2dfc

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[[Image:2dfc.gif|left|200px]]
 
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==Xylanase II from Tricoderma reesei at 293K==
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The line below this paragraph, containing "STRUCTURE_2dfc", creates the "Structure Box" on the page.
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<StructureSection load='2dfc' size='340' side='right'caption='[[2dfc]], [[Resolution|resolution]] 1.19&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2dfc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Trichoderma_reesei Trichoderma reesei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DFC FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 1.19&#8491;</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=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
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{{STRUCTURE_2dfc| PDB=2dfc | SCENE= }}
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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=2dfc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfc OCA], [https://pdbe.org/2dfc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dfc RCSB], [https://www.ebi.ac.uk/pdbsum/2dfc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dfc ProSAT]</span></td></tr>
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</table>
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'''Xylanase II from Tricoderma reesei at 293K'''
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== Function ==
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[https://www.uniprot.org/uniprot/XYN2_HYPJR XYN2_HYPJR] Glycoside hydrolase involved in the hydrolysis of xylan, a major plant cell wall hemicellulose made up of 1,4-beta-linked D-xylopyranose residues. Catalyzes the endohydrolysis of the main-chain 1,4-beta-glycosidic bonds connecting the xylose subunits yielding various xylooligosaccharides and xylose (PubMed:1369024, Ref.5). The catalysis proceeds by a double-displacement reaction mechanism with a putative covalent glycosyl-enzyme intermediate, with retention of the anomeric configuration (PubMed:7988708). Produces xylobiose and xylose as the main degradation products (PubMed:19556747).<ref>PMID:1369024</ref> <ref>PMID:19556747</ref> <ref>PMID:7988708</ref> <ref>PMID:1369024</ref>
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== Evolutionary Conservation ==
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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/df/2dfc_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2dfc ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
An orthorhombic crystal of xylanase II from Trichoderma reesei was grown in the presence of sodium iodide. Crystal structures at atomic resolution were determined at 100 and 293 K. Protein molecules were aligned along a crystallographic twofold screw axis, forming a helically extended polymer-like chain mediated by an iodide ion. The iodide ion connected main-chain peptide groups between two adjacent molecules by an N-H...I-...H-N hydrogen-bond bridge, thus contributing to regulation of the molecular arrangement and suppression of the rigid-body motion in the crystal with high diffraction quality. The structure at 293 K showed considerable thermal motion in the loop regions connecting the beta-strands that form the active-site cleft. TLS model analysis of the thermal motion and a comparison between this structure and that at 100 K suggest that the fluctuation of these loop regions is attributable to the hinge-like movement of the beta-strands.
An orthorhombic crystal of xylanase II from Trichoderma reesei was grown in the presence of sodium iodide. Crystal structures at atomic resolution were determined at 100 and 293 K. Protein molecules were aligned along a crystallographic twofold screw axis, forming a helically extended polymer-like chain mediated by an iodide ion. The iodide ion connected main-chain peptide groups between two adjacent molecules by an N-H...I-...H-N hydrogen-bond bridge, thus contributing to regulation of the molecular arrangement and suppression of the rigid-body motion in the crystal with high diffraction quality. The structure at 293 K showed considerable thermal motion in the loop regions connecting the beta-strands that form the active-site cleft. TLS model analysis of the thermal motion and a comparison between this structure and that at 100 K suggest that the fluctuation of these loop regions is attributable to the hinge-like movement of the beta-strands.
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==About this Structure==
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Structure of an orthorhombic form of xylanase II from Trichoderma reesei and analysis of thermal displacement.,Watanabe N, Akiba T, Kanai R, Harata K Acta Crystallogr D Biol Crystallogr. 2006 Jul;62(Pt 7):784-92. Epub 2006, Jun 20. PMID:16790934<ref>PMID:16790934</ref>
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2DFC is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Hypocrea_jecorina Hypocrea jecorina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFC OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structure of an orthorhombic form of xylanase II from Trichoderma reesei and analysis of thermal displacement., Watanabe N, Akiba T, Kanai R, Harata K, Acta Crystallogr D Biol Crystallogr. 2006 Jul;62(Pt 7):784-92. Epub 2006, Jun 20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16790934 16790934]
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</div>
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[[Category: Endo-1,4-beta-xylanase]]
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<div class="pdbe-citations 2dfc" style="background-color:#fffaf0;"></div>
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[[Category: Hypocrea jecorina]]
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== References ==
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[[Category: Single protein]]
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<references/>
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[[Category: Akiba, T.]]
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__TOC__
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[[Category: Harata, K.]]
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</StructureSection>
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[[Category: Bent beta sheet]]
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[[Category: Large Structures]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 00:18:56 2008''
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[[Category: Trichoderma reesei]]
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[[Category: Akiba T]]
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[[Category: Harata K]]

Current revision

Xylanase II from Tricoderma reesei at 293K

PDB ID 2dfc

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