acidification of the cell (PubMed:9437863). Involved in wound induction of jasmonic acid (PubMed:11090221). May be involved in membrane lipid remodeling (PubMed:11239826). Probably involved in freezing tolerance by modulating the cold-responsive genes and accumulation of osmolytes (PubMed:16949955). Can use phosphatidylcholine (PC), phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) as substrates, both in presence or in absence of PIP2 (PubMed:9578608). Its main substrate is phosphatidylcholine (PubMed:11239826). Stimulates the intrinsic GTPase activity of GPA1 upon binding (PubMed:14594812). Mediates the abscisic acid effects on stomata through interaction with GPA1 and the production of phosphatidic acid that bind to ABI1 (PubMed:17261695, PubMed:17565616). Involved in seed aging and deterioration (PubMed:17565616). Involved in microtubule stabilization and salt tolerance (PubMed:23150630). Involved in abscisic acid-induced stomatal closure (PubMed:22392280).<ref>PMID:10441386</ref> <ref>PMID:11090221</ref> <ref>PMID:11239826</ref> <ref>PMID:14594812</ref> <ref>PMID:16614222</ref> <ref>PMID:16949955</ref> <ref>PMID:17261695</ref> <ref>PMID:17565616</ref> <ref>PMID:22392280</ref> <ref>PMID:23150630</ref> <ref>PMID:9437863</ref> <ref>PMID:9578608</ref>	+	[https://www.uniprot.org/uniprot/PLDA1_ARATH PLDA1_ARATH] Hydrolyzes glycerol-phospholipids at the terminal phosphodiesteric bond to generate phosphatidic acids (PA). Plays an important role in various cellular processes, including phytohormone action and response to stress, characterized by acidification of the cell (PubMed:9437863). Involved in wound induction of jasmonic acid (PubMed:11090221). May be involved in membrane lipid remodeling (PubMed:11239826). Probably involved in freezing tolerance by modulating the cold-responsive genes and accumulation of osmolytes (PubMed:16949955). Can use phosphatidylcholine (PC), phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) as substrates, both in presence or in absence of PIP2 (PubMed:9578608). Its main substrate is phosphatidylcholine (PubMed:11239826). Stimulates the intrinsic GTPase activity of GPA1 upon binding (PubMed:14594812). Mediates the abscisic acid effects on stomata through interaction with GPA1 and the production of phosphatidic acid that bind to ABI1 (PubMed:17261695, PubMed:17565616). Involved in seed aging and deterioration (PubMed:17565616). Involved in microtubule stabilization and salt tolerance (PubMed:23150630). Involved in abscisic acid-induced stomatal closure (PubMed:22392280).<ref>PMID:10441386</ref> <ref>PMID:11090221</ref> <ref>PMID:11239826</ref> <ref>PMID:14594812</ref> <ref>PMID:16614222</ref> <ref>PMID:16949955</ref> <ref>PMID:17261695</ref> <ref>PMID:17565616</ref> <ref>PMID:22392280</ref> <ref>PMID:23150630</ref> <ref>PMID:9437863</ref> <ref>PMID:9578608</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Phospholipase D (PLD) hydrolyzes the phosphodiester bond of glycerophospholipids and produces phosphatidic acid (PA), which acts as a second messenger in many living organisms. A large number of PLDs have been identified in eukaryotes, and are viewed as promising targets for drug design because these enzymes are known to be tightly regulated and to function in the pathophysiology of many human diseases. However, the underlying molecular mechanisms of catalysis and regulation of eukaryotic PLD remain elusive. Here, we determined the crystal structure of full-length plant PLDalpha1 in the apo state and in complex with PA. The structure shows that the N-terminal C2 domain hydrophobically interacts with the C-terminal catalytic domain that features two HKD motifs. Our analysis reveals the catalytic site, substrate-binding mechanism, and a new Ca(2+)-binding site that is required for the activation of PLD. In addition, we tested several efficient small-molecule inhibitors against PLDalpha1, and suggested a possible competitive inhibition mechanism according to structure-based docking analysis. This study explains many long-standing questions about PLDs and provides structural insights into PLD-targeted inhibitor/drug design.	+
-		+
-	Crystal structure of plant PLDalpha1 reveals catalytic and regulatory mechanisms of eukaryotic phospholipase D.,Li J, Yu F, Guo H, Xiong R, Zhang W, He F, Zhang M, Zhang P Cell Res. 2019 Oct 16. pii: 10.1038/s41422-019-0244-6. doi:, 10.1038/s41422-019-0244-6. PMID:31619765<ref>PMID:31619765</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6kz8" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
-	*[[Phospholipase D\|Phospholipase D]]	+	*[[Phospholipase D 3D structures\|Phospholipase D 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arath~~]]	+	[[Category: Arabidopsis thaliana]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Phospholipase D]]~~	+	[[Category: Li JX]]
-	[[Category: Li~~, J X~~]]	+	[[Category: Yu F]]
-	[[Category: Yu, F]]	+	[[Category: Zhang P]]
-	[[Category: Zhang, P]]	+
-	~~[[Category: C2 domain]]~~	+
-	~~[[Category: Calcium activation]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Phosphatidic acid]]~~	+
-	~~[[Category: Phospholipase d~~]]	+

