|
|
| (One intermediate revision not shown.) |
| Line 3: |
Line 3: |
| | <StructureSection load='2rgl' size='340' side='right'caption='[[2rgl]], [[Resolution|resolution]] 2.20Å' scene=''> | | <StructureSection load='2rgl' size='340' side='right'caption='[[2rgl]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2rgl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Japanese_rice Japanese rice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RGL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RGL FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2rgl]] 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=2RGL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RGL FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2rgm|2rgm]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Os3bglu7 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Japanese rice])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-glucosidase Beta-glucosidase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=2rgl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rgl OCA], [https://pdbe.org/2rgl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rgl RCSB], [https://www.ebi.ac.uk/pdbsum/2rgl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rgl ProSAT]</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=2rgl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rgl OCA], [https://pdbe.org/2rgl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rgl RCSB], [https://www.ebi.ac.uk/pdbsum/2rgl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rgl ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[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>
| + | [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]] |
| Line 17: |
Line 15: |
| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rg/2rgl_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rg/2rgl_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> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
| Line 38: |
Line 36: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Beta-glucosidase]] | |
| - | [[Category: Japanese rice]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Cairns, J R.Ketudat]] | + | [[Category: Oryza sativa Japonica Group]] |
| - | [[Category: Chen, C J]] | + | [[Category: Chen C-J]] |
| - | [[Category: Chuenchor, W]] | + | [[Category: Chuenchor W]] |
| - | [[Category: Pengthaisong, S]] | + | [[Category: Ketudat Cairns JR]] |
| - | [[Category: Robinson, R C]] | + | [[Category: Pengthaisong S]] |
| - | [[Category: Yuvaniyama, J]] | + | [[Category: Robinson RC]] |
| - | [[Category: Beta-alpha-barrel]] | + | [[Category: Yuvaniyama J]] |
| - | [[Category: Glycosidase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
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
The structures of rice BGlu1 beta-glucosidase, a plant beta-glucosidase active in hydrolyzing cell wall-derived oligosaccharides, and its covalent intermediate with 2-deoxy-2-fluoroglucoside have been solved at 2.2 A and 1.55 A resolution, respectively. The structures were similar to the known structures of other glycosyl hydrolase family 1 (GH1) beta-glucosidases, but showed several differences in the loops around the active site, which lead to an open active site with a narrow slot at the bottom, compatible with the hydrolysis of long beta-1,4-linked oligosaccharides. Though this active site structure is somewhat similar to that of the Paenibacillus polymyxa beta-glucosidase B, which hydrolyzes similar oligosaccharides, molecular docking studies indicate that the residues interacting with the substrate beyond the conserved -1 site are completely different, reflecting the independent evolution of plant and microbial GH1 exo-beta-glucanase/beta-glucosidases. The complex with the 2-fluoroglucoside included a glycerol molecule, which appears to be in a position to make a nucleophilic attack on the anomeric carbon in a transglycosylation reaction. The coordination of the hydroxyl groups suggests that sugars are positioned as acceptors for transglycosylation by their interactions with E176, the catalytic acid/base, and Y131, which is conserved in barley BGQ60/beta-II beta-glucosidase, that has oligosaccharide hydrolysis and transglycosylation activity similar to rice BGlu1. As the rice and barley enzymes have different preferences for cellobiose and cellotriose, residues that appeared to interact with docked oligosaccharides were mutated to those of the barley enzyme to see if the relative activities of rice BGlu1 toward these substrates could be changed to those of BGQ60. Although no single residue appeared to be responsible for these differences, I179, N190 and N245 did appear to interact with the substrates.
Structural insights into rice BGlu1 beta-glucosidase oligosaccharide hydrolysis and transglycosylation.,Chuenchor W, Pengthaisong S, Robinson RC, Yuvaniyama J, Oonanant W, Bevan DR, Esen A, Chen CJ, Opassiri R, Svasti J, Cairns JR J Mol Biol. 2008 Apr 4;377(4):1200-15. Epub 2008 Feb 4. PMID:18308333[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, 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
|
