2zox: Difference between revisions

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{{Seed}}
[[Image:2zox.jpg|left|200px]]


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==Crystal Structure of the Covalent Intermediate of Human Cytosolic beta-Glucosidase==
The line below this paragraph, containing "STRUCTURE_2zox", creates the "Structure Box" on the page.
<StructureSection load='2zox' size='340' side='right'caption='[[2zox]], [[Resolution|resolution]] 1.90&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'>[[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>
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]] 1.9&#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=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>
{{STRUCTURE_2zox|  PDB=2zox  |  SCENE=  }}
<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===
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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2zox" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_18662675}}, adds the Publication Abstract to the page
*[[Beta-glucosidase 3D structures|Beta-glucosidase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 18662675 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_18662675}}
__TOC__
 
</StructureSection>
==About this Structure==
2ZOX is a [[Single protein]] structure of sequence from [http://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].
 
==Reference==
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:[http://www.ncbi.nlm.nih.gov/pubmed/18662675 18662675]
[[Category: Beta-glucosidase]]
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Baba, Y.]]
[[Category: Baba Y]]
[[Category: Hayashi, Y.]]
[[Category: Hayashi Y]]
[[Category: Ito, M.]]
[[Category: Ito M]]
[[Category: Kakuta, Y.]]
[[Category: Kakuta Y]]
[[Category: Kimura, M.]]
[[Category: Kimura M]]
[[Category: Noguchi, J.]]
[[Category: Noguchi J]]
[[Category: Okino, N.]]
[[Category: Okino N]]
[[Category: Alternative splicing]]
[[Category: Cytoplasm]]
[[Category: Glycosidase]]
[[Category: Hydrolase]]
[[Category: Polymorphism]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct  1 21:39:45 2008''

Latest revision as of 08:42, 30 October 2024

Crystal Structure of the Covalent Intermediate of Human Cytosolic beta-Glucosidase

2zox, resolution 1.90Å

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