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| | ==Crystal structure of beta-xylosidase mutant (E186Q) from Bacillus pumilus== | | ==Crystal structure of beta-xylosidase mutant (E186Q) from Bacillus pumilus== |
| - | <StructureSection load='5zqx' size='340' side='right' caption='[[5zqx]], [[Resolution|resolution]] 2.00Å' scene=''> | + | <StructureSection load='5zqx' size='340' side='right'caption='[[5zqx]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5zqx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_7061 Atcc 7061]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZQX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZQX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5zqx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_pumilus Bacillus pumilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZQX FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BXP:4-O-BETA-D-XYLOPYRANOSYL-BETA-D-XYLOPYRANOSE'>BXP</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]] 2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5zqj|5zqj]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PRD_900116:4beta-beta-xylobiose'>PRD_900116</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">xynB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1408 ATCC 7061])</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=5zqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zqx OCA], [https://pdbe.org/5zqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zqx RCSB], [https://www.ebi.ac.uk/pdbsum/5zqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zqx 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/Xylan_1,4-beta-xylosidase Xylan 1,4-beta-xylosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.37 3.2.1.37] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5zqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zqx OCA], [http://pdbe.org/5zqx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zqx RCSB], [http://www.ebi.ac.uk/pdbsum/5zqx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zqx ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/XYNB_BACPU XYNB_BACPU]] Beta-xylosidase is an intracellular xylan-degrading enzyme. | + | [https://www.uniprot.org/uniprot/XYNB_BACPU XYNB_BACPU] Beta-xylosidase is an intracellular xylan-degrading enzyme. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 5zqx" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5zqx" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Xylosidase 3D structures|Xylosidase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 7061]] | + | [[Category: Bacillus pumilus]] |
| - | [[Category: Xylan 1,4-beta-xylosidase]] | + | [[Category: Large Structures]] |
| - | [[Category: Ha, N C]] | + | [[Category: Ha NC]] |
| - | [[Category: Hong, S]] | + | [[Category: Hong S]] |
| - | [[Category: Jo, I]] | + | [[Category: Jo I]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Xylobiose hydrolysis]]
| + | |
| Structural highlights
Function
XYNB_BACPU Beta-xylosidase is an intracellular xylan-degrading enzyme.
Publication Abstract from PubMed
Xylobiose consists of two molecules of xylose and has been highly recognized as a food supplement because it possesses high prebiotic functions. beta-xylosidase exhibits enzymatic activity to hydrolyze xylobiose, and the enzyme can also catalyze the reverse reaction in the presence of high concentrations of xylose. Previously, beta-xylosidase from Bacillus pumilus IPO (BpXynB), belonging to GH family 43, was employed to produce xylobiose from xylose. To improve the enzymatic efficiency, this study determined the high-resolution structure of BpXynB in a complex with xylobiose and engineered BpXynB based on the structures. The structure of BpXynB deciphered the residues involved in the recognition of the xylobiose. A site-directed mutation at the residue for xylobiose recognition increased the yield of xylobiose by 20% compared to a similar activity of the wild type enzyme. The complex structure of the mutant enzyme and xylobiose provided the structural basis for a higher yield of the engineered protein. This engineered enzyme would enable a higher economic production of xylobiose, and a similar engineering strategy could be applied within the same family of enzymes.
Structure-based protein engineering of bacterial beta-xylosidase to increase the production yield of xylobiose from xylose.,Hong S, Kyung M, Jo I, Kim YR, Ha NC Biochem Biophys Res Commun. 2018 Jun 27;501(3):703-710. doi:, 10.1016/j.bbrc.2018.05.051. PMID:29752942[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Hong S, Kyung M, Jo I, Kim YR, Ha NC. Structure-based protein engineering of bacterial beta-xylosidase to increase the production yield of xylobiose from xylose. Biochem Biophys Res Commun. 2018 Jun 27;501(3):703-710. doi:, 10.1016/j.bbrc.2018.05.051. PMID:29752942 doi:http://dx.doi.org/10.1016/j.bbrc.2018.05.051
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