OCA at 05:45, 13 May 2020

OCA — Wed, 13 May 2020 05:45:30 GMT

←Older revision		Revision as of 05:45, 13 May 2020
Line 1:		Line 1:

-	==Crystal structure of plant Phospholipase D alpha ~~comlex~~ with phosphatidic acid==	+	==Crystal structure of plant Phospholipase D alpha complex with phosphatidic acid==
	<StructureSection load='6kz8' size='340' side='right'caption='[[6kz8]], [[Resolution\|resolution]] 2.29Å' scene=''>		<StructureSection load='6kz8' size='340' side='right'caption='[[6kz8]], [[Resolution\|resolution]] 2.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kz8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6KZ8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kz8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KZ8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PA8:1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE'>PA8</scene></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=PA8:1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE'>PA8</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PLDALPHA1, PLD1, At3g15730, MSJ11.13 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PLDALPHA1, PLD1, At3g15730, MSJ11.13 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phospholipase_D Phospholipase D], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.4 3.1.4.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phospholipase_D Phospholipase D], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.4 3.1.4.4] </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=6kz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kz8 OCA], [http://pdbe.org/6kz8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kz8 RCSB], [http://www.ebi.ac.uk/pdbsum/6kz8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kz8 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=6kz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kz8 OCA], [http://pdbe.org/6kz8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kz8 RCSB], [http://www.ebi.ac.uk/pdbsum/6kz8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kz8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 16:37, 22 January 2020

OCA — Wed, 22 Jan 2020 16:37:17 GMT

←Older revision		Revision as of 16:37, 22 January 2020
Line 3:		Line 3:
	<StructureSection load='6kz8' size='340' side='right'caption='[[6kz8]], [[Resolution\|resolution]] 2.29Å' scene=''>		<StructureSection load='6kz8' size='340' side='right'caption='[[6kz8]], [[Resolution\|resolution]] 2.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kz8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KZ8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kz8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KZ8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PA8:1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE'>PA8</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PA8:1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE'>PA8</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PLDALPHA1, PLD1, At3g15730, MSJ11.13 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phospholipase_D Phospholipase D], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.4 3.1.4.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phospholipase_D Phospholipase D], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.4 3.1.4.4] </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=6kz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kz8 OCA], [http://pdbe.org/6kz8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kz8 RCSB], [http://www.ebi.ac.uk/pdbsum/6kz8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kz8 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=6kz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kz8 OCA], [http://pdbe.org/6kz8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kz8 RCSB], [http://www.ebi.ac.uk/pdbsum/6kz8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kz8 ProSAT]</span></td></tr>
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 6kz8" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6kz8" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phospholipase D\|Phospholipase D]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Arath]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Phospholipase D]]		[[Category: Phospholipase D]]

