3nj3 - Revision history

OCA at 10:00, 14 February 2024

OCA — Wed, 14 Feb 2024 10:00:39 GMT

←Older revision		Revision as of 10:00, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='3nj3' size='340' side='right'caption='[[3nj3]], [[Resolution\|resolution]] 1.88Å' scene=''>		<StructureSection load='3nj3' size='340' side='right'caption='[[3nj3]], [[Resolution\|resolution]] 1.88Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3nj3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Thep1 Thep1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NJ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NJ3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3nj3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_petrophila_RKU-1 Thermotoga petrophila RKU-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NJ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NJ3 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.88Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3niy\|3niy]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PRD_900116:4beta-beta-xylobiose'>PRD_900116</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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">Tpet_0854 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=390874 THEP1])</td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Endo~~-~~1,4~~-~~beta-xylanase Endo-1,4-beta-xylanase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=3nj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nj3 OCA], [https://pdbe.org/3nj3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nj3 RCSB], [https://www.ebi.ac.uk/pdbsum/3nj3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nj3 ProSAT]</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=3nj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nj3 OCA], [https://pdbe.org/3nj3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nj3 RCSB], [https://www.ebi.ac.uk/pdbsum/3nj3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nj3 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A5IL00_THEP1 A5IL00_THEP1]
-	Endo-xylanases play a key role in the depolymerization of xylan and recently, they have attracted much attention owing to their potential applications on biofuels and paper industries. In this work, we have investigated the molecular basis for the action mode of xylanases 10B at high temperatures using biochemical, biophysical and crystallographic methods. The crystal structure of xylanase 10B from hyperthermophilic bacterium Thermotoga petrophila RKU-1 (TpXyl10B) has been solved in the native state and in complex with xylobiose. The complex crystal structure showed a classical binding mode shared among other xylanases, which encompasses the -1 and -2 subsites. Interestingly, TpXyl10B displayed a temperature-dependent action mode producing xylobiose and xylotriose at 20 degrees C, and exclusively xylobiose at 90 degrees C as assessed by capillary zone electrophoresis. Moreover, circular dichroism spectroscopy suggested a coupling effect of temperature-induced structural changes with this particular enzymatic behavior. Molecular dynamics simulations supported the CD analysis suggesting that an open conformational state adopted by the catalytic loop (Trp297-Lys326) provokes significant modifications in the product release area (+1,+2 and +3 subsites), which drives the enzymatic activity to the specific release of xylobiose at high temperatures.	+
-		+
-	~~Thermal-induced conformational changes in the product release area drive the enzymatic activity of xylanases 10B~~: Crystal structure, conformational stability and functional characterization of the xylanase 10B from Thermotoga petrophila RKU-1.,Santos CR, Meza AN, Hoffmam ZB, Silva JC, Alvarez TM, Ruller R, Giesel GM, Verli H, Squina FM, Prade RA, Murakami MT Biochem Biophys Res Commun. 2010 Dec 10;403(2):214-9. Epub 2010 Nov 9. PMID:21070746<ref>PMID:21070746</~~ref>~~	+
-		+
-	~~From MEDLINE®~~/~~PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 3nj3" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thep1~~]]	+	[[Category: Thermotoga petrophila RKU-1]]
-	[[Category: Meza~~, A N~~]]	+	[[Category: Meza AN]]
-	[[Category: Murakami~~, M T~~]]	+	[[Category: Murakami MT]]
-	[[Category: Prade~~, R A~~]]	+	[[Category: Prade RA]]
-	[[Category: Ruller, R]]	+	[[Category: Ruller R]]
-	[[Category: Santos~~, C R~~]]	+	[[Category: Santos CR]]
-	[[Category: Squina~~, F M~~]]	+	[[Category: Squina FM]]
-	[[Category: Trindade~~, D M]]~~	+	[[Category: Trindade DM]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Tim barrel]]~~	+
-	~~[[Category: Xylanase~~]]	+

OCA at 07:03, 12 May 2022

OCA — Thu, 12 May 2022 07:03:18 GMT

←Older revision		Revision as of 07:03, 12 May 2022
Line 1:		Line 1:

