3rlh

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==Crystal structure of a class II phospholipase D from Loxosceles intermedia venom==
==Crystal structure of a class II phospholipase D from Loxosceles intermedia venom==
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<StructureSection load='3rlh' size='340' side='right' caption='[[3rlh]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
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<StructureSection load='3rlh' size='340' side='right'caption='[[3rlh]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3rlh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Brown_spider Brown spider]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RLH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RLH FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3rlh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Loxosceles_intermedia Loxosceles intermedia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RLH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RLH FirstGlance]. <br>
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</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.72&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3rlg|3rlg]]</td></tr>
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<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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase_D Sphingomyelin phosphodiesterase D], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.41 3.1.4.41] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3rlh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rlh OCA], [https://pdbe.org/3rlh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rlh RCSB], [https://www.ebi.ac.uk/pdbsum/3rlh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rlh ProSAT]</span></td></tr>
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<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=3rlh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rlh OCA], [http://pdbe.org/3rlh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3rlh RCSB], [http://www.ebi.ac.uk/pdbsum/3rlh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3rlh ProSAT]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/A1HA_LOXIN A1HA_LOXIN]] Catalyzes the hydrolysis of sphingomyelin, lysophosphatidylcholine, and lyso-platelet activating factor but not that of phosphatidylcholine. Shows a high enzymatic activity. Induces dermonecrosis, blood vessel permeability and platelet aggregation (PubMed:9790962). Is directly toxic to kidney (PubMed:16005484) and liver (PubMed:18765244). Also induces hemolysis in a complement-dependent manner (PubMed:9790962) as well as in a complement-independent manner. The hemolysis provoked in a complement-independent manner is composed of several steps. The toxin binds to erythrocyte membranes, hydrolyzes membrane phospholipids (sphingomyelin and lysophosphatidylcholine) thus generating metabolism products that cause hemolysis, probably by provoking an increase of calcium inside cells. The calcium influx is due to the opening of L-type calcium channels, since L-type calcium channel blockers inhibit calcium influx (PubMed:21590705).<ref>PMID:16005484</ref> <ref>PMID:18760322</ref> <ref>PMID:18765244</ref> <ref>PMID:19455508</ref> <ref>PMID:21590705</ref> <ref>PMID:9790962</ref>
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[https://www.uniprot.org/uniprot/A1HA_LOXIN A1HA_LOXIN] Catalyzes the hydrolysis of sphingomyelin, lysophosphatidylcholine, and lyso-platelet activating factor but not that of phosphatidylcholine. Shows a high enzymatic activity. Induces dermonecrosis, blood vessel permeability and platelet aggregation (PubMed:9790962). Is directly toxic to kidney (PubMed:16005484) and liver (PubMed:18765244). Also induces hemolysis in a complement-dependent manner (PubMed:9790962) as well as in a complement-independent manner. The hemolysis provoked in a complement-independent manner is composed of several steps. The toxin binds to erythrocyte membranes, hydrolyzes membrane phospholipids (sphingomyelin and lysophosphatidylcholine) thus generating metabolism products that cause hemolysis, probably by provoking an increase of calcium inside cells. The calcium influx is due to the opening of L-type calcium channels, since L-type calcium channel blockers inhibit calcium influx (PubMed:21590705).<ref>PMID:16005484</ref> <ref>PMID:18760322</ref> <ref>PMID:18765244</ref> <ref>PMID:19455508</ref> <ref>PMID:21590705</ref> <ref>PMID:9790962</ref>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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==See Also==
==See Also==
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*[[Phospholipase D|Phospholipase D]]
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*[[Phospholipase D 3D structures|Phospholipase D 3D structures]]
*[[Sphingomyelinase|Sphingomyelinase]]
*[[Sphingomyelinase|Sphingomyelinase]]
== References ==
== References ==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Brown spider]]
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[[Category: Large Structures]]
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[[Category: Sphingomyelin phosphodiesterase D]]
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[[Category: Loxosceles intermedia]]
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[[Category: Arni, R K]]
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[[Category: Arni RK]]
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[[Category: Giuseppe, P O]]
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[[Category: Giuseppe PO]]
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[[Category: Murakami, M T]]
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[[Category: Murakami MT]]
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[[Category: Ullah, A]]
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[[Category: Ullah A]]
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[[Category: Veiga, S S]]
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[[Category: Veiga SS]]
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[[Category: Class ii pld]]
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[[Category: Hydrolase]]
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[[Category: Phospholipase d]]
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[[Category: Plc-like phosphodiesterase]]
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[[Category: Tim beta/alpha-barrel superfamily]]
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[[Category: Venom]]
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Current revision

Crystal structure of a class II phospholipase D from Loxosceles intermedia venom

PDB ID 3rlh

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