2zox: Difference between revisions
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New page: '''Unreleased structure''' The entry 2zox is ON HOLD until sometime in the future Authors: Noguchi, J., Hayashi, Y., Baba, Y., Okino, N., Kimura, M., Ito, M., Kakuta, Y. Description: C... |
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==Crystal Structure of the Covalent Intermediate of Human Cytosolic beta-Glucosidase== | |||
<StructureSection load='2zox' size='340' side='right'caption='[[2zox]], [[Resolution|resolution]] 1.90Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2zox]] 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=2ZOX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZOX 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]] 1.9Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OLA:OLEIC+ACID'>OLA</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=PNG:4-NITROPHENYL-ALPHA-D-GLUCOPYRANOSIDE'>PNG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=2zox FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zox OCA], [https://pdbe.org/2zox PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zox RCSB], [https://www.ebi.ac.uk/pdbsum/2zox PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zox ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[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> | |||
== 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/zo/2zox_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=2zox ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Human cytosolic beta-glucosidase, also known as klotho-related protein (KLrP, GBA3), is an enzyme that hydrolyzes various beta-D-glucosides, including glucosylceramide. We recently reported the crystal structure of KLrP in complex with glucose [Y. Hayashi, N. Okino, Y. Kakuta, T. Shikanai, M. Tani, H. Narimatsu, M. Ito, Klotho-related protein is a novel cytosolic neutral beta-glycosylceramidase, J. Biol. Chem. 282 (2007) 30889-30900]. Here, we report the crystal structure of a covalent intermediate of the KLrP mutant E165Q, in which glucose was covalently bound to a nucleophile, Glu(373). The structure confirms the double displacement mechanism of the retaining beta-glucosidase. In addition, the structure suggests that a water molecule could be involved in the stabilization of transition states through a sugar, 2-hydroxyl. | |||
Crystal structure of the covalent intermediate of human cytosolic beta-glucosidase.,Noguchi J, Hayashi Y, Baba Y, Okino N, Kimura M, Ito M, Kakuta Y Biochem Biophys Res Commun. 2008 Sep 26;374(3):549-52. Epub 2008 Jul 26. PMID:18662675<ref>PMID:18662675</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2zox" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Beta-glucosidase 3D structures|Beta-glucosidase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Homo sapiens]] | |||
[[Category: Large Structures]] | |||
[[Category: Baba Y]] | |||
[[Category: Hayashi Y]] | |||
[[Category: Ito M]] | |||
[[Category: Kakuta Y]] | |||
[[Category: Kimura M]] | |||
[[Category: Noguchi J]] | |||
[[Category: Okino N]] | |||
Latest revision as of 11:42, 30 October 2024
Crystal Structure of the Covalent Intermediate of Human Cytosolic beta-GlucosidaseCrystal Structure of the Covalent Intermediate of Human Cytosolic beta-Glucosidase
Structural highlights
FunctionGBA3_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.[1] [2] [3] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedHuman cytosolic beta-glucosidase, also known as klotho-related protein (KLrP, GBA3), is an enzyme that hydrolyzes various beta-D-glucosides, including glucosylceramide. We recently reported the crystal structure of KLrP in complex with glucose [Y. Hayashi, N. Okino, Y. Kakuta, T. Shikanai, M. Tani, H. Narimatsu, M. Ito, Klotho-related protein is a novel cytosolic neutral beta-glycosylceramidase, J. Biol. Chem. 282 (2007) 30889-30900]. Here, we report the crystal structure of a covalent intermediate of the KLrP mutant E165Q, in which glucose was covalently bound to a nucleophile, Glu(373). The structure confirms the double displacement mechanism of the retaining beta-glucosidase. In addition, the structure suggests that a water molecule could be involved in the stabilization of transition states through a sugar, 2-hydroxyl. Crystal structure of the covalent intermediate of human cytosolic beta-glucosidase.,Noguchi J, Hayashi Y, Baba Y, Okino N, Kimura M, Ito M, Kakuta Y Biochem Biophys Res Commun. 2008 Sep 26;374(3):549-52. Epub 2008 Jul 26. PMID:18662675[4] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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