2zox

From Proteopedia

(Difference between revisions)

Current revision

Crystal 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.
Method:	X-ray diffraction, Resolution 1.9Å
Ligands:	, , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[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 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^[4]

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

References

↑ Berrin JG, McLauchlan WR, Needs P, Williamson G, Puigserver A, Kroon PA, Juge N. Functional expression of human liver cytosolic beta-glucosidase in Pichia pastoris. Insights into its role in the metabolism of dietary glucosides. Eur J Biochem. 2002 Jan;269(1):249-58. PMID:11784319
↑ Nemeth K, Plumb GW, Berrin JG, Juge N, Jacob R, Naim HY, Williamson G, Swallow DM, Kroon PA. Deglycosylation by small intestinal epithelial cell beta-glucosidases is a critical step in the absorption and metabolism of dietary flavonoid glycosides in humans. Eur J Nutr. 2003 Jan;42(1):29-42. PMID:12594539 doi:http://dx.doi.org/10.1007/s00394-003-0397-3
↑ Hayashi Y, Okino N, Kakuta Y, Shikanai T, Tani M, Narimatsu H, Ito M. Klotho-related protein is a novel cytosolic neutral beta-glycosylceramidase. J Biol Chem. 2007 Oct 19;282(42):30889-900. Epub 2007 Jun 26. PMID:17595169 doi:10.1074/jbc.M700832200
↑ 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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
 ==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=''>
+<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/Human Human]. 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>
+<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='ligand'><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></td></tr>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2e9l|2e9l]], [[2e9m|2e9m]]</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='gene'><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 HUMAN])</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>
-<tr id='activity'><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 id='resources'><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://pdbe.org/2zox PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zox RCSB], [http://www.ebi.ac.uk/pdbsum/2zox PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zox ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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]]
@@ Line 17: / Line 15: @@
   <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>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 33: / Line 31: @@
 ==See Also==
-*[[Beta-glucosidase|Beta-glucosidase]]
+*[[Beta-glucosidase 3D structures|Beta-glucosidase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Beta-glucosidase]]
+[[Category: Homo sapiens]]
-[[Category: Human]]
+[[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: Glycosidase]]
-[[Category: Hydrolase]]

2zox

From Proteopedia

Current revision

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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