5z5i - Revision history

OCA at 08:45, 22 November 2023

OCA — Wed, 22 Nov 2023 08:45:50 GMT

←Older revision		Revision as of 08:45, 22 November 2023
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	==Crystal structure of a thermostable glycoside hydrolase family 43 {beta}-1,4-xylosidase from Geobacillus thermoleovorans IT-08 in complex with L-arabinose and D-xylose==		==Crystal structure of a thermostable glycoside hydrolase family 43 {beta}-1,4-xylosidase from Geobacillus thermoleovorans IT-08 in complex with L-arabinose and D-xylose==
-	<StructureSection load='5z5i' size='340' side='right' caption='[[5z5i]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5z5i' size='340' side='right'caption='[[5z5i]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z5i]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_43513 Atcc 43513~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z5I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Z5I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z5i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_thermoleovorans Geobacillus thermoleovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z5I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z5I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FUB:BETA-L-ARABINOFURANOSE'>FUB</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</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]] 1.7Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">xyl ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33941 ATCC 43513])</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FUB:BETA-L-ARABINOFURANOSE'>FUB</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=5z5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z5i OCA], [https://pdbe.org/5z5i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z5i RCSB], [https://www.ebi.ac.uk/pdbsum/5z5i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z5i 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=5z5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z5i OCA], [~~http~~://pdbe.org/5z5i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5z5i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5z5i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5z5i ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q2I2N4_GEOTH Q2I2N4_GEOTH]
	<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 5z5i" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5z5i" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Xylosidase 3D structures\|Xylosidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 43513~~]]	+	[[Category: Geobacillus thermoleovorans]]
-	[[Category: ~~Xylan 1,4-beta-xylosidase~~]]	+	[[Category: Large Structures]]
-	[[Category: Dijkstra~~, B W]]~~	+	[[Category: Dijkstra BW]]
-	~~[[Category: Oosterwijk, N van~~]]	+	[[Category: Puspaningsih NNT]]
-	[[Category: Puspaningsih~~, N N.T~~]]	+	[[Category: Rohman A]]
-	[[Category: Rohman, A]]	+	[[Category: Van Oosterwijk N]]
-	[[Category: ~~Gh43]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Oligosaccharide]]~~	+
-	~~[[Category: Saccharification]]~~	+
-	~~[[Category: Xylanolytic~~]]	+

OCA at 05:55, 16 May 2018

OCA — Wed, 16 May 2018 05:55:47 GMT

←Older revision		Revision as of 05:55, 16 May 2018
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	<StructureSection load='5z5i' size='340' side='right' caption='[[5z5i]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5z5i' size='340' side='right' caption='[[5z5i]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z5i]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z5I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z5i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43513 Atcc 43513]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z5I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FUB:BETA-L-ARABINOFURANOSE'>FUB</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FUB:BETA-L-ARABINOFURANOSE'>FUB</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">xyl ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33941 ATCC 43513])</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=5z5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z5i OCA], [http://pdbe.org/5z5i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z5i RCSB], [http://www.ebi.ac.uk/pdbsum/5z5i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z5i 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=5z5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z5i OCA], [http://pdbe.org/5z5i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z5i RCSB], [http://www.ebi.ac.uk/pdbsum/5z5i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z5i ProSAT]</span></td></tr>
Line 10:		Line 11:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~The main enzymes involved in~~ xylan-backbone ~~hydrolysis are~~ endo-1,4-~~beta~~-~~xylanase and~~ beta~~-xylosidase. beta-Xylosidase converts the xylo-oligosaccharides produced by endo~~-1,4-~~beta-xylanase~~ into xylose monomers. The beta-xylosidase from ~~the thermophilic~~ Geobacillus thermoleovorans IT-08, a ~~member of glycoside hydrolase family 43~~, ~~was crystallized at room temperature using~~ the ~~hanging-drop vapour-diffusion method~~. ~~Two crystal forms were observed. Bipyramid-shaped crystals belonging~~ to ~~space group P4(3)2(1)2~~, with ~~unit-cell parameters a = b = 62.53~~, ~~c = 277.4 A diffracted to~~ 1.55 A resolution. The ~~rectangular crystals belonged~~ to ~~space group P2(1), with unit-cell parameters a = 57~~.94, ~~b = 142~~.1, ~~c = 153~~.~~9 A, beta = 90.5 degrees ,~~ and ~~diffracted to 1.80 A resolution~~.	+	Complete degradation of the xylan backbone of hemicellulosic plant cell walls requires the synergistic action of endo-xylanases and beta-1,4-xylosidases. While endo-xylanases produce xylooligosaccharides from xylan, beta-1,4-xylosidases degrade the xylooligosaccharides into xylose monomers. The glycoside hydrolase family 43 beta-1,4-xylosidase from Geobacillus thermoleovorans IT-08 is a promising, heat stable catalyst for the saccharification of hemicellulosic material into simple fermentable sugars, but it is competitively inhibited by its products arabinose and xylose. As a first step to help overcome this problem, we elucidated crystal structures of the enzyme in the unliganded form and with bound products, at 1.7-2.0 A resolution. The structures are very similar to those of other enzymes belonging to glycoside hydrolase family 43. Unexpectedly, the monosaccharides are bound in very different ways. Arabinose preferentially binds in subsite -1, while xylose exclusively interacts with subsite +1. These structures and sugar binding preferences suggest ways for improving the catalytic performance of the enzyme by rational mutational design.

