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| | ==Semi-active E176Q mutant of rice BGlu1, a plant exoglucanase/beta-glucosidase== | | ==Semi-active E176Q mutant of rice BGlu1, a plant exoglucanase/beta-glucosidase== |
| - | <StructureSection load='3f5j' size='340' side='right' caption='[[3f5j]], [[Resolution|resolution]] 1.95Å' scene=''> | + | <StructureSection load='3f5j' size='340' side='right'caption='[[3f5j]], [[Resolution|resolution]] 1.95Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3f5j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Japanese_rice Japanese rice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F5J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3F5J FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3f5j]] is a 2 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=3F5J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F5J FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CTT:BETA-D-GLUCOPYRANOSYL-(1- 4)-BETA-D-GLUCOPYRANOSYL-(1- 4)-BETA-D-GLUCOPYRANOSYL-(1- 4)-BETA-D-GLUCOPYRANOSE'>CTT</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.95Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2rgl|2rgl]], [[2rgm|2rgm]], [[3f4v|3f4v]], [[3ahv|3ahv]], [[3f5k|3f5k]], [[3f5l|3f5l]], [[3aht|3aht]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=PRD_900011:beta-cellotetraose'>PRD_900011</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Os3bglu7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Japanese rice])</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=3f5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f5j OCA], [https://pdbe.org/3f5j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f5j RCSB], [https://www.ebi.ac.uk/pdbsum/3f5j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f5j 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=3f5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f5j OCA], [http://pdbe.org/3f5j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3f5j RCSB], [http://www.ebi.ac.uk/pdbsum/3f5j PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/BGL07_ORYSJ BGL07_ORYSJ]] Hydrolyzes p-nitrophenyl beta-D-glucoside, p-nitrophenyl beta-D-mannoside, p-nitrophenyl beta-D-galactoside, p-nitrophenyl beta-D-xyloside, p-nitrophenyl beta-D-fucoside, p-nitrophenyl beta-L-arabinoside, oligosaccharides, pyridoxine beta-D-glucoside and the cyanogenic glucosides amygdalin, prunasin and dhurrin. Possesses pyridoxine transglucosylation activity.<ref>PMID:14692878</ref> <ref>PMID:19766588</ref> <ref>PMID:18308333</ref> | + | [https://www.uniprot.org/uniprot/BGL07_ORYSJ BGL07_ORYSJ] Hydrolyzes p-nitrophenyl beta-D-glucoside, p-nitrophenyl beta-D-mannoside, p-nitrophenyl beta-D-galactoside, p-nitrophenyl beta-D-xyloside, p-nitrophenyl beta-D-fucoside, p-nitrophenyl beta-L-arabinoside, oligosaccharides, pyridoxine beta-D-glucoside and the cyanogenic glucosides amygdalin, prunasin and dhurrin. Possesses pyridoxine transglucosylation activity.<ref>PMID:14692878</ref> <ref>PMID:19766588</ref> <ref>PMID:18308333</ref> |
| | == 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/f5/3f5j_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f5/3f5j_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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| | ==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: Beta-glucosidase]] | + | [[Category: Large Structures]] |
| - | [[Category: Japanese rice]] | + | [[Category: Oryza sativa Japonica Group]] |
| - | [[Category: Cairns, J R.Ketudat]] | + | [[Category: Chen C-J]] |
| - | [[Category: Chen, C J]] | + | [[Category: Chuenchor W]] |
| - | [[Category: Chuenchor, W]] | + | [[Category: Ketudat Cairns JR]] |
| - | [[Category: Pengthaisong, S]] | + | [[Category: Pengthaisong S]] |
| - | [[Category: Robinson, R C]] | + | [[Category: Robinson RC]] |
| - | [[Category: Yuvaniyama, J]] | + | [[Category: Yuvaniyama J]] |
| - | [[Category: Beta-alpha-barrel]]
| + | |
