6r3m - Revision history

OCA at 12:14, 24 January 2024

2024-01-24T12:14:21Z

←Older revision		Revision as of 12:14, 24 January 2024
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	<StructureSection load='6r3m' size='340' side='right'caption='[[6r3m]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='6r3m' size='340' side='right'caption='[[6r3m]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6r3m]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R3M OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6R3M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6r3m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetivibrio_thermocellus_ATCC_27405 Acetivibrio thermocellus ATCC 27405]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R3M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6R3M 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=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.45Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1v0a\|1v0a]]</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=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cellulase Cellulase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.4 3.2.1.4] </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=6r3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r3m OCA], [https://pdbe.org/6r3m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6r3m RCSB], [https://www.ebi.ac.uk/pdbsum/6r3m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6r3m 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=6r3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r3m OCA], [~~http~~://pdbe.org/6r3m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6r3m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6r3m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6r3m ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~GUNH_CLOTH GUNH_CLOTH]~~] This enzyme catalyzes the endohydrolysis of 1,4-beta-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.	+	[https://www.uniprot.org/uniprot/GUNH_ACET2 GUNH_ACET2] This enzyme catalyzes the endohydrolysis of 1,4-beta-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
	<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 6r3m" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6r3m" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Glucanase 3D structures\|Glucanase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Cellulase~~]]	+	[[Category: Acetivibrio thermocellus ATCC 27405]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Carvalho~~, A L~~]]	+	[[Category: Carvalho AL]]
-	[[Category: Ribeiro~~, D O]]~~	+	[[Category: Ribeiro DO]]
-	~~[[Category: 3-1]]~~	+
-	~~[[Category: 4-mixed-linked glucan clostridium thermocellum]]~~	+
-	~~[[Category: Ctcbm11 beta-1]]~~	+
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 08:06, 5 February 2020

2020-02-05T08:06:40Z

←Older revision		Revision as of 08:06, 5 February 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6r3m is ~~ON HOLD until Paper~~ Publication	+	==Family 11 Carbohydrate-Binding Module from Clostridium thermocellum in complex with beta-1,3-1,4-mixed-linked tetrasaccharide==
		+	<StructureSection load='6r3m' size='340' side='right'caption='[[6r3m]], [[Resolution\|resolution]] 1.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6r3m]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R3M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R3M 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=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1v0a\|1v0a]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cellulase Cellulase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.4 3.2.1.4] </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=6r3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r3m OCA], [http://pdbe.org/6r3m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r3m RCSB], [http://www.ebi.ac.uk/pdbsum/6r3m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r3m ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GUNH_CLOTH GUNH_CLOTH]] This enzyme catalyzes the endohydrolysis of 1,4-beta-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Understanding the specific molecular interactions between proteins and beta1,3-1,4-mixed-linked d-glucans is fundamental to harvest the full biological and biotechnological potential of these carbohydrates and of proteins that specifically recognize them. The family 11 carbohydrate-binding module from Clostridium thermocellum (CtCBM11) is known for its binding preference for beta1,3-1,4-mixed-linked over beta1,4-linked glucans. Despite the growing industrial interest of this protein for the biotransformation of lignocellulosic biomass, the molecular determinants of its ligand specificity are not well defined. In this report, a combined approach of methodologies was used to unravel, at a molecular level, the ligand recognition of CtCBM11. The analysis of the interaction by carbohydrate microarrays and NMR and the crystal structures of CtCBM11 bound to beta1,3-1,4-linked glucose oligosaccharides showed that both the chain length and the position of the beta1,3-linkage are important for recognition, and identified the tetrasaccharide Glcbeta1,4Glcbeta1,4Glcbeta1,3Glc sequence as a minimum epitope required for binding. The structural data, along with site-directed mutagenesis and ITC studies, demonstrated the specificity of CtCBM11 for the twisted conformation of beta1,3-1,4-mixed-linked glucans. This is mediated by a conformation-selection mechanism of the ligand in the binding cleft through CH-pi stacking and a hydrogen bonding network, which is dependent not only on ligand chain length, but also on the presence of a beta1,3-linkage at the reducing end and at specific positions along the beta1,4-linked glucan chain. The understanding of the detailed mechanism by which CtCBM11 can distinguish between linear and mixed-linked beta-glucans strengthens its exploitation for the design of new biomolecules with improved capabilities and applications in health and agriculture. DATABASE: Structural data are available in the Protein Data Bank under the accession codes 6R3M and 6R31.

-	~~Authors~~:	+	Molecular basis for the preferential recognition of beta1,3-1,4-glucans by the family 11 carbohydrate-binding module from Clostridium thermocellum.,Ribeiro DO, Viegas A, Pires VMR, Medeiros-Silva J, Bule P, Chai W, Marcelo F, Fontes CMGA, Cabrita EJ, Palma AS, Carvalho AL FEBS J. 2019 Dec 3. doi: 10.1111/febs.15162. PMID:31794092<ref>PMID:31794092</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6r3m" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cellulase]]
		+	[[Category: Large Structures]]
		+	[[Category: Carvalho, A L]]
		+	[[Category: Ribeiro, D O]]
		+	[[Category: 3-1]]
		+	[[Category: 4-mixed-linked glucan clostridium thermocellum]]
		+	[[Category: Ctcbm11 beta-1]]
		+	[[Category: Sugar binding protein]]

OCA at 04:54, 3 April 2019

2019-04-03T04:54:27Z

←Older revision		Revision as of 04:54, 3 April 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6r3m is ON HOLD	+	The entry 6r3m is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6r3m" [edit=sysop:move=sysop]

2019-03-27T05:16:21Z

Protected "6r3m" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:16, 27 March 2019

OCA: New page: '''Unreleased structure''' The entry 6r3m is ON HOLD Authors: Description: Category: Unreleased Structures

2019-03-27T05:16:19Z

New page: '''Unreleased structure''' The entry 6r3m is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6r3m is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]