2d97: Difference between revisions
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<StructureSection load='2d97' size='340' side='right'caption='[[2d97]], [[Resolution|resolution]] 2.01Å' scene=''> | <StructureSection load='2d97' size='340' side='right'caption='[[2d97]], [[Resolution|resolution]] 2.01Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2d97]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[2d97]] 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=2D97 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D97 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]] 2.01Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IYR:3-IODO-TYROSINE'>IYR</scene>, <scene name='pdbligand=TYI:3,5-DIIODOTYROSINE'>TYI</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=2d97 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d97 OCA], [https://pdbe.org/2d97 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d97 RCSB], [https://www.ebi.ac.uk/pdbsum/2d97 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d97 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=2d97 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d97 OCA], [https://pdbe.org/2d97 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d97 RCSB], [https://www.ebi.ac.uk/pdbsum/2d97 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d97 ProSAT]</span></td></tr> | ||
</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]] | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Trichoderma reesei]] | ||
[[Category: | [[Category: Hasegawa T]] | ||
[[Category: | [[Category: Miyatake H]] | ||
[[Category: | [[Category: Yamano A]] | ||
Revision as of 14:35, 22 May 2024
Structure of VIL-xylanaseStructure of VIL-xylanase
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 PubMedNew techniques are presented for the preparation of iodine derivatives, involving vapour diffusion of iodine. Firstly, in the vaporizing iodine labelling (VIL) technique, a small amount of KI/I(2) solution is enclosed in a crystallization well, with the result that gaseous I(2) molecules diffuse into the crystallization droplets without exerting substantial changes in ionic strength in the target crystals. Once they have diffused into the droplet, the I(2) molecules sometimes iodinate accessible tyrosines at ortho positions. Secondly, when iodination is insufficient, the hydrogen peroxide VIL (HYPER-VIL) technique can be further applied to increase the iodination ratio by the addition of a small droplet of hydrogen peroxide (H(2)O(2)) to the crystallization well; the gaseous H(2)O(2) also diffuses into the crystallization droplet to emphasize the iodination. These techniques are most effective for phase determination when coupled with softer X-rays, such as those from Cu Kalpha or Cr Kalpha radiation. The effectiveness of these techniques was assessed using five different crystals. Four of the crystals were successfully iodinated, providing sufficient phasing power for structure determination. New methods to prepare iodinated derivatives by vaporizing iodine labelling (VIL) and hydrogen peroxide VIL (HYPER-VIL).,Miyatake H, Hasegawa T, Yamano A Acta Crystallogr D Biol Crystallogr. 2006 Mar;62(Pt 3):280-9. Epub 2006, Feb 22. PMID:16510975[5] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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