| - | [[Category: Glycosidase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
3f5j is a 2 chain structure with sequence from Oryza sativa Japonica Group. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.95Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
BGL07_ORYSJ Hydrolyzes p-nitrophenyl beta-D-glucoside, p-nitrophenyl beta-D-mannoside, p-nitrophenyl beta-D-galactoside, p-nitrophenyl beta-D-xyloside, p-nitrophenyl beta-D-fucoside, p-nitrophenyl beta-L-arabinoside, oligosaccharides, pyridoxine beta-D-glucoside and the cyanogenic glucosides amygdalin, prunasin and dhurrin. Possesses pyridoxine transglucosylation activity.[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
Rice BGlu1 beta-glucosidase is an oligosaccharide exoglucosidase that binds to six beta-(1-->4)-linked glucosyl residues in its active site cleft. Here, we demonstrate that a BGlu1 E176Q active site mutant can be effectively rescued by small nucleophiles, such as acetate, azide and ascorbate, for hydrolysis of aryl glycosides in a pH-independent manner above pH5, consistent with the role of E176 as the catalytic acid-base. Cellotriose, cellotetraose, cellopentaose, cellohexaose and laminaribiose are not hydrolyzed by the mutant and instead exhibit competitive inhibition. The structures of the BGlu1 E176Q, its complexes with cellotetraose, cellopentaose and laminaribiose, and its covalent intermediate with 2-deoxy-2-fluoroglucoside were determined at 1.65, 1.95, 1.80, 2.80, and 1.90A resolution, respectively. The Q176Nepsilon was found to hydrogen bond to the glycosidic oxygen of the scissile bond, thereby explaining its high activity. The enzyme interacts with cellooligosaccharides through direct hydrogen bonds to the nonreducing terminal glucosyl residue. However, interaction with the other glucosyl residues is predominantly mediated through water molecules, with the exception of a direct hydrogen bond from N245 to glucosyl residue 3, consistent with the apparent high binding energy at this residue. Hydrophobic interactions with the aromatic sidechain of W358 appear to orient glucosyl residues 2 and 3, while Y341 orients glucosyl residues 4 and 5. In contrast, laminaribiose has its second glucosyl residue positioned to allow direct hydrogen bonding between its O2 and Q176 Oepsilon and O1 and N245. These are the first GH1 glycoside hydrolase family structures to show oligosaccharide binding in the hydrolytic configuration.
The structural basis of oligosaccharide binding by rice BGlu1 beta-glucosidase.,Chuenchor W, Pengthaisong S, Robinson RC, Yuvaniyama J, Svasti J, Cairns JR J Struct Biol. 2011 Jan;173(1):169-79. Epub 2010 Sep 25. PMID:20884352[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Opassiri R, Hua Y, Wara-Aswapati O, Akiyama T, Svasti J, Esen A, Ketudat Cairns JR. Beta-glucosidase, exo-beta-glucanase and pyridoxine transglucosylase activities of rice BGlu1. Biochem J. 2004 Apr 1;379(Pt 1):125-31. PMID:14692878 doi:http://dx.doi.org/10.1042/BJ20031485
- ↑ Kuntothom T, Luang S, Harvey AJ, Fincher GB, Opassiri R, Hrmova M, Ketudat Cairns JR. Rice family GH1 glycoside hydrolases with beta-D-glucosidase and beta-D-mannosidase activities. Arch Biochem Biophys. 2009 Nov;491(1-2):85-95. doi: 10.1016/j.abb.2009.09.004., Epub 2009 Sep 18. PMID:19766588 doi:http://dx.doi.org/10.1016/j.abb.2009.09.004
- ↑ Chuenchor W, Pengthaisong S, Robinson RC, Yuvaniyama J, Oonanant W, Bevan DR, Esen A, Chen CJ, Opassiri R, Svasti J, Cairns JR. Structural insights into rice BGlu1 beta-glucosidase oligosaccharide hydrolysis and transglycosylation. J Mol Biol. 2008 Apr 4;377(4):1200-15. Epub 2008 Feb 4. PMID:18308333 doi:10.1016/j.jmb.2008.01.076
- ↑ Chuenchor W, Pengthaisong S, Robinson RC, Yuvaniyama J, Svasti J, Cairns JR. The structural basis of oligosaccharide binding by rice BGlu1 beta-glucosidase. J Struct Biol. 2011 Jan;173(1):169-79. Epub 2010 Sep 25. PMID:20884352 doi:10.1016/j.jsb.2010.09.021
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