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3vst

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Current revision (08:41, 20 March 2024) (edit) (undo)
 
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<StructureSection load='3vst' size='340' side='right'caption='[[3vst]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
<StructureSection load='3vst' size='340' side='right'caption='[[3vst]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3vst]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VST OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VST FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3vst]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoanaerobacterium_saccharolyticum_JW/SL-YS485 Thermoanaerobacterium saccharolyticum JW/SL-YS485]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VST OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VST 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=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 1.75&#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;'>[[3vsu|3vsu]], [[3vsv|3vsv]]</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=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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/Xylan_1,4-beta-xylosidase Xylan 1,4-beta-xylosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.37 3.2.1.37] </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=3vst FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vst OCA], [https://pdbe.org/3vst PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vst RCSB], [https://www.ebi.ac.uk/pdbsum/3vst PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vst 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=3vst FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vst OCA], [https://pdbe.org/3vst PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vst RCSB], [https://www.ebi.ac.uk/pdbsum/3vst PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vst 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/A2ICH1_THESW A2ICH1_THESW]
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Xylan-1,4-beta-xylosidase (beta-xylosidase) hydrolyses xylo-oligomers at their non-reducing ends into individual xylose units. Recently, XylC, a beta-xylosidase from Thermoanaerobacterium saccharolyticum JW/SL-YS485, was found to be structurally different from corresponding glycosyl hydrolases in the CAZy database (http://www.cazy.org/), and was subsequently classified as the first member of a novel family of glycoside hydrolases (GH120). In the present paper, we report three crystal structures of XylC in complex with Tris, xylobiose and xylose at 1.48-2.05 A (1 A=0.1 nm) resolution. XylC assembles into a tetramer, and each monomer comprises two distinct domains. The core domain is a right-handed parallel beta-helix (residues 1-75 and 201-638) and the flanking region (residues 76-200) folds into a beta-sandwich domain. The enzyme contains an open carbohydrate-binding cleft, allowing accommodation of longer xylo-oligosaccharides. On the basis of the crystal structures and in agreement with previous kinetic data, we propose that XylC cleaves the glycosidic bond by the retaining mechanism using two acidic residues Asp382 (nucleophile) and Glu405 (general acid/base). In addition to the active site, nine other xylose-binding sites were consistently observed in each of the four monomers, providing a possible reason for the high tolerance of product inhibition.
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The substrate/product-binding modes of a novel GH120 beta-xylosidase (XylC) from Thermoanaerobacterium saccharolyticum JW/SL-YS485.,Huang CH, Sun Y, Ko TP, Chen CC, Zheng Y, Chan HC, Pang X, Wiegel J, Shao W, Guo RT Biochem J. 2012 Dec 15;448(3):401-7. doi: 10.1042/BJ20121359. PMID:22992047<ref>PMID:22992047</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 3vst" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Xylosidase 3D structures|Xylosidase 3D structures]]
*[[Xylosidase 3D structures|Xylosidase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Xylan 1,4-beta-xylosidase]]
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[[Category: Thermoanaerobacterium saccharolyticum JW/SL-YS485]]
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[[Category: Chan, H C]]
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[[Category: Chan HC]]
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[[Category: Chen, C C]]
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[[Category: Chen CC]]
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[[Category: Guo, R T]]
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[[Category: Guo RT]]
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[[Category: Huang, C H]]
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[[Category: Huang CH]]
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[[Category: Ko, T P]]
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[[Category: Ko TP]]
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[[Category: Ma, Y]]
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[[Category: Ma Y]]
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[[Category: Pang, X]]
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[[Category: Pang X]]
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[[Category: Shao, W]]
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[[Category: Shao W]]
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[[Category: Sun, Y]]
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[[Category: Sun Y]]
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[[Category: Wiegel, J]]
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[[Category: Wiegel J]]
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[[Category: Zheng, Y]]
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[[Category: Zheng Y]]
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[[Category: Beta-xylosidase]]
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[[Category: Glycoside hydrolase]]
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[[Category: Hydrolase]]
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[[Category: Product inhibition]]
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Current revision

The complex structure of XylC with Tris

PDB ID 3vst

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