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==Crystal structure of sphingomyelinase from Bacillus cereus with magnesium ion==
==Crystal structure of sphingomyelinase from Bacillus cereus with magnesium ion==
<StructureSection load='2ddt' size='340' side='right' caption='[[2ddt]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='2ddt' size='340' side='right'caption='[[2ddt]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2ddt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_14579 Atcc 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DDT FirstGlance]. <br>
<table><tr><td colspan='2'>[[2ddt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DDT FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.8&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2ddr|2ddr]], [[2dds|2dds]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12] </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=2ddt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddt OCA], [https://pdbe.org/2ddt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ddt RCSB], [https://www.ebi.ac.uk/pdbsum/2ddt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ddt ProSAT], [https://www.topsan.org/Proteins/RSGI/2ddt TOPSAN]</span></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=2ddt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddt OCA], [http://pdbe.org/2ddt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ddt RCSB], [http://www.ebi.ac.uk/pdbsum/2ddt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ddt ProSAT], [http://www.topsan.org/Proteins/RSGI/2ddt TOPSAN]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/PHL2_BACCE PHL2_BACCE]] Required, with sphingomyelinase, to effect target cell lysis (hemolysis).  
[https://www.uniprot.org/uniprot/PHL2_BACCE PHL2_BACCE] Required, with sphingomyelinase, to effect target cell lysis (hemolysis).
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=2ddt ConSurf].
</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=2ddt ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Sphingomyelinase (SMase) from Bacillus cereus (Bc-SMase) hydrolyzes sphingomyelin to phosphocholine and ceramide in a divalent metal ion-dependent manner. Bc-SMase is a homologue of mammalian neutral SMase (nSMase) and mimics the actions of the endogenous mammalian nSMase in causing differentiation, development, aging, and apoptosis. Thus Bc-SMase may be a good model for the poorly characterized mammalian nSMase. The metal ion activation of sphingomyelinase activity of Bc-SMase was in the order Co2+ &gt; or = Mn2+ &gt; or = Mg2+ &gt;&gt; Ca2+ &gt; or = Sr2+. The first crystal structures of Bc-SMase bound to Co2+, Mg2+, or Ca2+ were determined. The water-bridged double divalent metal ions at the center of the cleft in both the Co2+- and Mg2+-bound forms were concluded to be the catalytic architecture required for sphingomyelinase activity. In contrast, the architecture of Ca2+ binding at the site showed only one binding site. A further single metal-binding site exists at one side edge of the cleft. Based on the highly conserved nature of the residues of the binding sites, the crystal structure of Bc-SMase with bound Mg2+ or Co2+ may provide a common structural framework applicable to phosphohydrolases belonging to the DNase I-like folding superfamily. In addition, the structural features and site-directed mutagenesis suggest that the specific beta-hairpin with the aromatic amino acid residues participates in binding to the membrane-bound sphingomyelin substrate.
Structural basis of the sphingomyelin phosphodiesterase activity in neutral sphingomyelinase from Bacillus cereus.,Ago H, Oda M, Takahashi M, Tsuge H, Ochi S, Katunuma N, Miyano M, Sakurai J J Biol Chem. 2006 Jun 9;281(23):16157-67. Epub 2006 Apr 4. PMID:16595670<ref>PMID:16595670</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2ddt" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Sphingomyelinase|Sphingomyelinase]]
*[[Sphingomyelinase|Sphingomyelinase]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 14579]]
[[Category: Bacillus cereus]]
[[Category: Sphingomyelin phosphodiesterase]]
[[Category: Large Structures]]
[[Category: Ago, H]]
[[Category: Ago H]]
[[Category: Katunuma, N]]
[[Category: Katunuma N]]
[[Category: Miyano, M]]
[[Category: Miyano M]]
[[Category: Oda, M]]
[[Category: Oda M]]
[[Category: Structural genomic]]
[[Category: Sakurai J]]
[[Category: Sakurai, J]]
[[Category: Tsuge H]]
[[Category: Tsuge, H]]
[[Category: Dnase i like folding]]
[[Category: Hydrolase]]
[[Category: Rsgi]]

Latest revision as of 16:47, 13 March 2024

Crystal structure of sphingomyelinase from Bacillus cereus with magnesium ionCrystal structure of sphingomyelinase from Bacillus cereus with magnesium ion

Structural highlights

2ddt is a 2 chain structure with sequence from Bacillus cereus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.8Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

PHL2_BACCE Required, with sphingomyelinase, to effect target cell lysis (hemolysis).

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2ddt, resolution 1.80Å

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