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[[Image:2ddt.gif|left|200px]]<br /><applet load="2ddt" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2ddt, resolution 1.80&Aring;" />
'''Crystal structure of sphingomyelinase from Bacillus cereus with magnesium ion'''<br />


==Overview==
==Crystal structure of sphingomyelinase from Bacillus cereus with magnesium ion==
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.
<StructureSection load='2ddt' size='340' side='right'caption='[[2ddt]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
<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='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='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='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>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PHL2_BACCE PHL2_BACCE] Required, with sphingomyelinase, to effect target cell lysis (hemolysis).
== 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/dd/2ddt_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2ddt ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2DDT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=MES:'>MES</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDT OCA].
*[[Sphingomyelinase|Sphingomyelinase]]
 
__TOC__
==Reference==
</StructureSection>
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16595670 16595670]
[[Category: Bacillus cereus]]
[[Category: Bacillus cereus]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Sphingomyelin phosphodiesterase]]
[[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: Sakurai J]]
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
[[Category: Tsuge H]]
[[Category: Sakurai, J.]]
[[Category: Tsuge, H.]]
[[Category: MES]]
[[Category: MG]]
[[Category: SO4]]
[[Category: dnase i like folding]]
[[Category: riken structural genomics/proteomics initiative]]
[[Category: rsgi]]
[[Category: structural genomics]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:57:46 2008''

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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