7ymp - Revision history

OCA at 18:10, 29 November 2023

OCA — Wed, 29 Nov 2023 18:10:38 GMT

←Older revision		Revision as of 18:10, 29 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7ymp]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermocrispum_sp._RD004668 Thermocrispum sp. RD004668]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7YMP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YMP FirstGlance]. <br>		<table><tr><td colspan='2'>[[7ymp]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermocrispum_sp._RD004668 Thermocrispum sp. RD004668]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7YMP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YMP FirstGlance]. <br>
-	</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=7ymp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ymp OCA], [https://pdbe.org/7ymp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ymp RCSB], [https://www.ebi.ac.uk/pdbsum/7ymp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ymp ProSAT]</span></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]] 2.57Å</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=7ymp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ymp OCA], [https://pdbe.org/7ymp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ymp RCSB], [https://www.ebi.ac.uk/pdbsum/7ymp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ymp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 7ymp" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7ymp" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phospholipase D 3D structures\|Phospholipase D 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:44, 8 February 2023

OCA — Wed, 08 Feb 2023 06:44:11 GMT

←Older revision		Revision as of 06:44, 8 February 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 7ymp is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of lysoplasmalogen specific phospholipase D==
		+	<StructureSection load='7ymp' size='340' side='right'caption='[[7ymp]], [[Resolution\|resolution]] 2.57Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7ymp]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermocrispum_sp._RD004668 Thermocrispum sp. RD004668]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7YMP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YMP FirstGlance]. <br>
		+	</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=7ymp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ymp OCA], [https://pdbe.org/7ymp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ymp RCSB], [https://www.ebi.ac.uk/pdbsum/7ymp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ymp ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0U4VTN7_9PSEU A0A0U4VTN7_9PSEU]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Lysoplasmalogen-specific phospholipase D (LyPls-PLD) hydrolyzes choline lysoplasmalogen to choline and 1-(1-alkenyl)-sn-glycero-3-phosphate. Mutation of F211 to leucine altered its substrate specificity from lysoplasmalogen to 1-O-hexadecyl-2-hydroxy-sn-glycero-3-phosphocholine (lysoPAF). Enzymes specific to lysoPAF have good potential for clinical application, and understanding the mechanism of their activity is important. The crystal structure of LyPls-PLD exhibited a TIM barrel fold assigned to glycerophosphocholine phosphodiesterase, a member of glycerophosphodiester phosphodiesterase. LyPls-PLD possesses a hydrophobic cleft for the binding of the aliphatic chain of the substrate. In the structure of the F211L mutant, Met232 and Tyr258 form a "small lid" structure that stabilizes the binding of the aliphatic chain of the substrate. In contrast, F211 may inhibit small lid formation in the wild-type structure. LysoPAF possesses a flexible aliphatic chain; therefore, a small lid is effective for stabilizing the substrate during catalytic reactions.

-	~~Authors: Murayama, K~~., Kato-Murayama, M., ~~Sugimori, D.~~, Shirouzu, M., ~~Hamana~~, H.	+	Structural basis for the substrate specificity switching of lysoplasmalogen-specific phospholipase D from Thermocrispum sp. RD004668.,Hamana H, Yasutake Y, Kato-Murayama M, Hosaka T, Shirouzu M, Sakasegawa SI, Sugimori D, Murayama K Biosci Biotechnol Biochem. 2022 Dec 21;87(1):74-81. doi: 10.1093/bbb/zbac169. PMID:36307380<ref>PMID:36307380</ref>

-	~~Description: Crystal structure~~ of ~~lysoplasmalogen specific phospholipase D~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Kato-Murayama, M~~]]	+	<div class="pdbe-citations 7ymp" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Sugimori, D~~]]	+	== References ==
-	[[Category: ~~Hamana, H~~]]	+	<references/>
-	[[Category: Shirouzu, M]]	+	__TOC__
-	[[Category: ~~Murayama, K~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Thermocrispum sp. RD004668]]
		+	[[Category: Hamana H]]
		+	[[Category: Kato-Murayama M]]
		+	[[Category: Murayama K]]
		+	[[Category: Shirouzu M]]
		+	[[Category: Sugimori D]]

OCA at 03:34, 25 August 2022

OCA — Thu, 25 Aug 2022 03:34:19 GMT

←Older revision		Revision as of 03:34, 25 August 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7ymp is ON HOLD	+	The entry 7ymp is ON HOLD until Paper Publication

	Authors: Murayama, K., Kato-Murayama, M., Sugimori, D., Shirouzu, M., Hamana, H.		Authors: Murayama, K., Kato-Murayama, M., Sugimori, D., Shirouzu, M., Hamana, H.

OCA at 03:31, 18 August 2022

OCA — Thu, 18 Aug 2022 03:31:37 GMT

←Older revision		Revision as of 03:31, 18 August 2022
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	Authors: Murayama, K., Kato-Murayama, M., Sugimori, D., Shirouzu, M., Hamana, H.		Authors: Murayama, K., Kato-Murayama, M., Sugimori, D., Shirouzu, M., Hamana, H.

-	Description: ~~crystal~~ structure of lysoplasmalogen specific phospholipase D	+	Description: Crystal structure of lysoplasmalogen specific phospholipase D
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Hamana, H]]
	[[Category: Kato-Murayama, M]]		[[Category: Kato-Murayama, M]]
-	[[Category: Shirouzu, M]]
	[[Category: Sugimori, D]]		[[Category: Sugimori, D]]
		+	[[Category: Hamana, H]]
		+	[[Category: Shirouzu, M]]
	[[Category: Murayama, K]]		[[Category: Murayama, K]]

OCA: Protected "7ymp" [edit=sysop:move=sysop]

OCA — Wed, 03 Aug 2022 03:43:14 GMT

Protected "7ymp" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:43, 3 August 2022

OCA: New page: '''Unreleased structure''' The entry 7ymp is ON HOLD Authors: Murayama, K., Kato-Murayama, M., Sugimori, D., Shirouzu, M., Hamana, H. Description: crystal structure of lysoplasmalogen ...

OCA — Wed, 03 Aug 2022 03:43:13 GMT

New page: '''Unreleased structure''' The entry 7ymp is ON HOLD Authors: Murayama, K., Kato-Murayama, M., Sugimori, D., Shirouzu, M., Hamana, H. Description: crystal structure of lysoplasmalogen ...

New page

'''Unreleased structure'''

The entry 7ymp is ON HOLD

Authors: Murayama, K., Kato-Murayama, M., Sugimori, D., Shirouzu, M., Hamana, H.

Description: crystal structure of lysoplasmalogen specific phospholipase D
[[Category: Unreleased Structures]]
[[Category: Hamana, H]]
[[Category: Kato-Murayama, M]]
[[Category: Shirouzu, M]]
[[Category: Sugimori, D]]
[[Category: Murayama, K]]