-	~~Purification, crystallization~~ and ~~preliminary X-ray analysis~~ of a thermostable ~~glycoside hydrolase family 43~~ beta-xylosidase from Geobacillus thermoleovorans IT-08.,Rohman A, van Oosterwijk N, ~~Kralj S, Dijkhuizen L~~, Dijkstra BW~~, Puspaningsih NN Acta Crystallogr Sect F Struct Biol Cryst Commun~~. ~~2007 Nov 1~~;63(~~Pt 11~~):~~932-5~~., doi: 10.~~1107~~/~~S1744309107046015~~. ~~Epub 2007 Oct 24~~. PMID:~~18007043~~<ref>PMID:~~18007043~~</ref>	+	Structural basis of product inhibition by arabinose and xylose of the thermostable GH43 beta-1,4-xylosidase from Geobacillus thermoleovorans IT-08.,Rohman A, van Oosterwijk N, Puspaningsih NNT, Dijkstra BW PLoS One. 2018 Apr 26;13(4):e0196358. doi: 10.1371/journal.pone.0196358., eCollection 2018. PMID:29698436<ref>PMID:29698436</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 43513]]
	[[Category: Xylan 1,4-beta-xylosidase]]		[[Category: Xylan 1,4-beta-xylosidase]]
	[[Category: Dijkstra, B W]]		[[Category: Dijkstra, B W]]

OCA at 05:30, 25 April 2018

OCA — Wed, 25 Apr 2018 05:30:48 GMT

←Older revision		Revision as of 05:30, 25 April 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5z5i is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of a thermostable glycoside hydrolase family 43 {beta}-1,4-xylosidase from Geobacillus thermoleovorans IT-08 in complex with L-arabinose and D-xylose==
		+	<StructureSection load='5z5i' size='340' side='right' caption='[[5z5i]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5z5i]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z5I FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FUB:BETA-L-ARABINOFURANOSE'>FUB</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></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=5z5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z5i OCA], [http://pdbe.org/5z5i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z5i RCSB], [http://www.ebi.ac.uk/pdbsum/5z5i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z5i ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The main enzymes involved in xylan-backbone hydrolysis are endo-1,4-beta-xylanase and beta-xylosidase. beta-Xylosidase converts the xylo-oligosaccharides produced by endo-1,4-beta-xylanase into xylose monomers. The beta-xylosidase from the thermophilic Geobacillus thermoleovorans IT-08, a member of glycoside hydrolase family 43, was crystallized at room temperature using the hanging-drop vapour-diffusion method. Two crystal forms were observed. Bipyramid-shaped crystals belonging to space group P4(3)2(1)2, with unit-cell parameters a = b = 62.53, c = 277.4 A diffracted to 1.55 A resolution. The rectangular crystals belonged to space group P2(1), with unit-cell parameters a = 57.94, b = 142.1, c = 153.9 A, beta = 90.5 degrees , and diffracted to 1.80 A resolution.

-	~~Authors~~:	+	Purification, crystallization and preliminary X-ray analysis of a thermostable glycoside hydrolase family 43 beta-xylosidase from Geobacillus thermoleovorans IT-08.,Rohman A, van Oosterwijk N, Kralj S, Dijkhuizen L, Dijkstra BW, Puspaningsih NN Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Nov 1;63(Pt 11):932-5., doi: 10.1107/S1744309107046015. Epub 2007 Oct 24. PMID:18007043<ref>PMID:18007043</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5z5i" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Xylan 1,4-beta-xylosidase]]
		+	[[Category: Dijkstra, B W]]
		+	[[Category: Oosterwijk, N van]]
		+	[[Category: Puspaningsih, N N.T]]
		+	[[Category: Rohman, A]]
		+	[[Category: Gh43]]
		+	[[Category: Hydrolase]]
		+	[[Category: Oligosaccharide]]
		+	[[Category: Saccharification]]
		+	[[Category: Xylanolytic]]

OCA: Protected "5z5i" [edit=sysop:move=sysop]

OCA — Wed, 07 Feb 2018 04:58:56 GMT

Protected "5z5i" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:58, 7 February 2018

OCA: New page: '''Unreleased structure''' The entry 5z5i is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 07 Feb 2018 04:58:55 GMT

New page: '''Unreleased structure''' The entry 5z5i is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5z5i is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]