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| | <StructureSection load='6jwb' size='340' side='right'caption='[[6jwb]], [[Resolution|resolution]] 1.15Å' scene=''> | | <StructureSection load='6jwb' size='340' side='right'caption='[[6jwb]], [[Resolution|resolution]] 1.15Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6jwb]] 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=6JWB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JWB FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6jwb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Trichoderma_reesei_RUT_C-30 Trichoderma reesei RUT C-30]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JWB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JWB FirstGlance]. <br> |
| - | </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>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</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]] 1.15Å</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]], [[4hko|4hko]]</div></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>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=PRD_900117:4beta-beta-xylotriose'>PRD_900117</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6jwb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jwb OCA], [https://pdbe.org/6jwb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jwb RCSB], [https://www.ebi.ac.uk/pdbsum/6jwb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jwb ProSAT]</span></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=6jwb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jwb OCA], [http://pdbe.org/6jwb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jwb RCSB], [http://www.ebi.ac.uk/pdbsum/6jwb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jwb ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == 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> | + | [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> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Endo-1,4-beta-xylanase]] | |
| - | [[Category: Hypjr]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Li, C]] | + | [[Category: Trichoderma reesei RUT C-30]] |
| - | [[Category: Wan, Q]] | + | [[Category: Li C]] |
| - | [[Category: Complex]] | + | [[Category: Wan Q]] |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
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).[1] [2] [3] [4]
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[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Torronen A, Mach RL, Messner R, Gonzalez R, Kalkkinen N, Harkki A, Kubicek CP. The two major xylanases from Trichoderma reesei: characterization of both enzymes and genes. Biotechnology (N Y). 1992 Nov;10(11):1461-5. PMID:1369024
- ↑ Jun H, Bing Y, Keying Z, Xuemei D, Daiwen C. Sequencing and expression of the xylanase gene 2 from Trichoderma reesei Rut C-30 and characterization of the recombinant enzyme and its activity on xylan. J Mol Microbiol Biotechnol. 2009;17(3):101-9. doi: 10.1159/000226590. Epub 2009, Jun 26. PMID:19556747 doi:http://dx.doi.org/10.1159/000226590
- ↑ Biely P, Kremnicky L, Alfoldi J, Tenkanen M. Stereochemistry of the hydrolysis of glycosidic linkage by endo-beta-1,4-xylanases of Trichoderma reesei. FEBS Lett. 1994 Dec 12;356(1):137-40. PMID:7988708
- ↑ Torronen A, Mach RL, Messner R, Gonzalez R, Kalkkinen N, Harkki A, Kubicek CP. The two major xylanases from Trichoderma reesei: characterization of both enzymes and genes. Biotechnology (N Y). 1992 Nov;10(11):1461-5. PMID:1369024
- ↑ Li Z, Zhang X, Li C, Kovalevsky A, Wan Q. Studying the Role of a Single Mutation of a Family 11 Glycoside Hydrolase Using High-Resolution X-ray Crystallography. Protein J. 2020 Dec;39(6):671-680. doi: 10.1007/s10930-020-09938-5. Epub 2020 Oct, 31. PMID:33128114 doi:http://dx.doi.org/10.1007/s10930-020-09938-5
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