3vpl

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Current revision (12:31, 8 November 2023) (edit) (undo)
 
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<StructureSection load='3vpl' size='340' side='right'caption='[[3vpl]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
<StructureSection load='3vpl' size='340' side='right'caption='[[3vpl]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3vpl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Listonella_sp. Listonella sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VPL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VPL FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3vpl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_sp. Vibrio sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VPL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VPL 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=DNX:3,4-DINITROPHENOL'>DNX</scene>, <scene name='pdbligand=BXF:2-DEOXY-2-FLUORO-BETA-D-XYLOPYRANOSE'>BXF</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</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]] 1.2&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">xyl4 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=678 Listonella sp.])</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=BXF:2-DEOXY-2-FLUORO-BETA-D-XYLOPYRANOSE'>BXF</scene>, <scene name='pdbligand=DNX:3,4-DINITROPHENOL'>DNX</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</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/Endo-1,3-beta-xylanase Endo-1,3-beta-xylanase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.32 3.2.1.32] </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=3vpl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vpl OCA], [https://pdbe.org/3vpl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vpl RCSB], [https://www.ebi.ac.uk/pdbsum/3vpl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vpl 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=3vpl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vpl OCA], [https://pdbe.org/3vpl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vpl RCSB], [https://www.ebi.ac.uk/pdbsum/3vpl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vpl ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/3XYN1_VIBSX 3XYN1_VIBSX]] Catalyzes the hydrolysis of beta-1,3-xylan into oligosaccharides, mainly xylobiose, xylotriose and xylotetraose. Converts beta-1,3-xylotriose into xylose and xylobiose, converts beta-1,3-xylotetraose mainly into xylotriose and xylose, converts beta-1,3-xylopentaose into xylobiose and xylotriose. Does not hydrolyze beta-1,4-xylan, beta-1,4-mannan, beta-1,4-glucan, beta-1,3-xylobiose or p-nitrophenyl-beta-xyloside.<ref>PMID:15743273</ref>
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[https://www.uniprot.org/uniprot/3XYN1_VIBSX 3XYN1_VIBSX] Catalyzes the hydrolysis of beta-1,3-xylan into oligosaccharides, mainly xylobiose, xylotriose and xylotetraose. Converts beta-1,3-xylotriose into xylose and xylobiose, converts beta-1,3-xylotetraose mainly into xylotriose and xylose, converts beta-1,3-xylopentaose into xylobiose and xylotriose. Does not hydrolyze beta-1,4-xylan, beta-1,4-mannan, beta-1,4-glucan, beta-1,3-xylobiose or p-nitrophenyl-beta-xyloside.<ref>PMID:15743273</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Xylanases capable of degrading the crystalline microfibrils of 1,3-xylan that reinforce the cell walls of some red and siphonous green algae have not been well studied, yet they could prove to be of great utility in algaculture for the production of food and renewable chemical feedstocks. To gain a better mechanistic understanding of these enzymes, a suite of reagents was synthesized and evaluated as substrates and inhibitors of an endo-1,3-xylanase. With these reagents, a retaining mechanism was confirmed for the xylanase, its catalytic nucleophile identified, and the existence of -3 to +2 substrate-binding subsites demonstrated. Protein crystal X-ray diffraction methods provided a high resolution structure of a trapped covalent glycosyl-enzyme intermediate, indicating that the 1,3-xylanases likely utilize the (1)S(3) --&gt; (4)H(3) --&gt; (4)C(1) conformational itinerary to effect catalysis.
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Mechanistic insights into the 1,3-xylanases: useful enzymes for manipulation of algal biomass.,Goddard-Borger ED, Sakaguchi K, Reitinger S, Watanabe N, Ito M, Withers SG J Am Chem Soc. 2012 Feb 29;134(8):3895-902. doi: 10.1021/ja211836t. Epub 2012 Feb, 16. PMID:22296113<ref>PMID:22296113</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 3vpl" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Endo-1,3-beta-xylanase]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Listonella sp]]
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[[Category: Vibrio sp]]
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[[Category: Sakaguchi, K]]
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[[Category: Sakaguchi K]]
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[[Category: Watanabe, N]]
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[[Category: Watanabe N]]
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[[Category: 3-xylanase]]
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[[Category: Beta-1]]
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[[Category: Glycoside hydrolase]]
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[[Category: Hydrolase]]
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[[Category: Tim barrel]]
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Current revision

Crystal structure of a 2-fluoroxylotriosyl complex of the Vibrio sp. AX-4 Beta-1,3-xylanase

PDB ID 3vpl

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