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2jfe

From Proteopedia

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Current revision

The crystal structure of human cytosolic beta-glucosidase

Structural highlights

2jfe 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 2.7Å
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 (hCBG) is a xenobiotic-metabolizing enzyme that hydrolyses certain flavonoid glucosides, with specificity depending on the aglycone moiety, the type of sugar and the linkage between them. In this study, the substrate preference of this enzyme was investigated by mutational analysis, X-ray crystallography and homology modelling. The crystal structure of hCBG was solved by the molecular replacement method and refined at 2.7 A resolution. The main-chain fold of the enzyme belongs to the (beta/alpha)(8) barrel structure, which is common to family 1 glycoside hydrolases. The active site is located at the bottom of a pocket (about 16 A deep) formed by large surface loops, surrounding the C termini of the barrel of beta-strands. As for all the clan of GH-A enzymes, the two catalytic glutamate residues are located on strand 4 (the acid/base Glu165) and on strand 7 (the nucleophile Glu373). Although many features of hCBG were shown to be very similar to previously described enzymes from this family, crucial differences were observed in the surface loops surrounding the aglycone binding site, and these are likely to strongly influence the substrate specificity. The positioning of a substrate molecule (quercetin-4'-glucoside) by homology modelling revealed that hydrophobic interactions dominate the binding of the aglycone moiety. In particular, Val168, Trp345, Phe225, Phe179, Phe334 and Phe433 were identified as likely to be important in determining substrate specificity in hCBG, and site-directed mutagenesis supported a key role for some of these residues.

The crystal structure of human cytosolic beta-glucosidase unravels the substrate aglycone specificity of a family 1 glycoside hydrolase.,Tribolo S, Berrin JG, Kroon PA, Czjzek M, Juge N J Mol Biol. 2007 Jul 27;370(5):964-75. Epub 2007 May 18. PMID:17555766^[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
↑ Tribolo S, Berrin JG, Kroon PA, Czjzek M, Juge N. The crystal structure of human cytosolic beta-glucosidase unravels the substrate aglycone specificity of a family 1 glycoside hydrolase. J Mol Biol. 2007 Jul 27;370(5):964-75. Epub 2007 May 18. PMID:17555766 doi:10.1016/j.jmb.2007.05.034

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/2jfe"

@@ Line 1: / Line 1: @@
-==THE CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC BETA-GLUCOSIDASE==
-<StructureSection load='2jfe' size='340' side='right' caption='[[2jfe]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+==The crystal structure of human cytosolic beta-glucosidase==
+<StructureSection load='2jfe' size='340' side='right'caption='[[2jfe]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2jfe]] 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=2JFE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JFE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2jfe]] 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=2JFE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JFE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.7&#8491;</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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=2jfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jfe OCA], [http://pdbe.org/2jfe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jfe RCSB], [http://www.ebi.ac.uk/pdbsum/2jfe PDBsum]</span></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=2jfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jfe OCA], [https://pdbe.org/2jfe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jfe RCSB], [https://www.ebi.ac.uk/pdbsum/2jfe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jfe 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]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jf/2jfe_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jf/2jfe_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].
+</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=2jfe ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 30: / 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: Berrin, J G]]
+[[Category: Berrin JG]]
-[[Category: Czjzek, M]]
+[[Category: Czjzek M]]
-[[Category: Juge, N]]
+[[Category: Juge N]]
-[[Category: Kroon, P A]]
+[[Category: Kroon PA]]
-[[Category: Tribolo, S]]
+[[Category: Tribolo S]]
-[[Category: Family gh1 beta- glucosidase]]
-[[Category: Flavonoid-glycosidase]]
-[[Category: Glycosidase]]
-[[Category: Human cytosolic beta-glucosidase]]
-[[Category: Hydrolase]]

2jfe

From Proteopedia

Current revision

The crystal structure 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?)

Views

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