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3ptm

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Current revision (13:33, 1 March 2024) (edit) (undo)
 
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<StructureSection load='3ptm' size='340' side='right'caption='[[3ptm]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
<StructureSection load='3ptm' size='340' side='right'caption='[[3ptm]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3ptm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Orysa Orysa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PTM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PTM FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3ptm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa Oryza sativa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PTM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PTM FirstGlance]. <br>
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</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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ptk|3ptk]], [[3ptq|3ptq]]</div></td></tr>
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<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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Os04g0474800 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4530 ORYSA])</td></tr>
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<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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ptm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ptm OCA], [https://pdbe.org/3ptm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ptm RCSB], [https://www.ebi.ac.uk/pdbsum/3ptm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ptm 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=3ptm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ptm OCA], [https://pdbe.org/3ptm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ptm RCSB], [https://www.ebi.ac.uk/pdbsum/3ptm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ptm ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/BGL12_ORYSI BGL12_ORYSI] Hydrolyzes p-nitrophenyl beta-D-glucoside, p-nitrophenyl beta-D-galactoside, p-nitrophenyl beta-D-xyloside, p-nitrophenyl beta-D-fucoside, p-nitrophenyl beta-L-arabinoside, cello-oligosaccharides and laminaribiose.[UniProtKB:Q7XKV4]
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Rice Os4BGlu12, a glycoside hydrolase family 1 (GH1) beta-glucosidase, hydrolyzes beta-(1,4)-linked oligosaccharides of 3-6 glucosyl residues and the beta-(1,3)-linked disaccharide laminaribiose, as well as certain glycosides. The crystal structures of apo Os4BGlu12, and its complexes with 2,4-dinitrophenyl-2-deoxyl-2-fluoroglucoside (DNP2FG) and 2-deoxy-2-fluoroglucose (G2F) were solved at 2.50, 2.45 and 2.40A resolution, respectively. The overall structure of rice Os4BGlu12 is typical of GH1 enzymes, but it contains an extra disulfide bridge in the loop B region. The glucose ring of the G2F in the covalent intermediate was found in a (4)C(1) chair conformation, while that of the noncovalently bound DNP2FG had a (1)S(3) skew boat, consistent with hydrolysis via a (4)H(3) half-chair transition state. The position of the catalytic nucleophile (Glu393) in the G2F structure was more similar to that of the Sinapsis alba myrosinase G2F complex than to that in covalent intermediates of other O-glucosidases, such as rice Os3BGlu6 and Os3BGlu7 beta-glucosidases. This correlated with a significant thioglucosidase activity for Os4BGlu12, although with 200- to 1200-fold lower k(cat)/K(m) values for S-glucosides than the comparable O-glucosides, while hydrolysis of S-glucosides was undetectable for Os3BGlu6 and Os3BGlu7.
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The crystal structure of rice (Oryza sativa L.) Os4BGlu12, an oligosaccharide and tuberonic acid glucoside-hydrolyzing beta-glucosidase with significant thioglucohydrolase activity.,Sansenya S, Opassiri R, Kuaprasert B, Chen CJ, Ketudat Cairns JR Arch Biochem Biophys. 2011 Jun 1;510(1):62-72. Epub 2011 Apr 16. PMID:21521631<ref>PMID:21521631</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3ptm" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Beta-glucosidase 3D structures|Beta-glucosidase 3D structures]]
*[[Beta-glucosidase 3D structures|Beta-glucosidase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Beta-glucosidase]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Orysa]]
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[[Category: Oryza sativa]]
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[[Category: Cairns, J R.Ketudat]]
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[[Category: Chen CJ]]
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[[Category: Chen, C J]]
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[[Category: Ketudat Cairns JR]]
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[[Category: Kuaprasert, B]]
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[[Category: Kuaprasert B]]
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[[Category: Opassiri, R]]
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[[Category: Opassiri R]]
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[[Category: Sansenya, S]]
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[[Category: Sansenya S]]
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[[Category: Beta-alpha barrel]]
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[[Category: Glycosidase]]
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[[Category: Hydrolase]]
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Current revision

The crystal structure of rice (Oryza sativa L.) Os4BGlu12 with 2-fluoroglucopyranoside

PDB ID 3ptm

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