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==ENDO-1,4-BETA-XYLANASE II COMPLEX WITH 4,5-EPOXYPENTYL-BETA-D-XYLOSIDE== | ==ENDO-1,4-BETA-XYLANASE II COMPLEX WITH 4,5-EPOXYPENTYL-BETA-D-XYLOSIDE== | ||
<StructureSection load='1red' size='340' side='right' caption='[[1red]], [[Resolution|resolution]] 1.60Å' scene=''> | <StructureSection load='1red' size='340' side='right'caption='[[1red]], [[Resolution|resolution]] 1.60Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1red]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[1red]] is a 2 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=1RED OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RED FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=C5X:4,5-EPOXYPENTYL-BETA-D-XYLOSIDE'>C5X</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></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=1red FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1red OCA], [https://pdbe.org/1red PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1red RCSB], [https://www.ebi.ac.uk/pdbsum/1red PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1red ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[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> | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/re/1red_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/re/1red_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/ | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </jmolCheckbox> | ||
</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/ | </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=1red ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
| Line 31: | Line 33: | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Trichoderma reesei]] | [[Category: Trichoderma reesei]] | ||
[[Category: Havukainen | [[Category: Havukainen R]] | ||
[[Category: Rouvinen | [[Category: Rouvinen J]] | ||
[[Category: Torronen | [[Category: Torronen A]] | ||
Latest revision as of 12:41, 25 December 2024
ENDO-1,4-BETA-XYLANASE II COMPLEX WITH 4,5-EPOXYPENTYL-BETA-D-XYLOSIDEENDO-1,4-BETA-XYLANASE II COMPLEX WITH 4,5-EPOXYPENTYL-BETA-D-XYLOSIDE
Structural highlights
FunctionXYN2_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).[1] [2] [3] [4] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe three-dimensional structures of endo-1,4-xylanase II (XYNII) from Trichoderma reesei complexed with 4,5-epoxypentyl beta-D-xyloside (X-O-C5),3,4-epoxybutyl beta-D-xyloside (X-O-C4), and 2,3-epoxypropyl beta-D-xyloside (X-O-C3) were determined by X-ray crystallography. High-resolution measurement revealed clear electron densities for each ligand. Both X-O-C5 and X-O-C3 were found to form a covalent bond with the putative nucleophile Glu86. Unexpectedly, X-O-C4 was found to bind to the putative acid/base catalyst Glu177. In all three complexes, clear conformational changes were found in XYNII compared to the native structure. These changes were largest in the X-O-C3 complex structure. Covalent binding of three epoxyalkyl xylosides to the active site of endo-1,4-xylanase II from Trichoderma reesei.,Havukainen R, Torronen A, Laitinen T, Rouvinen J Biochemistry. 1996 Jul 23;35(29):9617-24. PMID:8755744[5] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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