2dds: Difference between revisions

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-{{Seed}}
-[[Image:2dds.png|left|200px]]
-<!--
+==Crystal structure of sphingomyelinase from Bacillus cereus with cobalt ion==
-The line below this paragraph, containing "STRUCTURE_2dds", creates the "Structure Box" on the page.
+<StructureSection load='2dds' size='340' side='right'caption='[[2dds]], [[Resolution|resolution]] 1.80&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'>[[2dds]] is a 4 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=2DDS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DDS 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]] 1.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></td></tr>
-{{STRUCTURE_2dds|  PDB=2dds  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dds OCA], [https://pdbe.org/2dds PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dds RCSB], [https://www.ebi.ac.uk/pdbsum/2dds PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dds ProSAT], [https://www.topsan.org/Proteins/RSGI/2dds 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/2dds_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=2dds ConSurf].
+<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.
-===Crystal structure of sphingomyelinase from Bacillus cereus with cobalt ion===
+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 2dds" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16595670}}, adds the Publication Abstract to the page
+*[[Sphingomyelinase|Sphingomyelinase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16595670 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16595670}}
+__TOC__
+</StructureSection>
-==About this Structure==
-DDS is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDS OCA].
-==Reference==
-<ref group="xtra">PMID:16595670</ref><references group="xtra"/>
 [[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: Ochi, S.]]
+[[Category: Ochi S]]
-[[Category: Oda, M.]]
+[[Category: Oda M]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Sakurai J]]
-[[Category: Sakurai, J.]]
+[[Category: Takahashi M]]
-[[Category: Takahashi, M.]]
+[[Category: Tsuge H]]
-[[Category: Tsuge, H.]]
-[[Category: Dnase i like folding]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 12:57:30 2009''