2f9r

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[[Image:2f9r.gif|left|200px]]
 
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{{Structure
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==Crystal structure of the inactive state of the Smase I, a sphingomyelinase D from Loxosceles laeta venom==
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|PDB= 2f9r |SIZE=350|CAPTION= <scene name='initialview01'>2f9r</scene>, resolution 1.85&Aring;
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<StructureSection load='2f9r' size='340' side='right'caption='[[2f9r]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID'>EPE</scene>
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<table><tr><td colspan='2'>[[2f9r]] 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=2F9R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F9R FirstGlance]. <br>
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|ACTIVITY= [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]
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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]] 1.85&#8491;</td></tr>
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|GENE=
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<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></td></tr>
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}}
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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=2f9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f9r OCA], [https://pdbe.org/2f9r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f9r RCSB], [https://www.ebi.ac.uk/pdbsum/2f9r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f9r ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f9/2f9r_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2f9r ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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'''Crystal structure of the inactive state of the Smase I, a sphingomyelinase D from Loxosceles laeta venom'''
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2f9r" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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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.
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*[[Sphingomyelinase|Sphingomyelinase]]
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== References ==
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==About this Structure==
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<references/>
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2F9R is a [[Single protein]] structure of sequence 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=2F9R OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Large Structures]]
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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:[http://www.ncbi.nlm.nih.gov/pubmed/15654080 15654080]
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[[Category: Loxosceles laeta]]
[[Category: Loxosceles laeta]]
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[[Category: Single protein]]
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[[Category: Arni RK]]
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[[Category: Sphingomyelin phosphodiesterase D]]
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[[Category: Betzel C]]
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[[Category: Arni, R K.]]
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[[Category: Fernandes-Pedrosa MF]]
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[[Category: Betzel, C.]]
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[[Category: Gabdoulkhakov A]]
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[[Category: Fernandes-Pedrosa, M F.]]
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[[Category: Murakami MT]]
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[[Category: Gabdoulkhakov, A.]]
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[[Category: Tambourgi DV]]
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[[Category: Murakami, M T.]]
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[[Category: Tambourgi, D V.]]
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[[Category: EPE]]
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[[Category: MG]]
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[[Category: catalytic activity]]
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[[Category: inactive state]]
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[[Category: magnesium-binding site]]
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[[Category: sphingomyelinase d]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:49:49 2008''
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Current revision

Crystal structure of the inactive state of the Smase I, a sphingomyelinase D from Loxosceles laeta venom

PDB ID 2f9r

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