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5egh

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Structure of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase in complex with phosphocholine

Structural highlights

5egh is a 2 chain structure with sequence from Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.803Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ENPP6_MOUSE Choline-specific glycerophosphodiester phosphodiesterase. The preferred substrate may be lysosphingomyelin (By similarity). Hydrolyzes lysophosphatidylcholine (LPC) to form monoacylglycerol and phosphorylcholine but not lysophosphatidic acid, showing it has a lysophospholipase C activity. Has a preference for LPC with short (12:0 and 14:0) or polyunsaturated (18:2 and 20:4) fatty acids. Also hydrolyzes glycerophosphorylcholine and sphingosylphosphorylcholine efficiently. Hydrolyzes the classical substrate for phospholipase C, p-nitrophenyl phosphorylcholine in vitro, while it does not hydrolyze the classical nucleotide phosphodiesterase substrate, p-nitrophenyl thymidine 5'-monophosphate. Does not hydrolyze diacyl phospholipids such as phosphatidylethanolamine, phosphatidylinositol, phosphatidylserine, phosphatidylglycerol and phosphatidic acid (By similarity).^[1]

Publication Abstract from PubMed

Choline is an essential nutrient for all living cells and is produced extracellularly by sequential degradation of phosphatidylcholine (PC). However, little is known about how choline is produced extracellularly. Here, we report that ENPP6, a choline-specific phosphodiesterase, hydrolyzes glycerophosphocholine (GPC), a degradation product of PC, as a physiological substrate and participates in choline metabolism. ENPP6 is highly expressed in liver sinusoidal endothelial cells and developing oligodendrocytes, which actively incorporate choline and synthesize PC. ENPP6-deficient mice exhibited fatty liver and hypomyelination, well known choline-deficient phenotypes. The choline moiety of GPC was incorporated into PC in an ENPP6-dependent manner both in vivo and in vitro. The crystal structure of ENPP6 in complex with phosphocholine revealed that the choline moiety of the phosphocholine is recognized by a choline-binding pocket formed by conserved aromatic and acidic residues. The present study provides the molecular basis for ENPP6-mediated choline metabolism at atomic, cellular and tissue levels.

Structure and biological function of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase.,Morita J, Kano K, Kato K, Takita H, Sakagami H, Yamamoto Y, Mihara E, Ueda H, Sato T, Tokuyama H, Arai H, Asou H, Takagi J, Ishitani R, Nishimasu H, Nureki O, Aoki J Sci Rep. 2016 Feb 18;6:20995. doi: 10.1038/srep20995. PMID:26888014^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Sakagami H, Aoki J, Natori Y, Nishikawa K, Kakehi Y, Natori Y, Arai H. Biochemical and molecular characterization of a novel choline-specific glycerophosphodiester phosphodiesterase belonging to the nucleotide pyrophosphatase/phosphodiesterase family. J Biol Chem. 2005 Jun 17;280(24):23084-93. Epub 2005 Mar 23. PMID:15788404 doi:http://dx.doi.org/10.1074/jbc.M413438200
↑ Morita J, Kano K, Kato K, Takita H, Sakagami H, Yamamoto Y, Mihara E, Ueda H, Sato T, Tokuyama H, Arai H, Asou H, Takagi J, Ishitani R, Nishimasu H, Nureki O, Aoki J. Structure and biological function of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase. Sci Rep. 2016 Feb 18;6:20995. doi: 10.1038/srep20995. PMID:26888014 doi:http://dx.doi.org/10.1038/srep20995

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5egh"

@@ Line 1: / Line 1: @@
 ==Structure of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase in complex with phosphocholine==
-<StructureSection load='5egh' size='340' side='right' caption='[[5egh]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='5egh' size='340' side='right'caption='[[5egh]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5egh]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EGH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EGH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5egh]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EGH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EGH FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PC:PHOSPHOCHOLINE'>PC</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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]] 1.803&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5ege|5ege]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PC:PHOSPHOCHOLINE'>PC</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5egh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5egh OCA], [http://pdbe.org/5egh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5egh RCSB], [http://www.ebi.ac.uk/pdbsum/5egh PDBsum]</span></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=5egh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5egh OCA], [https://pdbe.org/5egh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5egh RCSB], [https://www.ebi.ac.uk/pdbsum/5egh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5egh ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ENPP6_MOUSE ENPP6_MOUSE]] Choline-specific glycerophosphodiester phosphodiesterase. The preferred substrate may be lysosphingomyelin (By similarity). Hydrolyzes lysophosphatidylcholine (LPC) to form monoacylglycerol and phosphorylcholine but not lysophosphatidic acid, showing it has a lysophospholipase C activity. Has a preference for LPC with short (12:0 and 14:0) or polyunsaturated (18:2 and 20:4) fatty acids. Also hydrolyzes glycerophosphorylcholine and sphingosylphosphorylcholine efficiently. Hydrolyzes the classical substrate for phospholipase C, p-nitrophenyl phosphorylcholine in vitro, while it does not hydrolyze the classical nucleotide phosphodiesterase substrate, p-nitrophenyl thymidine 5'-monophosphate. Does not hydrolyze diacyl phospholipids such as phosphatidylethanolamine, phosphatidylinositol, phosphatidylserine, phosphatidylglycerol and phosphatidic acid (By similarity).<ref>PMID:15788404</ref>
+[https://www.uniprot.org/uniprot/ENPP6_MOUSE ENPP6_MOUSE] Choline-specific glycerophosphodiester phosphodiesterase. The preferred substrate may be lysosphingomyelin (By similarity). Hydrolyzes lysophosphatidylcholine (LPC) to form monoacylglycerol and phosphorylcholine but not lysophosphatidic acid, showing it has a lysophospholipase C activity. Has a preference for LPC with short (12:0 and 14:0) or polyunsaturated (18:2 and 20:4) fatty acids. Also hydrolyzes glycerophosphorylcholine and sphingosylphosphorylcholine efficiently. Hydrolyzes the classical substrate for phospholipase C, p-nitrophenyl phosphorylcholine in vitro, while it does not hydrolyze the classical nucleotide phosphodiesterase substrate, p-nitrophenyl thymidine 5'-monophosphate. Does not hydrolyze diacyl phospholipids such as phosphatidylethanolamine, phosphatidylinositol, phosphatidylserine, phosphatidylglycerol and phosphatidic acid (By similarity).<ref>PMID:15788404</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 5egh" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ectonucleotide pyrophosphatase/phosphodiesterase 3D structures|Ectonucleotide pyrophosphatase/phosphodiesterase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Aoki, J]]
+[[Category: Large Structures]]
-[[Category: Ishitani, R]]
+[[Category: Mus musculus]]
-[[Category: Kano, K]]
+[[Category: Aoki J]]
-[[Category: Kato, K]]
+[[Category: Ishitani R]]
-[[Category: Morita, J]]
+[[Category: Kano K]]
-[[Category: Nishimasu, H]]
+[[Category: Kato K]]
-[[Category: Nureki, O]]
+[[Category: Morita J]]
-[[Category: Takita, H]]
+[[Category: Nishimasu H]]
-[[Category: Choline metabolism]]
+[[Category: Nureki O]]
-[[Category: Hydrolase]]
+[[Category: Takita H]]
-[[Category: Phosphodiesterase]]

5egh

From Proteopedia

Current revision

Structure of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase in complex with phosphocholine

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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