View source for 7ymr


==Complex structure of lysoplasmalogen specific phopholipase D, F211L mutant with LPC==
<StructureSection load='7ymr' size='340' side='right'caption='[[7ymr]], [[Resolution|resolution]] 2.69&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[7ymr]] is a 4 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=7YMR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YMR 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]] 2.69&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KIP:[(2~{R})-2-oxidanyl-3-[oxidanyl-[2-(trimethyl-$l^{5}-azanyl)ethoxy]phosphoryl]oxy-propyl]+hexadecanoate'>KIP</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=7ymr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ymr OCA], [https://pdbe.org/7ymr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ymr RCSB], [https://www.ebi.ac.uk/pdbsum/7ymr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ymr 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.

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>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7ymr" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermocrispum sp. RD004668]]
[[Category: Hamana H]]
[[Category: Kato-Murayama M]]
[[Category: Murayama K]]
[[Category: Shirouzu M]]
[[Category: Sugimori D]]