3rlg: Difference between revisions

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 <StructureSection load='3rlg' size='340' side='right'caption='[[3rlg]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3rlg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Brown_spider Brown spider]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RLG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RLG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3rlg]] 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=3RLG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RLG FirstGlance]. <br>
-</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 1.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3rlh|3rlh]]</div></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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase_D Sphingomyelin phosphodiesterase D], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.41 3.1.4.41] </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=3rlg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rlg OCA], [https://pdbe.org/3rlg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rlg RCSB], [https://www.ebi.ac.uk/pdbsum/3rlg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rlg ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[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>
+[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;">
-== Publication Abstract from PubMed ==
-Phospholipases D are the major dermonecrotic component of Loxosceles venom and catalyze the hydrolysis of phospholipids, resulting in the formation of lipid mediators such as ceramide-1-phosphate and lysophosphatidic acid which can induce pathological and biological responses. Phospholipases D can be classified into two classes depending on their catalytic efficiency and the presence of an additional disulfide bridge. In this work, both wild-type and H12A-mutant forms of the class II phospholipase D from L. intermedia venom were crystallized. Wild-type and H12A-mutant crystals were grown under very similar conditions using PEG 200 as a precipitant and belonged to space group P12(1)1, with unit-cell parameters a = 50.1, b = 49.5, c = 56.5 A, beta = 105.9 degrees . Wild-type and H12A-mutant crystals diffracted to maximum resolutions of 1.95 and 1.60 A, respectively.
-Crystallization and preliminary X-ray diffraction analysis of a class II phospholipase D from Loxosceles intermedia venom.,Ullah A, de Giuseppe PO, Murakami MT, Trevisan-Silva D, Wille AC, Chaves-Moreira D, Gremski LH, da Silveira RB, Sennf-Ribeiro A, Chaim OM, Veiga SS, Arni RK Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Feb 1;67(Pt, 2):234-6. Epub 2011 Jan 22. PMID:21301094<ref>PMID:21301094</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3rlg" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Phospholipase D|Phospholipase D]]
+*[[Phospholipase D 3D structures|Phospholipase D 3D structures]]
 *[[Sphingomyelinase|Sphingomyelinase]]
 == References ==
@@ Line 28: / Line 18: @@
 __TOC__
 </StructureSection>
-[[Category: Brown spider]]
 [[Category: Large Structures]]
-[[Category: Sphingomyelin phosphodiesterase D]]
+[[Category: Loxosceles intermedia]]
-[[Category: Arni, R K]]
+[[Category: Arni RK]]
-[[Category: Giuseppe, P O]]
+[[Category: Giuseppe PO]]
-[[Category: Murakami, M T]]
+[[Category: Murakami MT]]
-[[Category: Ullah, A]]
+[[Category: Ullah A]]
-[[Category: Veiga, S S]]
+[[Category: Veiga SS]]
-[[Category: Hydrolase]]
-[[Category: Inactive mutant h12a phospholipase d]]
-[[Category: Plc-like phosphodiesterase]]
-[[Category: Tim beta/alpha-barrel]]