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2osw

From Proteopedia

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[[Image:2osw.jpg|left|200px]]<br /><applet load="2osw" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2osw, resolution 1.600&Aring;" />
 
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'''Endo-glycoceramidase II from Rhodococcus sp.'''<br />
 
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==Overview==
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==Endo-glycoceramidase II from Rhodococcus sp.==
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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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<StructureSection load='2osw' size='340' side='right'caption='[[2osw]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[2osw]] is a 2 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=2OSW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OSW FirstGlance]. <br>
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2OSW is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rhodococcus_sp. Rhodococcus sp.] with <scene name='pdbligand=NA:'>NA</scene> and <scene name='pdbligand=TRS:'>TRS</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Endoglycosylceramidase Endoglycosylceramidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.123 3.2.1.123] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OSW OCA].
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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]] 1.6&#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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
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==Reference==
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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=2osw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2osw OCA], [https://pdbe.org/2osw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2osw RCSB], [https://www.ebi.ac.uk/pdbsum/2osw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2osw ProSAT]</span></td></tr>
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=17329247 17329247]
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</table>
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[[Category: Endoglycosylceramidase]]
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== Function ==
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[[Category: Rhodococcus sp.]]
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[https://www.uniprot.org/uniprot/O33853_RHOSO O33853_RHOSO]
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[[Category: Single protein]]
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== Evolutionary Conservation ==
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[[Category: Caines, M E.C.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Strynadka, N C.J.]]
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Check<jmol>
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[[Category: NA]]
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<jmolCheckbox>
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[[Category: TRS]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/os/2osw_consurf.spt"</scriptWhenChecked>
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[[Category: (alpha/beta)8 (tim) barrel]]
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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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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:22:10 2008''
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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=2osw ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Rhodococcus sp]]
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[[Category: Caines MEC]]
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[[Category: Strynadka NCJ]]

Current revision

Endo-glycoceramidase II from Rhodococcus sp.

PDB ID 2osw

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