2y6h - Revision history

OCA at 07:11, 1 May 2024

OCA — Wed, 01 May 2024 07:11:52 GMT

←Older revision		Revision as of 07:11, 1 May 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q7WTN6_RHOMR Q7WTN6_RHOMR]		[https://www.uniprot.org/uniprot/Q7WTN6_RHOMR Q7WTN6_RHOMR]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Detection, immobilization and purification of carbohydrates can be done using molecular probes that specifically bind to targeted carbohydrate epitopes. Carbohydrate-binding modules (CBMs) are discrete parts of carbohydrate-hydrolyzing enzymes that can be engineered to bind and detect specifically a number of carbohydrates. Design and engineering of CBMs have benefited greatly from structural studies that have helped us to decipher the basis for specificity in carbohydrate-protein interactions. However, more studies are needed to predict which modifications in a CBM would generate probes with predetermined binding properties. In this report, we present the crystal structures of two highly related engineered CBMs with different binding specificity profiles: X-2, which is specific for xylans and the L110F mutant of X-2, which binds xyloglucans and beta-glucans in addition to xylans. The structures of the modules were solved both in the apo form and complexed with oligomers of xylose, as well as with an oligomer of glucose in the case of X-2 L110F. The mutation, leucine to phenylalanine, converting the specific module into a cross-reactive one, introduces a crucial hydrogen-pi interaction that allows the mutant to retain glucan-based ligands. The cross-reactivity of X-2 L110F is furthermore made possible by the plasticity of the protein, in particular, of residue R142, which permits accommodation of an extra hydroxymethyl group present in cellopentaose and not xylopentaose. Altogether, this study shows, in structural detail, altered protein-carbohydrate interactions that have high impact on the binding properties of a carbohydrate probe but are introduced through simple mutagenesis.
-
-	Structural basis for carbohydrate-binding specificity--a comparative assessment of two engineered carbohydrate-binding modules.,von Schantz L, Hakansson M, Logan DT, Walse B, Osterlin J, Nordberg-Karlsson E, Ohlin M Glycobiology. 2012 Jul;22(7):948-61. Epub 2012 Mar 20. PMID:22434778<ref>PMID:22434778</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2y6h" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:09, 23 August 2023

OCA — Wed, 23 Aug 2023 08:09:20 GMT

←Older revision		Revision as of 08:09, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='2y6h' size='340' side='right'caption='[[2y6h]], [[Resolution\|resolution]] 1.08Å' scene=''>		<StructureSection load='2y6h' size='340' side='right'caption='[[2y6h]], [[Resolution\|resolution]] 1.08Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2y6h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_43812 Atcc 43812~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y6H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y6H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2y6h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodothermus_marinus Rhodothermus marinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y6H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y6H FirstGlance]. <br>
-	</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>~~</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]] 1.08Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[2y64\|2y64]], [[2y6g\|2y6g]], [[2y6j\|2y6j]], [[2y6k\|2y6k]], [[2y6l\|2y6l]]</div></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></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=2y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y6h OCA], [https://pdbe.org/2y6h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2y6h RCSB], [https://www.ebi.ac.uk/pdbsum/2y6h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2y6h 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=2y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y6h OCA], [https://pdbe.org/2y6h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2y6h RCSB], [https://www.ebi.ac.uk/pdbsum/2y6h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2y6h ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q7WTN6_RHOMR Q7WTN6_RHOMR]
	<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: Atcc 43812]]
-	[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hakansson, M]]	+	[[Category: Rhodothermus marinus]]
-	[[Category: Logan~~, D T~~]]	+	[[Category: Hakansson M]]
-	[[Category: Nordberg-Karlsson, E]]	+	[[Category: Logan DT]]
-	[[Category: Ohlin, M]]	+	[[Category: Nordberg-Karlsson E]]
-	[[Category: Osterlin, J]]	+	[[Category: Ohlin M]]
-	~~[[Category: Schantz, L von~~]]	+	[[Category: Osterlin J]]
-	[[Category: Walse, B]]	+	[[Category: Walse B]]
-	[[Category: ~~Hydrolase~~]]	+	[[Category: Von Schantz L]]