OCA at 11:02, 13 November 2019

OCA — Wed, 13 Nov 2019 11:02:26 GMT

←Older revision		Revision as of 11:02, 13 November 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6kz8 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of plant Phospholipase D alpha comlex with phosphatidic acid==
		+	<StructureSection load='6kz8' size='340' side='right'caption='[[6kz8]], [[Resolution\|resolution]] 2.29Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6kz8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KZ8 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PA8:1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE'>PA8</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phospholipase_D Phospholipase D], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.4 3.1.4.4] </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=6kz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kz8 OCA], [http://pdbe.org/6kz8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kz8 RCSB], [http://www.ebi.ac.uk/pdbsum/6kz8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kz8 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PLDA1_ARATH PLDA1_ARATH]] Hydrolyzes glycerol-phospholipids at the terminal phosphodiesteric bond to generate phosphatidic acids (PA). Plays an important role in various cellular processes, including phytohormone action and response to stress, characterized by acidification of the cell (PubMed:9437863). Involved in wound induction of jasmonic acid (PubMed:11090221). May be involved in membrane lipid remodeling (PubMed:11239826). Probably involved in freezing tolerance by modulating the cold-responsive genes and accumulation of osmolytes (PubMed:16949955). Can use phosphatidylcholine (PC), phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) as substrates, both in presence or in absence of PIP2 (PubMed:9578608). Its main substrate is phosphatidylcholine (PubMed:11239826). Stimulates the intrinsic GTPase activity of GPA1 upon binding (PubMed:14594812). Mediates the abscisic acid effects on stomata through interaction with GPA1 and the production of phosphatidic acid that bind to ABI1 (PubMed:17261695, PubMed:17565616). Involved in seed aging and deterioration (PubMed:17565616). Involved in microtubule stabilization and salt tolerance (PubMed:23150630). Involved in abscisic acid-induced stomatal closure (PubMed:22392280).<ref>PMID:10441386</ref> <ref>PMID:11090221</ref> <ref>PMID:11239826</ref> <ref>PMID:14594812</ref> <ref>PMID:16614222</ref> <ref>PMID:16949955</ref> <ref>PMID:17261695</ref> <ref>PMID:17565616</ref> <ref>PMID:22392280</ref> <ref>PMID:23150630</ref> <ref>PMID:9437863</ref> <ref>PMID:9578608</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Phospholipase D (PLD) hydrolyzes the phosphodiester bond of glycerophospholipids and produces phosphatidic acid (PA), which acts as a second messenger in many living organisms. A large number of PLDs have been identified in eukaryotes, and are viewed as promising targets for drug design because these enzymes are known to be tightly regulated and to function in the pathophysiology of many human diseases. However, the underlying molecular mechanisms of catalysis and regulation of eukaryotic PLD remain elusive. Here, we determined the crystal structure of full-length plant PLDalpha1 in the apo state and in complex with PA. The structure shows that the N-terminal C2 domain hydrophobically interacts with the C-terminal catalytic domain that features two HKD motifs. Our analysis reveals the catalytic site, substrate-binding mechanism, and a new Ca(2+)-binding site that is required for the activation of PLD. In addition, we tested several efficient small-molecule inhibitors against PLDalpha1, and suggested a possible competitive inhibition mechanism according to structure-based docking analysis. This study explains many long-standing questions about PLDs and provides structural insights into PLD-targeted inhibitor/drug design.

-	~~Authors: Li~~, J~~.X.~~, Yu, F., Zhang, P.	+	Crystal structure of plant PLDalpha1 reveals catalytic and regulatory mechanisms of eukaryotic phospholipase D.,Li J, Yu F, Guo H, Xiong R, Zhang W, He F, Zhang M, Zhang P Cell Res. 2019 Oct 16. pii: 10.1038/s41422-019-0244-6. doi:, 10.1038/s41422-019-0244-6. PMID:31619765<ref>PMID:31619765</ref>

-	~~Description: Crystal structure~~ of ~~plant Phospholipase D alpha comlex with phosphatidic acid~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Zhang~~, P]]	+	<div class="pdbe-citations 6kz8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Phospholipase D]]
		+	[[Category: Li, J X]]
	[[Category: Yu, F]]		[[Category: Yu, F]]
-	[[Category: Li, ~~J.X~~]]	+	[[Category: Zhang, P]]
		+	[[Category: C2 domain]]
		+	[[Category: Calcium activation]]
		+	[[Category: Hydrolase]]
		+	[[Category: Inhibitor]]
		+	[[Category: Phosphatidic acid]]
		+	[[Category: Phospholipase d]]

OCA at 04:59, 6 November 2019

OCA — Wed, 06 Nov 2019 04:59:39 GMT

←Older revision		Revision as of 04:59, 6 November 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6kz8 is ON HOLD	+	The entry 6kz8 is ON HOLD until Paper Publication

	Authors: Li, J.X., Yu, F., Zhang, P.		Authors: Li, J.X., Yu, F., Zhang, P.

-	Description: Crystal structure of plant ~~PLD~~ alpha comlex with phosphatidic acid	+	Description: Crystal structure of plant Phospholipase D alpha comlex with phosphatidic acid
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Li, J.X]]
	[[Category: Zhang, P]]		[[Category: Zhang, P]]
	[[Category: Yu, F]]		[[Category: Yu, F]]
		+	[[Category: Li, J.X]]

OCA: Protected "6kz8" [edit=sysop:move=sysop]

OCA — Wed, 02 Oct 2019 07:01:49 GMT

Protected "6kz8" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:01, 2 October 2019

OCA: New page: '''Unreleased structure''' The entry 6kz8 is ON HOLD Authors: Li, J.X., Yu, F., Zhang, P. Description: Crystal structure of plant PLD alpha comlex with phosphatidic acid [[Category: Un...

OCA — Wed, 02 Oct 2019 07:01:47 GMT

New page: '''Unreleased structure''' The entry 6kz8 is ON HOLD Authors: Li, J.X., Yu, F., Zhang, P. Description: Crystal structure of plant PLD alpha comlex with phosphatidic acid [[Category: Un...

New page

'''Unreleased structure'''

The entry 6kz8 is ON HOLD

Authors: Li, J.X., Yu, F., Zhang, P.

Description: Crystal structure of plant PLD alpha comlex with phosphatidic acid
[[Category: Unreleased Structures]]
[[Category: Li, J.X]]
[[Category: Zhang, P]]
[[Category: Yu, F]]