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2osx

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[[Image:2osx.jpg|left|200px]]
 
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==Endo-glycoceramidase II from Rhodococcus sp.: Ganglioside GM3 Complex==
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The line below this paragraph, containing "STRUCTURE_2osx", creates the "Structure Box" on the page.
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<StructureSection load='2osx' size='340' side='right'caption='[[2osx]], [[Resolution|resolution]] 1.10&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2osx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_sp. Rhodococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OSX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OSX FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 1.1&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=16C:N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE'>16C</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene></td></tr>
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{{STRUCTURE_2osx| PDB=2osx | SCENE= }}
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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=2osx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2osx OCA], [https://pdbe.org/2osx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2osx RCSB], [https://www.ebi.ac.uk/pdbsum/2osx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2osx ProSAT]</span></td></tr>
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</table>
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'''Endo-glycoceramidase II from Rhodococcus sp.: Ganglioside GM3 Complex'''
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== Function ==
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[https://www.uniprot.org/uniprot/O33853_RHOSO O33853_RHOSO]
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== Evolutionary Conservation ==
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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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endo-Glycoceramidase, a membrane-associated family 5 glycosidase, deviates from the typical polysaccharide substrate specificity of other soluble members of the family, preferentially hydrolyzing glycosidic linkages between the oligosaccharide and ceramide moieties of gangliosides. Here we report the first x-ray crystal structures of an endo-glycoceramidase from Rhodococcus sp., in the apo form, in complex with the ganglioside G(M3) (Svennerholm ganglioside nomenclature (Svennerholm, L. (1964) J. Lipid Res. 5, 145-155)), and trapped as a glycosyl-enzyme intermediate. These snapshots provide the first molecular insight into enzyme recognition and association with gangliosides, revealing the structural adaptations necessary for glycosidase-catalyzed hydrolysis and detailing a novel ganglioside binding topology. Consistent with the chemical duality of the substrate, the active site of endo-glycoceramidase is split into a wide, polar cavity to bind the polyhydroxylated oligosaccharide moiety and a narrow, hydrophobic tunnel to bind the ceramide lipid chains. The specific interactions with the ceramide polar head group manifest a surprising aglycone specificity, an observation substantiated by our kinetic analyses. Collectively, the reported structural and kinetic data provide insight toward rational redesign of the synthetic glycosynthase mutant of endo-glycoceramidase to enable facile synthesis of nonnatural, therapeutically useful gangliosides.
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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/os/2osx_consurf.spt"</scriptWhenChecked>
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2OSX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rhodococcus_sp. Rhodococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OSX OCA].
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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==Reference==
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</jmolCheckbox>
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Structural and mechanistic analyses of endo-glycoceramidase II, a membrane-associated family 5 glycosidase in the Apo and GM3 ganglioside-bound forms., Caines ME, Vaughan MD, Tarling CA, Hancock SM, Warren RA, Withers SG, Strynadka NC, J Biol Chem. 2007 May 11;282(19):14300-8. Epub 2007 Feb 28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17329247 17329247]
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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=2osx ConSurf].
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[[Category: Endoglycosylceramidase]]
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<div style="clear:both"></div>
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[[Category: Rhodococcus sp.]]
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__TOC__
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[[Category: Single protein]]
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</StructureSection>
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[[Category: Caines, M E.C.]]
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[[Category: Large Structures]]
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[[Category: Strynadka, N C.J.]]
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[[Category: Rhodococcus sp]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 11:35:35 2008''
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[[Category: Caines MEC]]
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[[Category: Strynadka NCJ]]

Current revision

Endo-glycoceramidase II from Rhodococcus sp.: Ganglioside GM3 Complex

PDB ID 2osx

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