3gnr: Difference between revisions
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==Crystal Structure of a Rice Os3BGlu6 Beta-Glucosidase with covalently bound 2-deoxy-2-fluoroglucoside to the catalytic nucleophile E396== | ==Crystal Structure of a Rice Os3BGlu6 Beta-Glucosidase with covalently bound 2-deoxy-2-fluoroglucoside to the catalytic nucleophile E396== | ||
<StructureSection load='3gnr' size='340' side='right' caption='[[3gnr]], [[Resolution|resolution]] 1.81Å' scene=''> | <StructureSection load='3gnr' size='340' side='right'caption='[[3gnr]], [[Resolution|resolution]] 1.81Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3gnr]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3gnr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa_Japonica_Group Oryza sativa Japonica Group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GNR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GNR FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.81Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G2F:2-DEOXY-2-FLUORO-ALPHA-D-GLUCOPYRANOSE'>G2F</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr> | |||
<tr id=' | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3gnr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gnr OCA], [https://pdbe.org/3gnr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gnr RCSB], [https://www.ebi.ac.uk/pdbsum/3gnr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gnr ProSAT]</span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/BGL06_ORYSJ BGL06_ORYSJ] Hydrolyzes glycosides, oligosaccharides and hydrophobic glycosides. | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gn/3gnr_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gn/3gnr_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/ | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=3gnr ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 3gnr" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Beta-glucosidase|Beta-glucosidase]] | *[[Beta-glucosidase 3D structures|Beta-glucosidase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Oryza sativa | [[Category: Oryza sativa Japonica Group]] | ||
[[Category: Akiyama | [[Category: Akiyama T]] | ||
[[Category: Cairns | [[Category: Cairns JRK]] | ||
[[Category: Kuaprasert | [[Category: Kuaprasert B]] | ||
[[Category: Opassiri | [[Category: Opassiri R]] | ||
[[Category: Seshadri | [[Category: Seshadri S]] | ||
Latest revision as of 08:51, 17 October 2024
Crystal Structure of a Rice Os3BGlu6 Beta-Glucosidase with covalently bound 2-deoxy-2-fluoroglucoside to the catalytic nucleophile E396Crystal Structure of a Rice Os3BGlu6 Beta-Glucosidase with covalently bound 2-deoxy-2-fluoroglucoside to the catalytic nucleophile E396
Structural highlights
FunctionBGL06_ORYSJ Hydrolyzes glycosides, oligosaccharides and hydrophobic glycosides. 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 PubMedGlycoside hydrolase family 1 (GH1) beta-glucosidases play roles in many processes in plants, such as chemical defense, alkaloid metabolism, hydrolysis of cell wall-derived oligosaccharides, phytohormone regulation, and lignification. However, the functions of most of the 34 GH1 gene products in rice (Oryza sativa) are unknown. Os3BGlu6, a rice beta-glucosidase representing a previously uncharacterized phylogenetic cluster of GH1, was produced in recombinant Escherichia coli. Os3BGlu6 hydrolyzed p-nitrophenyl (pNP)-beta-d-fucoside (k(cat)/K(m) = 67 mm(-1) s(-1)), pNP-beta-d-glucoside (k(cat)/K(m) = 6.2 mm(-1) s(-1)), and pNP-beta-d-galactoside (k(cat)/K(m) = 1.6 mm(-1)s(-1)) efficiently but had little activity toward other pNP glycosides. It also had high activity toward n-octyl-beta-d-glucoside and beta-(1-->3)- and beta-(1-->2)-linked disaccharides and was able to hydrolyze apigenin beta-glucoside and several other natural glycosides. Crystal structures of Os3BGlu6 and its complexes with a covalent intermediate, 2-deoxy-2-fluoroglucoside, and a nonhydrolyzable substrate analog, n-octyl-beta-d-thioglucopyranoside, were solved at 1.83, 1.81, and 1.80 A resolution, respectively. The position of the covalently trapped 2-F-glucosyl residue in the enzyme was similar to that in a 2-F-glucosyl intermediate complex of Os3BGlu7 (rice BGlu1). The side chain of methionine-251 in the mouth of the active site appeared to block the binding of extended beta-(1-->4)-linked oligosaccharides and interact with the hydrophobic aglycone of n-octyl-beta-d-thioglucopyranoside. This correlates with the preference of Os3BGlu6 for short oligosaccharides and hydrophobic glycosides. Structural and enzymatic characterization of Os3BGlu6, a rice beta-glucosidase hydrolyzing hydrophobic glycosides and (1->3)- and (1->2)-linked disaccharides.,Seshadri S, Akiyama T, Opassiri R, Kuaprasert B, Cairns JK Plant Physiol. 2009 Sep;151(1):47-58. Epub 2009 Jul 8. PMID:19587102[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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