1xx1: Difference between revisions

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-{{Seed}}
-[[Image:1xx1.png|left|200px]]
-<!--
+==Structural basis for ion-coordination and the catalytic mechanism of sphingomyelinases D==
-The line below this paragraph, containing "STRUCTURE_1xx1", creates the "Structure Box" on the page.
+<StructureSection load='1xx1' size='340' side='right'caption='[[1xx1]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1xx1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Loxosceles_laeta Loxosceles laeta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XX1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XX1 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1xx1|  PDB=1xx1  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xx1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xx1 OCA], [https://pdbe.org/1xx1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xx1 RCSB], [https://www.ebi.ac.uk/pdbsum/1xx1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xx1 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A311_LOXLA A311_LOXLA] Catalyzes the hydrolysis of sphingomyelin. May also acts on other phosphatidyl esters. Induces complement-dependent hemolysis and dermonecrosis.<ref>PMID:12419302</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xx/1xx1_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1xx1 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Sphingomyelinases D (SMases D) from Loxosceles spider venom are the principal toxins responsible for the manifestation of dermonecrosis, intravascular hemolysis, and acute renal failure, which can result in death. These enzymes catalyze the hydrolysis of sphingomyelin, resulting in the formation of ceramide 1-phosphate and choline or the hydrolysis of lysophosphatidyl choline, generating the lipid mediator lysophosphatidic acid. This report represents the first crystal structure of a member of the sphingomyelinase D family from Loxosceles laeta (SMase I), which has been determined at 1.75-angstrom resolution using the "quick cryo-soaking" technique and phases obtained from a single iodine derivative and data collected from a conventional rotating anode x-ray source. SMase I folds as an (alpha/beta)8 barrel, the interfacial and catalytic sites encompass hydrophobic loops and a negatively charged surface. Substrate binding and/or the transition state are stabilized by a Mg2+ ion, which is coordinated by Glu32, Asp34, Asp91, and solvent molecules. In the proposed acid base catalytic mechanism, His12 and His47 play key roles and are supported by a network of hydrogen bonds between Asp34, Asp52, Trp230, Asp233, and Asn252.
-===Structural basis for ion-coordination and the catalytic mechanism of sphingomyelinases D===
+Structural basis for metal ion coordination and the catalytic mechanism of sphingomyelinases D.,Murakami MT, Fernandes-Pedrosa MF, Tambourgi DV, Arni RK J Biol Chem. 2005 Apr 8;280(14):13658-64. Epub 2005 Jan 14. PMID:15654080<ref>PMID:15654080</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1xx1" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15654080}}, adds the Publication Abstract to the page
+*[[Sphingomyelinase|Sphingomyelinase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15654080 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15654080}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-XX1 is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Loxosceles_laeta Loxosceles laeta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XX1 OCA].
-==Reference==
-<ref group="xtra">PMID:15654080</ref><references group="xtra"/>
 [[Category: Loxosceles laeta]]
-[[Category: Sphingomyelin phosphodiesterase D]]
+[[Category: Arni RK]]
-[[Category: Arni, R K.]]
+[[Category: Murakami MT]]
-[[Category: Murakami, M T.]]
+[[Category: Tambourgi DV]]
-[[Category: Tambourgi, D V.]]
-[[Category: Activity]]
-[[Category: Quick cryo-soaking]]
-[[Category: Smase d]]
-[[Category: Structure]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 07:48:07 2009''