2zox: Difference between revisions

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[[Image:2zox.png|left|200px]]
==Crystal Structure of the Covalent Intermediate of Human Cytosolic beta-Glucosidase==
<StructureSection load='2zox' size='340' side='right' caption='[[2zox]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2zox]] is a 1 chain structure with 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZOX FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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><br>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2e9l|2e9l]], [[2e9m|2e9m]]</td></tr>
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GBA3, CBG, CBGL1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zox FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zox OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zox RCSB], [http://www.ebi.ac.uk/pdbsum/2zox PDBsum]</span></td></tr>
<table>
== 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/initialview01.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/chain_selection.php?pdb_ID=2ata 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.


{{STRUCTURE_2zox|  PDB=2zox  |  SCENE=  }}
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>


===Crystal Structure of the Covalent Intermediate of Human Cytosolic beta-Glucosidase===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
{{ABSTRACT_PUBMED_18662675}}
 
==About this Structure==
[[2zox]] is a 1 chain structure with 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].


==See Also==
==See Also==
*[[Beta-glucosidase|Beta-glucosidase]]
*[[Beta-glucosidase|Beta-glucosidase]]
 
== References ==
==Reference==
<references/>
<ref group="xtra">PMID:018662675</ref><references group="xtra"/>
__TOC__
</StructureSection>
[[Category: Beta-glucosidase]]
[[Category: Beta-glucosidase]]
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]

Revision as of 10:49, 29 September 2014

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

Structural highlights

2zox is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, , , , , ,
Related:2e9l, 2e9m
Gene:GBA3, CBG, CBGL1 (Homo sapiens)
Activity:Beta-glucosidase, with EC number 3.2.1.21
Resources:FirstGlance, OCA, RCSB, PDBsum

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 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[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Noguchi J, Hayashi Y, Baba Y, Okino N, Kimura M, Ito M, Kakuta Y. Crystal structure of the covalent intermediate of human cytosolic beta-glucosidase. Biochem Biophys Res Commun. 2008 Sep 26;374(3):549-52. Epub 2008 Jul 26. PMID:18662675 doi:10.1016/j.bbrc.2008.07.089

2zox, resolution 1.90Å

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