OCA at 15:00, 17 November 2021

OCA — Wed, 17 Nov 2021 15:00:24 GMT

←Older revision		Revision as of 15:00, 17 November 2021
Line 3:		Line 3:
	<StructureSection load='2y6h' size='340' side='right'caption='[[2y6h]], [[Resolution\|resolution]] 1.08Å' scene=''>		<StructureSection load='2y6h' size='340' side='right'caption='[[2y6h]], [[Resolution\|resolution]] 1.08Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2y6h]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_43812 Atcc 43812]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y6H OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2Y6H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2y6h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43812 Atcc 43812]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y6H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y6H 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></td></tr>	+	</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></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2y64\|2y64]], [[2y6g\|2y6g]], [[2y6j\|2y6j]], [[2y6k\|2y6k]], [[2y6l\|2y6l]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2y64\|2y64]], [[2y6g\|2y6g]], [[2y6j\|2y6j]], [[2y6k\|2y6k]], [[2y6l\|2y6l]]</div></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=2y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y6h OCA], [~~http~~://pdbe.org/2y6h PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2y6h RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2y6h PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2y6h 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=2y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y6h OCA], [https://pdbe.org/2y6h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2y6h RCSB], [https://www.ebi.ac.uk/pdbsum/2y6h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2y6h ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 14:18, 25 December 2019

OCA — Wed, 25 Dec 2019 14:18:37 GMT

←Older revision		Revision as of 14:18, 25 December 2019
Line 1:		Line 1:

	==X-2 L110F CBM4-2 Carbohydrate Binding Module from a Thermostable Rhodothermus marinus Xylanase==		==X-2 L110F CBM4-2 Carbohydrate Binding Module from a Thermostable Rhodothermus marinus Xylanase==
-	<StructureSection load='2y6h' size='340' side='right' caption='[[2y6h]], [[Resolution\|resolution]] 1.08Å' scene=''>	+	<StructureSection load='2y6h' size='340' side='right'caption='[[2y6h]], [[Resolution\|resolution]] 1.08Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2y6h]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43812 Atcc 43812]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y6H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Y6H FirstGlance]. <br>		<table><tr><td colspan='2'>[[2y6h]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43812 Atcc 43812]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y6H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Y6H FirstGlance]. <br>
Line 24:		Line 24:
	[[Category: Atcc 43812]]		[[Category: Atcc 43812]]
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
		+	[[Category: Large Structures]]
	[[Category: Hakansson, M]]		[[Category: Hakansson, M]]
	[[Category: Logan, D T]]		[[Category: Logan, D T]]

OCA at 07:33, 17 January 2018

OCA — Wed, 17 Jan 2018 07:33:59 GMT

←Older revision		Revision as of 07:33, 17 January 2018
Line 25:		Line 25:
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Hakansson, M]]		[[Category: Hakansson, M]]
-	[[Category: Karlsson, E Nordberg]]
	[[Category: Logan, D T]]		[[Category: Logan, D T]]
		+	[[Category: Nordberg-Karlsson, E]]
	[[Category: Ohlin, M]]		[[Category: Ohlin, M]]
	[[Category: Osterlin, J]]		[[Category: Osterlin, J]]
-	[[Category: Schantz, L ~~Von~~]]	+	[[Category: Schantz, L von]]
	[[Category: Walse, B]]		[[Category: Walse, B]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 07:51, 5 August 2016

OCA — Fri, 05 Aug 2016 07:51:57 GMT

←Older revision		Revision as of 07:51, 5 August 2016
Line 1:		Line 1:
		+
	==X-2 L110F CBM4-2 Carbohydrate Binding Module from a Thermostable Rhodothermus marinus Xylanase==		==X-2 L110F CBM4-2 Carbohydrate Binding Module from a Thermostable Rhodothermus marinus Xylanase==
	<StructureSection load='2y6h' size='340' side='right' caption='[[2y6h]], [[Resolution\|resolution]] 1.08Å' scene=''>		<StructureSection load='2y6h' size='340' side='right' caption='[[2y6h]], [[Resolution\|resolution]] 1.08Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2y6h]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rhodothermus_marinus Rhodothermus marinus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y6H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Y6H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2y6h]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43812 Atcc 43812]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y6H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Y6H 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></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></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2y64\|2y64]], [[2y6g\|2y6g]], [[2y6j\|2y6j]], [[2y6k\|2y6k]], [[2y6l\|2y6l]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2y64\|2y64]], [[2y6g\|2y6g]], [[2y6j\|2y6j]], [[2y6k\|2y6k]], [[2y6l\|2y6l]]</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=2y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y6h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2y6h RCSB], [http://www.ebi.ac.uk/pdbsum/2y6h 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=2y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y6h OCA], [http://pdbe.org/2y6h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2y6h RCSB], [http://www.ebi.ac.uk/pdbsum/2y6h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2y6h ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 2y6h" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 43812]]
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
-	[[Category: Rhodothermus marinus]]
	[[Category: Hakansson, M]]		[[Category: Hakansson, M]]
	[[Category: Karlsson, E Nordberg]]		[[Category: Karlsson, E Nordberg]]

