5zqs: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 5zqs is ~~ON HOLD until Paper~~ Publication

==Crystal structure of beta-xylosidase mutant (E186Q/F503Y) from Bacillus pumilus==

== Structural highlights ==

<table><tr><td colspan='2'>[[5zqs]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZQS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZQS 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>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>

<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5zqj|5zqj]]</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=5zqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zqs OCA], [http://pdbe.org/5zqs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zqs RCSB], [http://www.ebi.ac.uk/pdbsum/5zqs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zqs ProSAT]</span></td></tr>

</table>

== Function ==

[[http://www.uniprot.org/uniprot/XYNB_BACPU 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.

~~Authors: Ha, N.C~~., Hong, S., Jo, I.

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<ref>PMID:29752942</ref>

~~Description~~: ~~Crystal structure of~~ beta-xylosidase ~~mutant (E186Q/F503Y) from Bacillus pumilus~~

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased Structures~~]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Xylan 1,4-beta-xylosidase]]

[[Category: Ha, N C]]

[[Category: Hong, S]]

[[Category: Jo, I]]

[[Category: ~~Ha, N.C~~]]

[[Category: Hydrolase]]

[[Category: ~~Hong, S~~]]

[[Category: Xylobiose hydrolysis]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5zqs is ON HOLD  until Paper Publication
+==Crystal structure of beta-xylosidase mutant (E186Q/F503Y) from Bacillus pumilus==
+<StructureSection load='5zqs' size='340' side='right' caption='[[5zqs]], [[Resolution|resolution]] 1.78&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5zqs]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZQS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZQS 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>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5zqj|5zqj]]</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=5zqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zqs OCA], [http://pdbe.org/5zqs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zqs RCSB], [http://www.ebi.ac.uk/pdbsum/5zqs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zqs ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/XYNB_BACPU XYNB_BACPU]] Beta-xylosidase is an intracellular xylan-degrading enzyme.
+<div style="background-color:#fffaf0;">
+== 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.
-Authors: Ha, N.C., Hong, S., Jo, I.
+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<ref>PMID:29752942</ref>
-Description: Crystal structure of beta-xylosidase mutant (E186Q/F503Y) from Bacillus pumilus
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 5zqs" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Xylan 1,4-beta-xylosidase]]
+[[Category: Ha, N C]]
+[[Category: Hong, S]]
 [[Category: Jo, I]]
-[[Category: Ha, N.C]]
+[[Category: Hydrolase]]
-[[Category: Hong, S]]
+[[Category: Xylobiose hydrolysis]]