This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2zox

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:47, 1 November 2023) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2zox.png|left|200px]]
 
-
<!--
+
==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>
-
-->
+
<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/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/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>
-
<!--
+
==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 1 chain 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==
+
-
<ref group="xtra">PMID:18662675</ref><references group="xtra"/>
+
-
[[Category: Beta-glucosidase]]
+
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Baba, Y.]]
+
[[Category: Large Structures]]
-
[[Category: Hayashi, Y.]]
+
[[Category: Baba Y]]
-
[[Category: Ito, M.]]
+
[[Category: Hayashi Y]]
-
[[Category: Kakuta, Y.]]
+
[[Category: Ito M]]
-
[[Category: Kimura, M.]]
+
[[Category: Kakuta Y]]
-
[[Category: Noguchi, J.]]
+
[[Category: Kimura M]]
-
[[Category: Okino, N.]]
+
[[Category: Noguchi J]]
-
[[Category: Alternative splicing]]
+
[[Category: Okino N]]
-
[[Category: Cytoplasm]]
+
-
[[Category: Glycosidase]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Polymorphism]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:40:54 2009''
+

Current revision

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

PDB ID 2zox

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2zox"
Personal tools