7ym0: Difference between revisions

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'''Unreleased structure'''


The entry 7ym0 is ON HOLD  until Paper Publication
==Lysoplasmalogen-specific phospholipase D (LyPls-PLD) with Ca2+==
<StructureSection load='7ym0' size='340' side='right'caption='[[7ym0]], [[Resolution|resolution]] 2.91&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[7ym0]] is a 2 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=7YM0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YM0 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.91&#8491;</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></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=7ym0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ym0 OCA], [https://pdbe.org/7ym0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ym0 RCSB], [https://www.ebi.ac.uk/pdbsum/7ym0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ym0 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: Yasutake, Y., Sakasegawa, S., Sugimori, D., Murayama, K.
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: Lysoplasmalogen-specific phospholipase D (LyPls-PLD) with Ca2+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Yasutake, Y]]
<div class="pdbe-citations 7ym0" style="background-color:#fffaf0;"></div>
[[Category: Sakasegawa, S]]
 
[[Category: Murayama, K]]
==See Also==
[[Category: Sugimori, D]]
*[[Phospholipase D 3D structures|Phospholipase D 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermocrispum sp. RD004668]]
[[Category: Murayama K]]
[[Category: Sakasegawa S]]
[[Category: Sugimori D]]
[[Category: Yasutake Y]]
Retrieved from "https://proteopedia.org/7ym0"