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| | <StructureSection load='3niy' size='340' side='right'caption='[[3niy]], [[Resolution|resolution]] 1.58Å' scene=''> | | <StructureSection load='3niy' size='340' side='right'caption='[[3niy]], [[Resolution|resolution]] 1.58Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3niy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thep1 Thep1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NIY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NIY FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3niy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_petrophila_RKU-1 Thermotoga petrophila RKU-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NIY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NIY FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.58Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3nj3|3nj3]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Tpet_0854 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=390874 THEP1])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=3niy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3niy OCA], [https://pdbe.org/3niy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3niy RCSB], [https://www.ebi.ac.uk/pdbsum/3niy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3niy 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=3niy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3niy OCA], [https://pdbe.org/3niy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3niy RCSB], [https://www.ebi.ac.uk/pdbsum/3niy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3niy ProSAT]</span></td></tr> |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/A5IL00_THEP1 A5IL00_THEP1] |
| - | Endo-xylanases play a key role in the depolymerization of xylan and recently, they have attracted much attention owing to their potential applications on biofuels and paper industries. In this work, we have investigated the molecular basis for the action mode of xylanases 10B at high temperatures using biochemical, biophysical and crystallographic methods. The crystal structure of xylanase 10B from hyperthermophilic bacterium Thermotoga petrophila RKU-1 (TpXyl10B) has been solved in the native state and in complex with xylobiose. The complex crystal structure showed a classical binding mode shared among other xylanases, which encompasses the -1 and -2 subsites. Interestingly, TpXyl10B displayed a temperature-dependent action mode producing xylobiose and xylotriose at 20 degrees C, and exclusively xylobiose at 90 degrees C as assessed by capillary zone electrophoresis. Moreover, circular dichroism spectroscopy suggested a coupling effect of temperature-induced structural changes with this particular enzymatic behavior. Molecular dynamics simulations supported the CD analysis suggesting that an open conformational state adopted by the catalytic loop (Trp297-Lys326) provokes significant modifications in the product release area (+1,+2 and +3 subsites), which drives the enzymatic activity to the specific release of xylobiose at high temperatures.
| + | |
| - | | + | |
| - | Thermal-induced conformational changes in the product release area drive the enzymatic activity of xylanases 10B: Crystal structure, conformational stability and functional characterization of the xylanase 10B from Thermotoga petrophila RKU-1.,Santos CR, Meza AN, Hoffmam ZB, Silva JC, Alvarez TM, Ruller R, Giesel GM, Verli H, Squina FM, Prade RA, Murakami MT Biochem Biophys Res Commun. 2010 Dec 10;403(2):214-9. Epub 2010 Nov 9. PMID:21070746<ref>PMID:21070746</ref>
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| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 3niy" style="background-color:#fffaf0;"></div>
| + | |
| - | == References ==
| + | |
| - | <references/>
| + | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Endo-1,4-beta-xylanase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Thep1]] | + | [[Category: Thermotoga petrophila RKU-1]] |
| - | [[Category: Meza, A N]] | + | [[Category: Meza AN]] |
| - | [[Category: Murakami, M T]] | + | [[Category: Murakami MT]] |
| - | [[Category: Prade, R A]] | + | [[Category: Prade RA]] |
| - | [[Category: Ruller, R]] | + | [[Category: Ruller R]] |
| - | [[Category: Santos, C R]] | + | [[Category: Santos CR]] |
| - | [[Category: Squina, F M]] | + | [[Category: Squina FM]] |
| - | [[Category: Trindade, D M]] | + | [[Category: Trindade DM]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Tim-barrel]]
| + | |
| - | [[Category: Xylanase]]
| + | |
