5la1 - Revision history

OCA at 16:12, 4 October 2023

OCA — Wed, 04 Oct 2023 16:12:47 GMT

←Older revision		Revision as of 16:12, 4 October 2023
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	==The mechanism by which arabinoxylanases can recognise highly decorated xylans==		==The mechanism by which arabinoxylanases can recognise highly decorated xylans==
-	<StructureSection load='5la1' size='340' side='right' caption='[[5la1]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5la1' size='340' side='right'caption='[[5la1]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5la1]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Clostridium_thermocellum_dsm_4150 Clostridium thermocellum dsm 4150~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LA1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5LA1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5la1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetivibrio_thermocellus_JW20 Acetivibrio thermocellus JW20]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LA1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LA1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=144:TRIS-HYDROXYMETHYL-METHYL-AMMONIUM'>144</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 1.9Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cther_1146 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=492476 Clostridium thermocellum DSM 4150])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=144:TRIS-HYDROXYMETHYL-METHYL-AMMONIUM'>144</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></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=5la1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5la1 OCA], [~~http~~://pdbe.org/5la1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5la1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5la1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5la1 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=5la1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5la1 OCA], [https://pdbe.org/5la1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5la1 RCSB], [https://www.ebi.ac.uk/pdbsum/5la1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5la1 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A3DHG6_ACET2 A3DHG6_ACET2]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Clostridium thermocellum dsm 4150~~]]	+	[[Category: Acetivibrio thermocellus JW20]]
-	[[Category: Basle, A]]	+	[[Category: Large Structures]]
-	[[Category: Crouch, L]]	+	[[Category: Basle A]]
-	[[Category: Cuskin, F]]	+	[[Category: Crouch L]]
-	[[Category: Gilbert, H]]	+	[[Category: Cuskin F]]
-	[[Category: Jackson, A]]	+	[[Category: Gilbert H]]
-	[[Category: Labourel, A]]	+	[[Category: Jackson A]]
-	[[Category: Rogowski, A]]	+	[[Category: Labourel A]]
-	~~[[Category: Arabinoxylanase glycoside hydrolase carbohydrate binding module arabinose clostridium thermocellum cellulosome]]~~	+	[[Category: Rogowski A]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 06:25, 24 October 2018

OCA — Wed, 24 Oct 2018 06:25:23 GMT

←Older revision		Revision as of 06:25, 24 October 2018
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	<StructureSection load='5la1' size='340' side='right' caption='[[5la1]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5la1' size='340' side='right' caption='[[5la1]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5la1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LA1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LA1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5la1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_thermocellum_dsm_4150 Clostridium thermocellum dsm 4150]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LA1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LA1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=144:TRIS-HYDROXYMETHYL-METHYL-AMMONIUM'>144</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=~~XYB~~:~~4-O-BETA-D-XYLOPYRANOSYL-~~BETA-D-XYLOPYRANOSE'>~~XYB~~</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=144:TRIS-HYDROXYMETHYL-METHYL-AMMONIUM'>144</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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">Cther_1146 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=492476 Clostridium thermocellum DSM 4150])</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=5la1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5la1 OCA], [http://pdbe.org/5la1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5la1 RCSB], [http://www.ebi.ac.uk/pdbsum/5la1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5la1 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=5la1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5la1 OCA], [http://pdbe.org/5la1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5la1 RCSB], [http://www.ebi.ac.uk/pdbsum/5la1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5la1 ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Clostridium thermocellum dsm 4150]]
	[[Category: Basle, A]]		[[Category: Basle, A]]
	[[Category: Crouch, L]]		[[Category: Crouch, L]]

