5zqs - Revision history

OCA at 09:04, 22 November 2023

OCA — Wed, 22 Nov 2023 09:04:06 GMT

←Older revision		Revision as of 09:04, 22 November 2023
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	==Crystal structure of beta-xylosidase mutant (E186Q/F503Y) from Bacillus pumilus==		==Crystal structure of beta-xylosidase mutant (E186Q/F503Y) from Bacillus pumilus==
-	<StructureSection load='5zqs' size='340' side='right' caption='[[5zqs]], [[Resolution\|resolution]] 1.78Å' scene=''>	+	<StructureSection load='5zqs' size='340' side='right'caption='[[5zqs]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zqs]] is a 2 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=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>	+	<table><tr><td colspan='2'>[[5zqs]] is a 2 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=5ZQS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/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>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.782Å</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=5zqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zqs OCA], [https://pdbe.org/5zqs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zqs RCSB], [https://www.ebi.ac.uk/pdbsum/5zqs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zqs 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=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>		</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 ==
Line 23:		Line 21:

	==See Also==		==See Also==
-	*[[Xylosidase\|Xylosidase]]	+	*[[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~~]]	+

OCA at 06:28, 18 October 2018

OCA — Thu, 18 Oct 2018 06:28:01 GMT

←Older revision		Revision as of 06:28, 18 October 2018
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5zqs" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5zqs" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Xylosidase\|Xylosidase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:17, 6 June 2018

OCA — Wed, 06 Jun 2018 06:17:33 GMT

←Older revision		Revision as of 06:17, 6 June 2018
Line 3:		Line 3:
	<StructureSection load='5zqs' size='340' side='right' caption='[[5zqs]], [[Resolution\|resolution]] 1.78Å' scene=''>		<StructureSection load='5zqs' size='340' side='right' caption='[[5zqs]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== 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>	+	<table><tr><td colspan='2'>[[5zqs]] is a 2 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=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>		</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5zqj\|5zqj]]</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='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='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>		<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>
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 7061]]
	[[Category: Xylan 1,4-beta-xylosidase]]		[[Category: Xylan 1,4-beta-xylosidase]]
	[[Category: Ha, N C]]		[[Category: Ha, N C]]

OCA at 05:30, 30 May 2018

OCA — Wed, 30 May 2018 05:30:32 GMT

←Older revision		Revision as of 05:30, 30 May 2018
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]] 1.78Å' 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®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: Jo, I]]	+	<div class="pdbe-citations 5zqs" style="background-color:#fffaf0;"></div>
-	[[Category: Ha, N.C]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Xylan 1,4-beta-xylosidase]]
		+	[[Category: Ha, N C]]
	[[Category: Hong, S]]		[[Category: Hong, S]]
		+	[[Category: Jo, I]]
		+	[[Category: Hydrolase]]
		+	[[Category: Xylobiose hydrolysis]]

OCA at 06:33, 2 May 2018

OCA — Wed, 02 May 2018 06:33:25 GMT

←Older revision		Revision as of 06:33, 2 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zqs is ON HOLD	+	The entry 5zqs is ON HOLD until Paper Publication

-	Authors: Ha, N.-C., Hong, S., Jo, I.	+	Authors: Ha, N.C., Hong, S., Jo, I.

	Description: Crystal structure of beta-xylosidase mutant (E186Q/F503Y) from Bacillus pumilus		Description: Crystal structure of beta-xylosidase mutant (E186Q/F503Y) from Bacillus pumilus
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Ha, N.-C]]
	[[Category: Jo, I]]		[[Category: Jo, I]]
		+	[[Category: Ha, N.C]]
	[[Category: Hong, S]]		[[Category: Hong, S]]

OCA: Protected "5zqs" [edit=sysop:move=sysop]

OCA — Wed, 25 Apr 2018 03:56:22 GMT

Protected "5zqs" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:56, 25 April 2018

OCA: New page: '''Unreleased structure''' The entry 5zqs is ON HOLD Authors: Ha, N.-C., Hong, S., Jo, I. Description: Crystal structure of beta-xylosidase mutant (E186Q/F503Y) from Bacillus pumilus [...

OCA — Wed, 25 Apr 2018 03:56:21 GMT

New page: '''Unreleased structure''' The entry 5zqs is ON HOLD Authors: Ha, N.-C., Hong, S., Jo, I. Description: Crystal structure of beta-xylosidase mutant (E186Q/F503Y) from Bacillus pumilus [...

New page

'''Unreleased structure'''

The entry 5zqs is ON HOLD

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

Description: Crystal structure of beta-xylosidase mutant (E186Q/F503Y) from Bacillus pumilus
[[Category: Unreleased Structures]]
[[Category: Ha, N.-C]]
[[Category: Jo, I]]
[[Category: Hong, S]]