	==Crystal structure of xylanase 10B from Thermotoga petrophila RKU-1 in complex with xylobiose==		==Crystal structure of xylanase 10B from Thermotoga petrophila RKU-1 in complex with xylobiose==
-	<StructureSection load='3nj3' size='340' side='right' caption='[[3nj3]], [[Resolution\|resolution]] 1.88Å' scene=''>	+	<StructureSection load='3nj3' size='340' side='right'caption='[[3nj3]], [[Resolution\|resolution]] 1.88Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3nj3]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Thep1 Thep1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NJ3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3NJ3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3nj3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thep1 Thep1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NJ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NJ3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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">[[3niy\|3niy]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3niy\|3niy]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tpet_0854 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=390874 THEP1])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tpet_0854 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=390874 THEP1])</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [https://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~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3nj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nj3 OCA], [~~http~~://pdbe.org/3nj3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3nj3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3nj3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3nj3 ProSAT]</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=3nj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nj3 OCA], [https://pdbe.org/3nj3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nj3 RCSB], [https://www.ebi.ac.uk/pdbsum/3nj3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nj3 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
		+	[[Category: Large Structures]]
	[[Category: Thep1]]		[[Category: Thep1]]
	[[Category: Meza, A N]]		[[Category: Meza, A N]]

OCA at 04:01, 10 December 2016

OCA — Sat, 10 Dec 2016 04:01:58 GMT

←Older revision		Revision as of 04:01, 10 December 2016
Line 1:		Line 1:
		+
	==Crystal structure of xylanase 10B from Thermotoga petrophila RKU-1 in complex with xylobiose==		==Crystal structure of xylanase 10B from Thermotoga petrophila RKU-1 in complex with xylobiose==
	<StructureSection load='3nj3' size='340' side='right' caption='[[3nj3]], [[Resolution\|resolution]] 1.88Å' scene=''>		<StructureSection load='3nj3' size='340' side='right' caption='[[3nj3]], [[Resolution\|resolution]] 1.88Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3nj3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermotoga_petrophila_rku-1 Thermotoga petrophila rku-1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NJ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NJ3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3nj3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thep1 Thep1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NJ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NJ3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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">[[3niy\|3niy]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3niy\|3niy]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tpet_0854 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=390874 ~~Thermotoga petrophila RKU-1~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tpet_0854 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=390874 THEP1])</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='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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3nj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nj3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nj3 RCSB], [http://www.ebi.ac.uk/pdbsum/3nj3 PDBsum]</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=3nj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nj3 OCA], [http://pdbe.org/3nj3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3nj3 RCSB], [http://www.ebi.ac.uk/pdbsum/3nj3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3nj3 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	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>
	</div>		</div>
		+	<div class="pdbe-citations 3nj3" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 22:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
-	[[Category: ~~Thermotoga petrophila rku-1~~]]	+	[[Category: Thep1]]
	[[Category: Meza, A N]]		[[Category: Meza, A N]]
	[[Category: Murakami, M T]]		[[Category: Murakami, M T]]