OCA at 14:01, 10 September 2016

OCA — Sat, 10 Sep 2016 14:01:19 GMT

←Older revision		Revision as of 14:01, 10 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5la1 is ~~ON HOLD until Paper~~ Publication	+	==The mechanism by which arabinoxylanases can recognise highly decorated xylans==
		+	<StructureSection load='5la1' size='340' side='right' caption='[[5la1]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5la1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LA1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LA1 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=144:TRIS-HYDROXYMETHYL-METHYL-AMMONIUM'>144</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=XYB:4-O-BETA-D-XYLOPYRANOSYL-BETA-D-XYLOPYRANOSE'>XYB</scene></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=5la1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5la1 OCA], [http://pdbe.org/5la1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5la1 RCSB], [http://www.ebi.ac.uk/pdbsum/5la1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5la1 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The enzymatic degradation of plant cell walls is an important biological process of increasing environmental and industrial significance. Xylan, a major component of the plant cell wall, consists of a backbone of xylose (Xylp) units that are often decorated with arabinofuranose (Araf) side chains. A large penta-modular arabinoxylanase, CtXyl5A, was shown previously to specifically target arabinoxylans. However, the mechanism of substrate recognition displayed by the enzyme remains unclear. Here we report the crystal structure of the tetra-modular arabinoxylanase, and the enzyme in complex with ligands. The data showed that the multi-modular protein adopts a rigid structure, which stabilises the catalytic domain. The C-terminal non-catalytic carbohydrate binding module could not be observed in the crystal structure indicating positional flexibility. The structure of the enzyme in complex with Xylp-1,4-Xylp-1,4-Xylp-[1,3-Araf]-1,4-Xylp showed that the Araf decoration linked O3 to the xylose in the active site is located in the pocket (-2* subsite) that abuts onto the catalytic centre. The -2* subsite can also bind to Xylp and Arap, explaining why the enzyme can utilize xylose and arabinose as specificity determinants. Alanine substitution of Glu68, Tyr92 or Asn139, which interact with arabinose and xylose side chains at the -2* subsite abrogate catalytic activity. Distal to the active site the xylan backbone makes limited apolar contacts with the enzyme and the hydroxyls are solvent exposed. This explains why CtXyl5A is capable of hydrolysing xylans that are extensively decorated, and which are recalcitrant to classic endo-xylanase attack.

-	~~Authors: Arnaud Basle~~, ~~Aurore~~ Labourel, ~~Fiona Cuskin~~, ~~Adan~~ Jackson, ~~Lucy Crouch, Artur~~ Rogowski, ~~Harry~~ Gilbert	+	The mechanism by which arabinoxylanases can recognise highly decorated xylans.,Labourel A, Crouch LI, Bras JL, Jackson A, Rogowski A, Gray J, Yadav MP, Henrissat B, Fontes CM, Gilbert HJ, Najmudin S, Basle A, Cuskin F J Biol Chem. 2016 Aug 16. pii: jbc.M116.743948. PMID:27531750<ref>PMID:27531750</ref>

-	~~Description~~: ~~The mechanism by which arabinoxylanases can recognise highly decorated xylans~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Arnaud Basle, Aurore Labourel~~, ~~Fiona~~ Cuskin, ~~Adan~~ Jackson, ~~Lucy Crouch~~, ~~Artur~~ Rogowski, ~~Harry Gilbert~~]]	+	<div class="pdbe-citations 5la1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Basle, A]]
		+	[[Category: Crouch, L]]
		+	[[Category: Cuskin, F]]
		+	[[Category: Gilbert, H]]
		+	[[Category: Jackson, A]]
		+	[[Category: Labourel, A]]
		+	[[Category: Rogowski, A]]
		+	[[Category: Arabinoxylanase glycoside hydrolase carbohydrate binding module arabinose clostridium thermocellum cellulosome]]
		+	[[Category: Hydrolase]]

OCA: Protected "5la1" [edit=sysop:move=sysop]

OCA — Thu, 23 Jun 2016 21:54:45 GMT

Protected "5la1" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:54, 23 June 2016

OCA: New page: '''Unreleased structure''' The entry 5la1 is ON HOLD until Paper Publication Authors: Arnaud Basle, Aurore Labourel, Fiona Cuskin, Adan Jackson, Lucy Crouch, Artur Rogowski, Harry Gilbe...

OCA — Thu, 23 Jun 2016 21:54:43 GMT

New page: '''Unreleased structure''' The entry 5la1 is ON HOLD until Paper Publication Authors: Arnaud Basle, Aurore Labourel, Fiona Cuskin, Adan Jackson, Lucy Crouch, Artur Rogowski, Harry Gilbe...

New page

'''Unreleased structure'''

The entry 5la1 is ON HOLD until Paper Publication

Authors: Arnaud Basle, Aurore Labourel, Fiona Cuskin, Adan Jackson, Lucy Crouch, Artur Rogowski, Harry Gilbert

Description: The mechanism by which arabinoxylanases can recognise highly decorated xylans
[[Category: Unreleased Structures]]
[[Category: Arnaud Basle, Aurore Labourel, Fiona Cuskin, Adan Jackson, Lucy Crouch, Artur Rogowski, Harry Gilbert]]