3f5k: Difference between revisions
New page: '''Unreleased structure''' The entry 3f5k is ON HOLD Authors: Chuenchor, W., Ketudat Cairns, J.R., Pengthaisong, S., Robinson, R.C., Yuvaniyama, J., Chen, C.-J. Description: Semi-activ... |
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The | ==Semi-active E176Q mutant of rice BGlu1, a plant exoglucanase/beta-glucosidase== | ||
<StructureSection load='3f5k' size='340' side='right'caption='[[3f5k]], [[Resolution|resolution]] 1.80Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3f5k]] 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=3F5K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F5K FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=PRD_900016:beta-cellopentaose'>PRD_900016</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=3f5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f5k OCA], [https://pdbe.org/3f5k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f5k RCSB], [https://www.ebi.ac.uk/pdbsum/3f5k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f5k ProSAT]</span></td></tr> | |||
</table> | |||
== 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> | |||
== 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/f5/3f5k_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/main_output.php?pdb_ID=3f5k ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:20884352</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3f5k" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Beta-glucosidase 3D structures|Beta-glucosidase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Oryza sativa Japonica Group]] | |||
[[Category: Chen C-J]] | |||
[[Category: Chuenchor W]] | |||
[[Category: Ketudat Cairns JR]] | |||
[[Category: Pengthaisong S]] | |||
[[Category: Robinson RC]] | |||
[[Category: Yuvaniyama J]] | |||