This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
7ymq
From Proteopedia
(Difference between revisions)
m (Protected "7ymq" [edit=sysop:move=sysop]) |
|||
| (2 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | '''Unreleased structure''' | ||
| - | + | ==Crystal structure of lysoplasmalogen specific phopholipase D, F211L mutant== | |
| + | <StructureSection load='7ymq' size='340' side='right'caption='[[7ymq]], [[Resolution|resolution]] 2.29Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[7ymq]] 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=7YMQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YMQ 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]] 2.29Å</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=7ymq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ymq OCA], [https://pdbe.org/7ymq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ymq RCSB], [https://www.ebi.ac.uk/pdbsum/7ymq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ymq 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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| - | [[Category: Hamana | + | <div class="pdbe-citations 7ymq" style="background-color:#fffaf0;"></div> |
| - | [[Category: Kato-Murayama | + | == References == |
| - | [[Category: | + | <references/> |
| - | [[Category: | + | __TOC__ |
| - | [[Category: | + | </StructureSection> |
| + | [[Category: Large Structures]] | ||
| + | [[Category: Thermocrispum sp. RD004668]] | ||
| + | [[Category: Hamana H]] | ||
| + | [[Category: Kato-Murayama M]] | ||
| + | [[Category: Murayama K]] | ||
| + | [[Category: Shirouzu M]] | ||
| + | [[Category: Sugimori D]] | ||
Current revision
Crystal structure of lysoplasmalogen specific phopholipase D, F211L mutant
| |||||||||||
