9vl3: Difference between revisions

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'''Unreleased structure'''


The entry 9vl3 is ON HOLD  until Paper Publication
==Cryo-EM structure of human lipid phosphate phosphatase 1 complexed with PO4 in nanodiscs==
<StructureSection load='9vl3' size='340' side='right'caption='[[9vl3]], [[Resolution|resolution]] 2.82&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9vl3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9VL3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9VL3 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.82&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LBN:[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy-propyl]+2-(trimethylazaniumyl)ethyl+phosphate'>LBN</scene>, <scene name='pdbligand=LPP:2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL+HEXADECANOATE'>LPP</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PT5:(1S)-2-{[(R)-HYDROXY{[(1R,2R,3S,4R,5R,6S)-2,3,6-TRIHYDROXY-4,5-BIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL]OXY}-1-[(OCTADECANOYLOXY)METHYL]ETHYL+(8E,11E)-ICOSA-5,8,11,14-TETRAENOATE'>PT5</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=9vl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9vl3 OCA], [https://pdbe.org/9vl3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9vl3 RCSB], [https://www.ebi.ac.uk/pdbsum/9vl3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9vl3 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PLPP1_HUMAN PLPP1_HUMAN] Magnesium-independent phospholipid phosphatase of the plasma membrane that catalyzes the dephosphorylation of a variety of glycerolipid and sphingolipid phosphate esters including phosphatidate/PA, lysophosphatidate/LPA, diacylglycerol pyrophosphate/DGPP, sphingosine 1-phosphate/S1P and ceramide 1-phosphate/C1P (PubMed:10962286, PubMed:17379599, PubMed:9305923, PubMed:9607309, PubMed:9705349). Also acts on N-oleoyl ethanolamine phosphate/N-(9Z-octadecenoyl)-ethanolamine phosphate, a potential physiological compound (PubMed:9607309). Through its extracellular phosphatase activity allows both the hydrolysis and the cellular uptake of these bioactive lipid mediators from the milieu, regulating signal transduction in different cellular processes (PubMed:10962286, PubMed:12909631, PubMed:15461590, PubMed:17379599). It is for instance essential for the extracellular hydrolysis of S1P and subsequent conversion into intracellular S1P (PubMed:17379599). Involved in the regulation of inflammation, platelets activation, cell proliferation and migration among other processes (PubMed:12909631, PubMed:15461590). May also have an intracellular activity to regulate phospholipid-mediated signaling pathways (By similarity).[UniProtKB:O08564]<ref>PMID:10962286</ref> <ref>PMID:12909631</ref> <ref>PMID:15461590</ref> <ref>PMID:17379599</ref> <ref>PMID:9305923</ref> <ref>PMID:9607309</ref> <ref>PMID:9705349</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Lipid phosphate phosphatases (LPPs) catalyze the dephosphorylation of a broad range of bioactive lipid phosphates, including lysophosphatidic acid and sphingosine-1-phosphate, playing essential roles in embryonic vasculogenesis, cell differentiation and inflammation. Here we present the cryo-electron microscopic structure of human LPP1 as a tetramer with C4 symmetry. We capture the phosphohistidine intermediate state by using vanadate as a phosphate analog, where vanadate is coordinated by positively charged residues from three conserved motifs (C1, C2 and C3). Structural investigations of LPP1 variants with mutations in two catalytic histidine residues confirm that the histidine in the C2 motif facilitates phosphate bond cleavage. Enzymatic assays validate our structural observations. Additionally, a phosphatidylinositol 4,5-bisphosphate (PIP(2)) molecule was discovered in the LPP1 structure, underscoring a potential regulatory role for PIP(2) in the catalytic activity of LPP1.


Authors:  
Structural basis for the catalytic mechanism of human lipid phosphate phosphatases.,Yang M, Sun C, He Y, Qian H Nat Chem Biol. 2026 Jan 9. doi: 10.1038/s41589-025-02121-w. PMID:41513850<ref>PMID:41513850</ref>


Description:  
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
<div class="pdbe-citations 9vl3" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Qian HW]]
[[Category: Yang M]]
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