7t7z - Revision history

OCA at 17:01, 18 October 2023

OCA — Wed, 18 Oct 2023 17:01:36 GMT

←Older revision		Revision as of 17:01, 18 October 2023
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	<StructureSection load='7t7z' size='340' side='right'caption='[[7t7z]], [[Resolution\|resolution]] 1.46Å' scene=''>		<StructureSection load='7t7z' size='340' side='right'caption='[[7t7z]], [[Resolution\|resolution]] 1.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7t7z]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7T7Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7T7Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7t7z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7T7Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7T7Z FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=LMR:(2S)-2-HYDROXYBUTANEDIOIC+ACID'>LMR</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.46Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7t7y\|7t7y]]</div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=LMR:(2S)-2-HYDROXYBUTANEDIOIC+ACID'>LMR</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=7t7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7t7z OCA], [https://pdbe.org/7t7z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7t7z RCSB], [https://www.ebi.ac.uk/pdbsum/7t7z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7t7z 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=7t7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7t7z OCA], [https://pdbe.org/7t7z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7t7z RCSB], [https://www.ebi.ac.uk/pdbsum/7t7z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7t7z ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/GUN6_DICDI GUN6_DICDI]] May digest the spore cell wall during germination, to release the enclosed amoeba.<ref>PMID:1869562</ref>	+	[https://www.uniprot.org/uniprot/GUN6_DICDI GUN6_DICDI] May digest the spore cell wall during germination, to release the enclosed amoeba.<ref>PMID:1869562</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 7t7z" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7t7z" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Glucanase 3D structures\|Glucanase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Dictyostelium discoideum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Campos~~, B M~~]]	+	[[Category: Campos BM]]
-	[[Category: Marcelo~~, M V~~]]	+	[[Category: Marcelo MV]]
-	[[Category: Squina~~, F M]]~~	+	[[Category: Squina FM]]
-	~~[[Category: Carbohydrate-binding protein]]~~	+
-	~~[[Category: Cazyme]]~~	+
-	~~[[Category: Cellulose]]~~	+
-	~~[[Category: Ligand specificity]]~~	+
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 10:26, 18 May 2022

OCA — Wed, 18 May 2022 10:26:47 GMT

←Older revision		Revision as of 10:26, 18 May 2022
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	==The crystal structure of family 8 carbohydrate-binding module from Dictyostelium discoideum==		==The crystal structure of family 8 carbohydrate-binding module from Dictyostelium discoideum==
-	<StructureSection load='7t7z' size='340' side='right'caption='[[7t7z]]' scene=''>	+	<StructureSection load='7t7z' size='340' side='right'caption='[[7t7z]], [[Resolution\|resolution]] 1.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7T7Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7T7Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7t7z]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7T7Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7T7Z FirstGlance]. <br>
-	</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=7t7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7t7z OCA], [https://pdbe.org/7t7z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7t7z RCSB], [https://www.ebi.ac.uk/pdbsum/7t7z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7t7z ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=LMR:(2S)-2-HYDROXYBUTANEDIOIC+ACID'>LMR</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7t7y\|7t7y]]</div></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=7t7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7t7z OCA], [https://pdbe.org/7t7z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7t7z RCSB], [https://www.ebi.ac.uk/pdbsum/7t7z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7t7z ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/GUN6_DICDI GUN6_DICDI]] May digest the spore cell wall during germination, to release the enclosed amoeba.<ref>PMID:1869562</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Deciphering how enzymes interact, modify, and recognize carbohydrates has long been a topic of interest in academic, pharmaceutical, and industrial research. Carbohydrate-binding modules (CBMs) are non-catalytic globular protein domains attached to carbohydrate-active enzymes (CAZymes) that strengthen enzyme affinity to substrates and increase enzymatic efficiency via targeting and proximity effects. CBMs are considered auspicious for various biotechnological purposes in textile, food, and feed industries, representing valuable tools in basic science research and biomedicine. Here, we present the first crystallographic structure of a CBM8 family member (CBM8), DdCBM8 from the slime mold Dictyostelium discoideum, which was identified attached to an endo-beta-1,4-glucanase (glycoside hydrolase family 9). We show that the planar carbohydrate binding site of DdCBM8, composed of aromatic residues, is similar to type A CBMs that are specific for crystalline (multi-chain) polysaccharides. Accordingly, pull-down assays indicated that DdCBM8 was able to bind insoluble forms of cellulose. However, affinity gel electrophoresis demonstrated that DdCBM8 also bound to soluble (single chain) polysaccharides, especially glucomannan, similar to type B CBMs, although it had no apparent affinity for oligosaccharides. Therefore, the structural characteristics and broad specificity of DdCBM8 represent exceptions to the canonical CBM classification. In addition, mutational analysis identified specific amino acid residues involved in ligand recognition, which are conserved throughout the CBM8 family. This advancement in the structural and functional characterization of CBMs contributes to our understanding of CAZymes and protein-carbohydrate interactions, pushing forward protein engineering strategies and enhancing the potential biotechnological applications of glycoside hydrolase accessory modules.
		+
		+	Unique properties of a Dictyostelium discoideum carbohydrate-binding module expand our understanding of CBM-ligand interactions.,Liberato MV, Campos BM, Tomazetto G, Crouch LI, Garcia W, Zeri ACM, Bolam DN, Squina FM J Biol Chem. 2022 Apr 1:101891. doi: 10.1016/j.jbc.2022.101891. PMID:35378128<ref>PMID:35378128</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7t7z" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Campos BM]]	+	[[Category: Campos, B M]]
-	[[Category: Marcelo MV]]	+	[[Category: Marcelo, M V]]
-	[[Category: Squina FM]]	+	[[Category: Squina, F M]]
		+	[[Category: Carbohydrate-binding protein]]
		+	[[Category: Cazyme]]
		+	[[Category: Cellulose]]
		+	[[Category: Ligand specificity]]
		+	[[Category: Sugar binding protein]]

OCA at 02:56, 21 April 2022

OCA — Thu, 21 Apr 2022 02:56:48 GMT

←Older revision		Revision as of 02:56, 21 April 2022
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-	'''Unreleased structure'''

-	The ~~entry~~ 7t7z is ~~ON HOLD until Paper Publication~~	+	==The crystal structure of family 8 carbohydrate-binding module from Dictyostelium discoideum==
-		+	<StructureSection load='7t7z' size='340' side='right'caption='[[7t7z]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7T7Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7T7Z FirstGlance]. <br>
-	~~Description~~:	+	</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=7t7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7t7z OCA], [https://pdbe.org/7t7z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7t7z RCSB], [https://www.ebi.ac.uk/pdbsum/7t7z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7t7z ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Campos BM]]
		+	[[Category: Marcelo MV]]
		+	[[Category: Squina FM]]

OCA at 05:57, 19 January 2022

OCA — Wed, 19 Jan 2022 05:57:23 GMT

←Older revision		Revision as of 05:57, 19 January 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7t7z is ON HOLD	+	The entry 7t7z is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7t7z" [edit=sysop:move=sysop]

OCA — Wed, 22 Dec 2021 14:09:43 GMT

Protected "7t7z" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:09, 22 December 2021

OCA: New page: '''Unreleased structure''' The entry 7t7z is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 22 Dec 2021 14:09:42 GMT

New page: '''Unreleased structure''' The entry 7t7z is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7t7z is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]