6xqf - Revision history

OCA at 14:59, 18 October 2023

OCA — Wed, 18 Oct 2023 14:59:11 GMT

←Older revision		Revision as of 14:59, 18 October 2023
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	<StructureSection load='6xqf' size='340' side='right'caption='[[6xqf]], [[Resolution\|resolution]] 1.58Å' scene=''>		<StructureSection load='6xqf' size='340' side='right'caption='[[6xqf]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6xqf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Uncultivated_bacterium Uncultivated~~ bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XQF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6xqf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Uncultured_bacterium Uncultured bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XQF FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<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></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]] 1.58Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[6xof\|6xof]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~sclam ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=77133 uncultivated bacterium])</td~~></tr>	+
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Glucan_endo-1,3-beta~~-D-~~glucosidase Glucan endo-1,3-beta-D-glucosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.39 3.2.1.39]~~ </~~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=6xqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xqf OCA], [https://pdbe.org/6xqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xqf RCSB], [https://www.ebi.ac.uk/pdbsum/6xqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xqf 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=6xqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xqf OCA], [https://pdbe.org/6xqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xqf RCSB], [https://www.ebi.ac.uk/pdbsum/6xqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xqf ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0B5H9B3_9BACT A0A0B5H9B3_9BACT]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
	*[[Glucanase 3D structures\|Glucanase 3D structures]]		*[[Glucanase 3D structures\|Glucanase 3D structures]]
		+	*[[Laminarase 3D structures\|Laminarase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Glucan endo-1,3-beta-D-glucosidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Uncultivated~~ bacterium]]	+	[[Category: Uncultured bacterium]]
-	[[Category: Liberato~~, M V~~]]	+	[[Category: Liberato MV]]
-	[[Category: Squina, F]]	+	[[Category: Squina F]]
-	~~[[Category: Endo-1]]~~	+
-	~~[[Category: Glycoside hydrolase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Metagenome]]~~	+
-	~~[[Category: Transglycosylation~~]]	+

OCA at 06:27, 25 August 2021

OCA — Wed, 25 Aug 2021 06:27:20 GMT

←Older revision		Revision as of 06:27, 25 August 2021
Line 1:		Line 1:

	==Crystal structure of SCLam E144S mutant, a non-specific endo-beta-1,3(4)-glucanase from family GH16, co-crystallized with 1,3-beta-D-cellotriosyl-glucose, presenting a 1,3-beta-D-cellobiosyl-glucose at active site==		==Crystal structure of SCLam E144S mutant, a non-specific endo-beta-1,3(4)-glucanase from family GH16, co-crystallized with 1,3-beta-D-cellotriosyl-glucose, presenting a 1,3-beta-D-cellobiosyl-glucose at active site==
-	<StructureSection load='6xqf' size='340' side='right'caption='[[6xqf]]' scene=''>	+	<StructureSection load='6xqf' size='340' side='right'caption='[[6xqf]], [[Resolution\|resolution]] 1.58Å' 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=6XQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XQF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6xqf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Uncultivated_bacterium Uncultivated bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XQF 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=6xqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xqf OCA], [https://pdbe.org/6xqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xqf RCSB], [https://www.ebi.ac.uk/pdbsum/6xqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xqf 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=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</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;'>[[6xof\|6xof]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">sclam ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=77133 uncultivated bacterium])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glucan_endo-1,3-beta-D-glucosidase Glucan endo-1,3-beta-D-glucosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.39 3.2.1.39] </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=6xqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xqf OCA], [https://pdbe.org/6xqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xqf RCSB], [https://www.ebi.ac.uk/pdbsum/6xqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xqf ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Glycoside hydrolases (GHs) are involved in the degradation of a wide diversity of carbohydrates and present several biotechnological applications. Many GH families are composed of enzymes with a single well-defined specificity. In contrast, enzymes from the GH16 family can act on a range of different polysaccharides, including beta-glucans and galactans. SCLam, a GH16 member derived from a soil metagenome, an endo-beta-1,3(4)-glucanase (EC 3.2.1.6), can cleave both beta-1,3 and beta-1,4 glycosidic bonds in glucans, such as laminarin, barley beta-glucan, and cello-oligosaccharides. A similar cleavage pattern was previously reported for other GH16 family members. However, the molecular mechanisms for this dual cleavage activity on (1,3)- and (1,4)-beta-D-glycosidic bonds by laminarinases have not been elucidated. In this sense, we determined the X-ray structure of a presumably inactive form of SCLam cocrystallized with different oligosaccharides. The solved structures revealed general bound products that are formed owing to residual activities of hydrolysis and transglycosylation. Biochemical and biophysical analyses and molecular dynamics simulations help to rationalize differences in activity toward different substrates. Our results depicted a bulky aromatic residue near the catalytic site critical to select the preferable configuration of glycosidic bonds in the binding cleft. Altogether, these data contribute to understanding the structural basis of recognition and hydrolysis of beta-1,3 and beta-1,4 glycosidic linkages of the laminarinase enzyme class, which is valuable for future studies on the GH16 family members and applications related to biomass conversion into feedstocks and bioproducts.
		+
		+	Insights into the dual cleavage activity of the GH16 laminarinase enzyme class on beta-1,3 and beta-1,4 glycosidic bonds.,Liberato MV, Teixeira Prates E, Goncalves TA, Bernardes A, Vilela N, Fattori J, Ematsu GC, Chinaglia M, Machi Gomes ER, Migliorini Figueira AC, Damasio A, Polikarpov I, Skaf MS, Squina FM J Biol Chem. 2021 Jan-Jun;296:100385. doi: 10.1016/j.jbc.2021.100385. Epub 2021, Feb 5. PMID:33556371<ref>PMID:33556371</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6xqf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Glucanase 3D structures\|Glucanase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Glucan endo-1,3-beta-D-glucosidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Liberato MV]]	+	[[Category: Uncultivated bacterium]]
-	[[Category: Squina F]]	+	[[Category: Liberato, M V]]
		+	[[Category: Squina, F]]
		+	[[Category: Endo-1]]
		+	[[Category: Glycoside hydrolase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Metagenome]]
		+	[[Category: Transglycosylation]]

OCA at 10:54, 10 February 2021

OCA — Wed, 10 Feb 2021 10:54:59 GMT

←Older revision		Revision as of 10:54, 10 February 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 6xqf ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of SCLam E144S mutant, a non-specific endo-beta-1,3(4)-glucanase from family GH16, co-crystallized with 1,3-beta-D-cellotriosyl-glucose, presenting a 1,3-beta-D-cellobiosyl-glucose at active site==
-		+	<StructureSection load='6xqf' size='340' side='right'caption='[[6xqf]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XQF 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=6xqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xqf OCA], [https://pdbe.org/6xqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xqf RCSB], [https://www.ebi.ac.uk/pdbsum/6xqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xqf ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Liberato MV]]
		+	[[Category: Squina F]]

OCA at 03:52, 5 August 2020

OCA — Wed, 05 Aug 2020 03:52:24 GMT

←Older revision		Revision as of 03:52, 5 August 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 22 Jul 2020 06:53:33 GMT

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

←Older revision

Revision as of 06:53, 22 July 2020

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

OCA — Wed, 22 Jul 2020 06:53:31 GMT

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

New page

'''Unreleased structure'''

The entry 6xqf is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]