OCA at 08:47, 15 February 2015

OCA — Sun, 15 Feb 2015 08:47:55 GMT

←Older revision		Revision as of 08:47, 15 February 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_3nj3~~\| ~~PDB~~=3nj3 \| ~~SCENE~~= }}	+	==Crystal structure of xylanase 10B from Thermotoga petrophila RKU-1 in complex with xylobiose==
-	===~~Crystal~~ structure of xylanase 10B from Thermotoga petrophila RKU-1 in complex with xylobiose~~===~~	+	<StructureSection load='3nj3' size='340' side='right' caption='[[3nj3]], [[Resolution\|resolution]] 1.88Å' scene=''>
-	~~{{ABSTRACT_PUBMED_21070746}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3nj3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_petrophila_rku-1 Thermotoga petrophila rku-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NJ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NJ3 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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">[[3niy\|3niy]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tpet_0854 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=390874 Thermotoga petrophila RKU-1])</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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3nj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nj3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nj3 RCSB], [http://www.ebi.ac.uk/pdbsum/3nj3 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Endo-xylanases play a key role in the depolymerization of xylan and recently, they have attracted much attention owing to their potential applications on biofuels and paper industries. In this work, we have investigated the molecular basis for the action mode of xylanases 10B at high temperatures using biochemical, biophysical and crystallographic methods. The crystal structure of xylanase 10B from hyperthermophilic bacterium Thermotoga petrophila RKU-1 (TpXyl10B) has been solved in the native state and in complex with xylobiose. The complex crystal structure showed a classical binding mode shared among other xylanases, which encompasses the -1 and -2 subsites. Interestingly, TpXyl10B displayed a temperature-dependent action mode producing xylobiose and xylotriose at 20 degrees C, and exclusively xylobiose at 90 degrees C as assessed by capillary zone electrophoresis. Moreover, circular dichroism spectroscopy suggested a coupling effect of temperature-induced structural changes with this particular enzymatic behavior. Molecular dynamics simulations supported the CD analysis suggesting that an open conformational state adopted by the catalytic loop (Trp297-Lys326) provokes significant modifications in the product release area (+1,+2 and +3 subsites), which drives the enzymatic activity to the specific release of xylobiose at high temperatures.

-	~~==About this Structure==~~	+	Thermal-induced conformational changes in the product release area drive the enzymatic activity of xylanases 10B: Crystal structure, conformational stability and functional characterization of the xylanase 10B from Thermotoga petrophila RKU-1.,Santos CR, Meza AN, Hoffmam ZB, Silva JC, Alvarez TM, Ruller R, Giesel GM, Verli H, Squina FM, Prade RA, Murakami MT Biochem Biophys Res Commun. 2010 Dec 10;403(2):214-9. Epub 2010 Nov 9. PMID:21070746<ref>PMID:21070746</ref>
-	~~[[3nj3]] is a 2 chain~~ structure ~~with sequence~~ from ~~[http://en.wikipedia.org/wiki/Thermotoga_petrophila_rku-1~~ Thermotoga petrophila ~~rku~~-1]. ~~Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=3NJ3 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:021070746</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Thermotoga petrophila rku-1]]		[[Category: Thermotoga petrophila rku-1]]
-	[[Category: Meza, A N.]]	+	[[Category: Meza, A N]]
-	[[Category: Murakami, M T.]]	+	[[Category: Murakami, M T]]
-	[[Category: Prade, R A.]]	+	[[Category: Prade, R A]]
-	[[Category: Ruller, R.]]	+	[[Category: Ruller, R]]
-	[[Category: Santos, C R.]]	+	[[Category: Santos, C R]]
-	[[Category: Squina, F M.]]	+	[[Category: Squina, F M]]
-	[[Category: Trindade, D M.]]	+	[[Category: Trindade, D M]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Tim barrel]]		[[Category: Tim barrel]]
	[[Category: Xylanase]]		[[Category: Xylanase]]

OCA at 11:56, 24 April 2013

OCA — Wed, 24 Apr 2013 11:56:29 GMT

←Older revision		Revision as of 11:56, 24 April 2013
Line 1:		Line 1:
-	[[Image:3nj3.jpg\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3nj3", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3nj3\| PDB=3nj3 \| SCENE= }}		{{STRUCTURE_3nj3\| PDB=3nj3 \| SCENE= }}
-
	===Crystal structure of xylanase 10B from Thermotoga petrophila RKU-1 in complex with xylobiose===		===Crystal structure of xylanase 10B from Thermotoga petrophila RKU-1 in complex with xylobiose===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_21070746}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 21070746 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_21070746}}		{{ABSTRACT_PUBMED_21070746}}