OCA at 23:25, 3 January 2015

OCA — Sat, 03 Jan 2015 23:25:27 GMT

←Older revision		Revision as of 23:25, 3 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2y6h]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodothermus_marinus Rhodothermus marinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y6H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Y6H FirstGlance]. <br>		<table><tr><td colspan='2'>[[2y6h]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodothermus_marinus Rhodothermus marinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y6H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Y6H FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><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></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2y64\|2y64]], [[2y6g\|2y6g]], [[2y6j\|2y6j]], [[2y6k\|2y6k]], [[2y6l\|2y6l]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2y64\|2y64]], [[2y6g\|2y6g]], [[2y6j\|2y6j]], [[2y6k\|2y6k]], [[2y6l\|2y6l]]</td></tr>
-	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y6h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2y6h RCSB], [http://www.ebi.ac.uk/pdbsum/2y6h 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=2y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y6h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2y6h RCSB], [http://www.ebi.ac.uk/pdbsum/2y6h PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 14:		Line 14:
	Structural basis for carbohydrate-binding specificity--a comparative assessment of two engineered carbohydrate-binding modules.,von Schantz L, Hakansson M, Logan DT, Walse B, Osterlin J, Nordberg-Karlsson E, Ohlin M Glycobiology. 2012 Jul;22(7):948-61. Epub 2012 Mar 20. PMID:22434778<ref>PMID:22434778</ref>		Structural basis for carbohydrate-binding specificity--a comparative assessment of two engineered carbohydrate-binding modules.,von Schantz L, Hakansson M, Logan DT, Walse B, Osterlin J, Nordberg-Karlsson E, Ohlin M Glycobiology. 2012 Jul;22(7):948-61. Epub 2012 Mar 20. PMID:22434778<ref>PMID:22434778</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 22:		Line 22:
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Rhodothermus marinus]]		[[Category: Rhodothermus marinus]]
-	[[Category: Hakansson, M.]]	+	[[Category: Hakansson, M]]
-	[[Category: Karlsson, E Nordberg.]]	+	[[Category: Karlsson, E Nordberg]]
-	[[Category: Logan, D T.]]	+	[[Category: Logan, D T]]
-	[[Category: Ohlin, M.]]	+	[[Category: Ohlin, M]]
-	[[Category: Osterlin, J.]]	+	[[Category: Osterlin, J]]
-	[[Category: Schantz, L Von.]]	+	[[Category: Schantz, L Von]]
-	[[Category: Walse, B.]]	+	[[Category: Walse, B]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 05:34, 4 June 2014

OCA — Wed, 04 Jun 2014 05:34:33 GMT

←Older revision		Revision as of 05:34, 4 June 2014
Line 1:		Line 1:
-	[[~~Image:~~2y6h.~~png~~\|~~left~~\|~~200px~~]]	+	==X-2 L110F CBM4-2 Carbohydrate Binding Module from a Thermostable Rhodothermus marinus Xylanase==
		+	<StructureSection load='2y6h' size='340' side='right' caption='[[2y6h]], [[Resolution\|resolution]] 1.08Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2y6h]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodothermus_marinus Rhodothermus marinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y6H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Y6H FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2y64\|2y64]], [[2y6g\|2y6g]], [[2y6j\|2y6j]], [[2y6k\|2y6k]], [[2y6l\|2y6l]]</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y6h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2y6h RCSB], [http://www.ebi.ac.uk/pdbsum/2y6h PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Detection, immobilization and purification of carbohydrates can be done using molecular probes that specifically bind to targeted carbohydrate epitopes. Carbohydrate-binding modules (CBMs) are discrete parts of carbohydrate-hydrolyzing enzymes that can be engineered to bind and detect specifically a number of carbohydrates. Design and engineering of CBMs have benefited greatly from structural studies that have helped us to decipher the basis for specificity in carbohydrate-protein interactions. However, more studies are needed to predict which modifications in a CBM would generate probes with predetermined binding properties. In this report, we present the crystal structures of two highly related engineered CBMs with different binding specificity profiles: X-2, which is specific for xylans and the L110F mutant of X-2, which binds xyloglucans and beta-glucans in addition to xylans. The structures of the modules were solved both in the apo form and complexed with oligomers of xylose, as well as with an oligomer of glucose in the case of X-2 L110F. The mutation, leucine to phenylalanine, converting the specific module into a cross-reactive one, introduces a crucial hydrogen-pi interaction that allows the mutant to retain glucan-based ligands. The cross-reactivity of X-2 L110F is furthermore made possible by the plasticity of the protein, in particular, of residue R142, which permits accommodation of an extra hydroxymethyl group present in cellopentaose and not xylopentaose. Altogether, this study shows, in structural detail, altered protein-carbohydrate interactions that have high impact on the binding properties of a carbohydrate probe but are introduced through simple mutagenesis.

