6jug
From Proteopedia
(Difference between revisions)
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==Crystal Structures of Endo-beta-1,4-xylanase II Complexed with Xylotriose== | ==Crystal Structures of Endo-beta-1,4-xylanase II Complexed with Xylotriose== | ||
| - | <StructureSection load='6jug' size='340' side='right'caption='[[6jug]]' scene=''> | + | <StructureSection load='6jug' size='340' side='right'caption='[[6jug]], [[Resolution|resolution]] 1.19Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JUG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JUG FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6jug]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Hypjr Hypjr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JUG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JUG FirstGlance]. <br> |
| - | </td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6jug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jug OCA], [http://pdbe.org/6jug PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jug RCSB], [http://www.ebi.ac.uk/pdbsum/6jug PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jug ProSAT]</span></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr> |
| + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2dfc|2dfc]], [[4hkw|4hkw]], [[4hk9|4hk9]], [[4hki|4hki]]</div></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">xyn2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1344414 HYPJR])</td></tr> | ||
| + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://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'>[http://proteopedia.org/fgij/fg.htm?mol=6jug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jug OCA], [http://pdbe.org/6jug PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jug RCSB], [http://www.ebi.ac.uk/pdbsum/6jug PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jug ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [[http://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> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | XynII is a family 11 glycoside hydrolase that uses the retaining mechanism for catalysis. In the active site, E177 works as the acid/base and E86 works as the nucleophile. Mutating an uncharged residue (N44) to an acidic residue (D) near E177 decreases the enzyme's optimal pH by ~ 1.0 unit. D44 was previously suggested to be a second proton carrier for catalysis. To test this hypothesis, we abolished the activity of E177 by mutating it to be Q, and mutated N44 to be D or E. These double mutants have dramatically decreased activities. Our high-resolution crystallographic structures and the microscopic pKa calculations show that D44 has similar position and pKa value during catalysis, indicating that D44 changes electrostatics around E177, which makes it prone to rotate as the acid/base in acidic conditions, thus decreases the pH optimum. Our results could be helpful to design enzymes with different pH optimum. | ||
| + | |||
| + | Studying the Role of a Single Mutation of a Family 11 Glycoside Hydrolase Using High-Resolution X-ray Crystallography.,Li Z, Zhang X, Li C, Kovalevsky A, Wan Q Protein J. 2020 Dec;39(6):671-680. doi: 10.1007/s10930-020-09938-5. Epub 2020 Oct, 31. PMID:33128114<ref>PMID:33128114</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6jug" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Endo-1,4-beta-xylanase]] | ||
| + | [[Category: Hypjr]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Li C]] | + | [[Category: Li, C]] |
| - | [[Category: Wan Q]] | + | [[Category: Wan, Q]] |
| + | [[Category: Complex]] | ||
| + | [[Category: Hydrolase]] | ||
| + | [[Category: Xylanase ii]] | ||
| + | [[Category: Xylotriose]] | ||
Revision as of 10:46, 24 December 2020
Crystal Structures of Endo-beta-1,4-xylanase II Complexed with Xylotriose
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Categories: Endo-1,4-beta-xylanase | Hypjr | Large Structures | Li, C | Wan, Q | Complex | Hydrolase | Xylanase ii | Xylotriose