	==About this Structure==		==About this Structure==
-	[[3nj3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacteria Bacteria~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NJ3 OCA].	+	[[3nj3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_petrophila_rku-1 Thermotoga petrophila rku-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NJ3 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:021070746</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021070746</ref><references group="xtra"/><references/>
-	~~[[Category: Bacteria]]~~	+
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
		+	[[Category: Thermotoga petrophila rku-1]]
	[[Category: Meza, A N.]]		[[Category: Meza, A N.]]
	[[Category: Murakami, M T.]]		[[Category: Murakami, M T.]]
Line 32:		Line 17:
	[[Category: Squina, F M.]]		[[Category: Squina, F M.]]
	[[Category: Trindade, D M.]]		[[Category: Trindade, D M.]]
		+	[[Category: Hydrolase]]
		+	[[Category: Tim barrel]]
		+	[[Category: Xylanase]]

OCA: Protected "3nj3" [edit=sysop:move=sysop]

OCA — Wed, 04 May 2011 06:49:20 GMT

Protected "3nj3" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:49, 4 May 2011

OCA at 06:49, 4 May 2011

OCA — Wed, 04 May 2011 06:49:16 GMT

←Older revision		Revision as of 06:49, 4 May 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3nj3.jpg\|left\|200px]]

-	The ~~entry 3nj3~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3nj3", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3nj3\| PDB=3nj3 \| SCENE= }}

-	~~Authors: Santos, C.R., Meza, A.N., Trindade, D.M., Ruller, R., Squina, F.M., Prade, R.A., Murakami, M.T.~~	+	===Crystal structure of xylanase 10B from Thermotoga petrophila RKU-1 in complex with xylobiose===

-	Description: Crystal structure of xylanase 10B from Thermotoga petrophila RKU-1 in complex with xylobiose

-	~~''Page seeded by~~ [http://oca.weizmann.ac.il/oca OCA ] ~~on Wed Jun 30 13~~:35:~~57 2010''~~	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21070746}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21070746 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21070746}}
		+
		+	==About this Structure==
		+	[[3nj3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteria Bacteria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NJ3 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021070746</ref><references group="xtra"/>
		+	[[Category: Bacteria]]
		+	[[Category: Endo-1,4-beta-xylanase]]
		+	[[Category: Meza, A N.]]
		+	[[Category: Murakami, M T.]]
		+	[[Category: Prade, R A.]]
		+	[[Category: Ruller, R.]]
		+	[[Category: Santos, C R.]]
		+	[[Category: Squina, F M.]]
		+	[[Category: Trindade, D M.]]

OCA at 09:30, 30 June 2010

OCA — Wed, 30 Jun 2010 09:30:22 GMT

←Older revision		Revision as of 09:30, 30 June 2010
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3nj3 is ON HOLD	+	The entry 3nj3 is ON HOLD until Paper Publication

	Authors: Santos, C.R., Meza, A.N., Trindade, D.M., Ruller, R., Squina, F.M., Prade, R.A., Murakami, M.T.		Authors: Santos, C.R., Meza, A.N., Trindade, D.M., Ruller, R., Squina, F.M., Prade, R.A., Murakami, M.T.
Line 7:		Line 7:
	Description: Crystal structure of xylanase 10B from Thermotoga petrophila RKU-1 in complex with xylobiose		Description: Crystal structure of xylanase 10B from Thermotoga petrophila RKU-1 in complex with xylobiose

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun ~~23 08~~:44:00 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 30 13:35:57 2010''

OCA: New page: '''Unreleased structure''' The entry 3nj3 is ON HOLD Authors: Santos, C.R., Meza, A.N., Trindade, D.M., Ruller, R., Squina, F.M., Prade, R.A., Murakami, M.T. Description: Crystal struc...

OCA — Wed, 23 Jun 2010 04:38:42 GMT

New page: '''Unreleased structure''' The entry 3nj3 is ON HOLD Authors: Santos, C.R., Meza, A.N., Trindade, D.M., Ruller, R., Squina, F.M., Prade, R.A., Murakami, M.T. Description: Crystal struc...

New page

'''Unreleased structure'''

The entry 3nj3 is ON HOLD

Authors: Santos, C.R., Meza, A.N., Trindade, D.M., Ruller, R., Squina, F.M., Prade, R.A., Murakami, M.T.

Description: Crystal structure of xylanase 10B from Thermotoga petrophila RKU-1 in complex with xylobiose

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 23 08:44:00 2010''