-	~~{{STRUCTURE_2y6h\| PDB=2y6h \| SCENE= }}~~	+	Structural basis for carbohydrate-binding specificity--a comparative assessment of two engineered carbohydrate-binding modules.,von Schantz L, Hakansson M, Logan DT, Walse B, Osterlin J, Nordberg-Karlsson E, Ohlin M Glycobiology. 2012 Jul;22(7):948-61. Epub 2012 Mar 20. PMID:22434778<ref>PMID:22434778</ref>

-	~~===X-2 L110F CBM4-2 Carbohydrate Binding Module from~~ a ~~Thermostable Rhodothermus marinus Xylanase===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_22434778}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2y6h]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Rhodothermus_marinus Rhodothermus marinus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2Y6H OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022434778<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Rhodothermus marinus]]		[[Category: Rhodothermus marinus]]

OCA at 05:08, 1 August 2012

OCA — Wed, 01 Aug 2012 05:08:00 GMT

←Older revision		Revision as of 05:08, 1 August 2012
Line 1:		Line 1:
-	[[Image:2y6h.~~jpg~~\|left\|200px]]	+	[[Image:2y6h.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2y6h", 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_2y6h\| PDB=2y6h \| SCENE= }}		{{STRUCTURE_2y6h\| PDB=2y6h \| SCENE= }}

	===X-2 L110F CBM4-2 Carbohydrate Binding Module from a Thermostable Rhodothermus marinus Xylanase===		===X-2 L110F CBM4-2 Carbohydrate Binding Module from a Thermostable Rhodothermus marinus Xylanase===

		+	{{ABSTRACT_PUBMED_22434778}}

	==About this Structure==		==About this Structure==
	[[2y6h]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodothermus_marinus Rhodothermus marinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y6H OCA].		[[2y6h]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodothermus_marinus Rhodothermus marinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y6H OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022434778</ref><references group="xtra"/>
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Rhodothermus marinus]]		[[Category: Rhodothermus marinus]]

OCA at 05:50, 8 March 2012

OCA — Thu, 08 Mar 2012 05:50:43 GMT

←Older revision		Revision as of 05:50, 8 March 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:2y6h.jpg\|left\|200px]]

-	The ~~entry 2y6h~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_2y6h", 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_2y6h\| PDB=2y6h \| SCENE= }}

-	~~Authors: Von Schantz, L., Hakansson, M., Logan, D.T., Walse, B., Osterlin, J., Nordberg Karlsson, E., Ohlin, M.~~	+	===X-2 L110F CBM4-2 Carbohydrate Binding Module from a Thermostable Rhodothermus marinus Xylanase===

-	~~Description~~: X-~~2 L110F CBM4~~-~~2 Carbohydrate Binding Module from a Thermostable~~ Rhodothermus marinus ~~Xylanase~~	+
		+	==About this Structure==
		+	[[2y6h]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodothermus_marinus Rhodothermus marinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y6H OCA].
		+	[[Category: Endo-1,4-beta-xylanase]]
		+	[[Category: Rhodothermus marinus]]
		+	[[Category: Hakansson, M.]]
		+	[[Category: Karlsson, E Nordberg.]]
		+	[[Category: Logan, D T.]]
		+	[[Category: Ohlin, M.]]
		+	[[Category: Osterlin, J.]]
		+	[[Category: Schantz, L Von.]]
		+	[[Category: Walse, B.]]
		+	[[Category: Hydrolase]]