2e9m

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[[Image:2e9m.gif|left|200px]]<br /><applet load="2e9m" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2e9m, resolution 1.80&Aring;" />
 
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'''Crystal Structure of human Cytosolic Neutral beta-Glycosylceramidase (Klotho-related Prote:KLrP) complex with Galactose and fatty acids'''<br />
 
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==Overview==
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==Crystal Structure of human Cytosolic Neutral beta-Glycosylceramidase (Klotho-related Prote:KLrP) complex with Galactose and fatty acids==
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Using C6-NBD-glucosylceramide (GlcCer) as a substrate, we detected the, activity of a conduritol B epoxide (CBE)-insensitive neutral, glycosylceramidase in cytosolic fractions of zebrafish embryos, mouse and, rat brains and human fibroblasts. The candidates for the enzyme were, assigned to the Klotho (KL) whose family members share a -glucosidase-like, domain but whose natural substrates unknown. Among this family, only the, KL-related protein (KLrP) is capable of degrading C6-NBD-GlcCer when, expressed in CHOP cells, in which Myc-tagged KLrP was exclusively, distributed in the cytosol. In addition, knockdown of the endogenous KLrP, by siRNA increased the cellular level of GlcCer. The purified recombinant, KLrP hydrolyzed 4-methylumbelliferyl-glucose, C6-NBD-GlcCer, and authentic, GlcCer at pH 6.0. The enzyme also hydrolyzed the corresponding galactosyl, derivatives but each kcat/Km was much lower than that for glucosyl, derivatives. The X-ray structure of KLrP at 1.6 resolution revealed that, KLrP is a (/)8 TIM barrel, in which E165 and E373 at the carboxyl termini, of -strands 4 and 7 could function as an acid/base catalyst and, nucleophile, respectively. The distance between carboxyl oxygens of these, two residues is 5.3 indicating the reaction proceeds with the anomeric, carbon retained upon cleavage, rather than inverted. The substrate-binding, cleft of the enzyme was occupied with palmitic acid and oleic acid when, the recombinant protein was crystallized in a complex with glucose. GlcCer, was found to well fit the cleft of the crystal structure of KLrP., Collectively, KLrP was identified as a cytosolic neutral, glycosylceramidase which could be involved in a novel non-lysosomal, catabolic pathway of GlcCer.
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<StructureSection load='2e9m' size='340' side='right'caption='[[2e9m]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2e9m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E9M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E9M FirstGlance]. <br>
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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]] 1.8&#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=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=OLA:OLEIC+ACID'>OLA</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene></td></tr>
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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=2e9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e9m OCA], [https://pdbe.org/2e9m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e9m RCSB], [https://www.ebi.ac.uk/pdbsum/2e9m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e9m ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/GBA3_HUMAN GBA3_HUMAN] Glycosidase probably involved in the intestinal absorption and metabolism of dietary flavonoid glycosides. Able to hydrolyze a broad variety of glycosides including phytoestrogens, flavonols, flavones, flavanones and cyanogens. Possesses beta-glycosylceramidase activity and may be involved in a nonlysosomal catabolic pathway of glycosylceramide.<ref>PMID:11784319</ref> <ref>PMID:12594539</ref> <ref>PMID:17595169</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e9/2e9m_consurf.spt"</scriptWhenChecked>
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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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</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=2e9m ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Using C6-NBD-glucosylceramide (GlcCer) as a substrate, we detected the activity of a conduritol B epoxide-insensitive neutral glycosylceramidase in cytosolic fractions of zebrafish embryos, mouse and rat brains, and human fibroblasts. The candidates for the enzyme were assigned to the Klotho (KL), whose family members share a beta-glucosidase-like domain but whose natural substrates are unknown. Among this family, only the KL-related protein (KLrP) is capable of degrading C6-NBD-GlcCer when expressed in CHOP cells, in which Myc-tagged KLrP was exclusively distributed in the cytosol. In addition, knockdown of the endogenous KLrP by small interfering RNA increased the cellular level of GlcCer. The purified recombinant KLrP hydrolyzed 4-methylumbelliferyl-glucose, C6-NBD-GlcCer, and authentic GlcCer at pH 6.0. The enzyme also hydrolyzed the corresponding galactosyl derivatives, but each k(cat)/Km was much lower than that for glucosyl derivatives. The x-ray structure of KLrP at 1.6A resolution revealed that KLrP is a (beta/alpha)8 TIM barrel, in which Glu(165) and Glu(373) at the carboxyl termini of beta-strands 4 and 7 could function as an acid/base catalyst and nucleophile, respectively. The substrate-binding cleft of the enzyme was occupied with palmitic acid and oleic acid when the recombinant protein was crystallized in a complex with glucose. GlcCer was found to fit well the cleft of the crystal structure of KLrP. Collectively, KLrP was identified as a cytosolic neutral glycosylceramidase that could be involved in a novel nonlysosomal catabolic pathway of GlcCer.
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==About this Structure==
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Klotho-related protein is a novel cytosolic neutral beta-glycosylceramidase.,Hayashi Y, Okino N, Kakuta Y, Shikanai T, Tani M, Narimatsu H, Ito M J Biol Chem. 2007 Oct 19;282(42):30889-900. Epub 2007 Jun 26. PMID:17595169<ref>PMID:17595169</ref>
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2E9M is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=GAL:'>GAL</scene>, <scene name='pdbligand=PLM:'>PLM</scene> and <scene name='pdbligand=OLA:'>OLA</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Beta-glucosidase Beta-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.21 3.2.1.21] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E9M OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Klotho-related protein is a novel cytosolic neutral beta -glycosylceramidase., Hayashi Y, Okino N, Kakuta Y, Shiknai T, Tani M, Narimatsu H, Ito M, J Biol Chem. 2007 Jun 26;. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17595169 17595169]
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</div>
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[[Category: Beta-glucosidase]]
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<div class="pdbe-citations 2e9m" style="background-color:#fffaf0;"></div>
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[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Hayashi, Y.]]
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[[Category: Ito, M.]]
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[[Category: Kakuta, Y.]]
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[[Category: Okino, N.]]
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[[Category: GAL]]
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[[Category: OLA]]
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[[Category: PLM]]
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[[Category: hydrolase]]
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[[Category: novel cytosolic neutral beta-glycosylceramidase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 13:38:10 2008''
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==See Also==
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*[[Beta-glucosidase 3D structures|Beta-glucosidase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Homo sapiens]]
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[[Category: Large Structures]]
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[[Category: Hayashi Y]]
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[[Category: Ito M]]
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[[Category: Kakuta Y]]
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[[Category: Okino N]]

Current revision

Crystal Structure of human Cytosolic Neutral beta-Glycosylceramidase (Klotho-related Prote:KLrP) complex with Galactose and fatty acids

PDB ID 2e9m

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