6ujf - Revision history

OCA at 07:52, 11 October 2023

2023-10-11T07:52:41Z

←Older revision		Revision as of 07:52, 11 October 2023
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	<StructureSection load='6ujf' size='340' side='right'caption='[[6ujf]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6ujf' size='340' side='right'caption='[[6ujf]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ujf]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_difficilis"_hall_and_o'toole_1935 "bacillus difficilis" hall and o'toole 1935~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UJF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6UJF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ujf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridioides_difficile Clostridioides difficile]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UJF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UJF 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>~~</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]] 2Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>celH, SAMEA1402348_00819 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1496~~ "~~Bacillus difficilis~~" ~~Hall and O'Toole 1935])</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></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=6ujf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ujf OCA], [https://pdbe.org/6ujf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ujf RCSB], [https://www.ebi.ac.uk/pdbsum/6ujf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ujf ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6ujf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ujf OCA], [~~http~~://pdbe.org/6ujf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ujf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ujf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ujf ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 6ujf" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6ujf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Glucanase 3D structures\|Glucanase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus difficilis hall and o'toole 1935]]~~	+	[[Category: Clostridioides difficile]]
-	~~[[Category: Cellulase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Anderson~~, A C~~]]	+	[[Category: Anderson AC]]
-	[[Category: Lowrance, B]]	+	[[Category: Lowrance B]]
-	[[Category: Scott, W]]	+	[[Category: Scott W]]
-	[[Category: Weadge~~, J T]]~~	+	[[Category: Weadge JT]]
-	~~[[Category: Biofilm]]~~	+
-	~~[[Category: Cellulose]]~~	+
-	~~[[Category: Gh8]]~~	+
-	~~[[Category: Glycosyl]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 06:48, 9 December 2020

2020-12-09T06:48:19Z

←Older revision		Revision as of 06:48, 9 December 2020
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	==Crystal structure of the Clostridial cellulose synthase subunit Z (CcsZ) from Clostridioides difficile==		==Crystal structure of the Clostridial cellulose synthase subunit Z (CcsZ) from Clostridioides difficile==
-	<StructureSection load='6ujf' size='340' side='right'caption='[[6ujf]]' scene=''>	+	<StructureSection load='6ujf' size='340' side='right'caption='[[6ujf]], [[Resolution\|resolution]] 2.00Å' 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=6UJF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6UJF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ujf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_difficilis"_hall_and_o'toole_1935 "bacillus difficilis" hall and o'toole 1935]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UJF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6UJF FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6ujf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ujf OCA], [http://pdbe.org/6ujf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ujf RCSB], [http://www.ebi.ac.uk/pdbsum/6ujf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ujf 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></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">celH, SAMEA1402348_00819 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1496 "Bacillus difficilis" Hall and O'Toole 1935])</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://proteopedia.org/fgij/fg.htm?mol=6ujf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ujf OCA], [http://pdbe.org/6ujf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ujf RCSB], [http://www.ebi.ac.uk/pdbsum/6ujf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ujf ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Biofilms are community structures of bacteria enmeshed in a self-produced matrix of exopolysaccharides. The biofilm matrix serves numerous roles, including resilience and persistence, making biofilms a subject of research interest among persistent clinical pathogens of global health importance. Our current understanding of the underlying biochemical pathways responsible for biosynthesis of these exopolysaccharides is largely limited to Gram-negative bacteria. Clostridia are a class of Gram-positive, anaerobic and spore-forming bacteria and include the important human pathogens Clostridium perfringens, Clostridium botulinum and Clostridioides difficile, among numerous others. Several species of Clostridia have been reported to produce a biofilm matrix that contains an acetylated glucan linked to a series of hypothetical genes. Here, we propose a model for the function of these hypothetical genes, which, using homology modelling, we show plausibly encode a synthase complex responsible for polymerization, modification and export of an O-acetylated cellulose exopolysaccharide. Specifically, the cellulose synthase is homologous to that of the known exopolysaccharide synthases in Gram-negative bacteria. The remaining proteins represent a mosaic of evolutionary lineages that differ from the described Gram-negative cellulose exopolysaccharide synthases, but their predicted functions satisfy all criteria required for a functional cellulose synthase operon. Accordingly, we named these hypothetical genes ccsZABHI, for the Clostridial cellulose synthase (Ccs), in keeping with naming conventions for exopolysaccharide synthase subunits and to distinguish it from the Gram-negative Bcs locus with which it shares only a single one-to-one ortholog. To test our model and assess the identity of the exopolysaccharide, we subcloned the putative glycoside hydrolase encoded by ccsZ and solved the X-ray crystal structure of both apo- and product-bound CcsZ, which belongs to glycoside hydrolase family 5 (GH-5). Although not homologous to the Gram-negative cellulose synthase, which instead encodes the structurally distinct BcsZ belonging to GH-8, we show CcsZ displays specificity for cellulosic materials. This specificity of the synthase-associated glycosyl hydrolase validates our proposal that these hypothetical genes are responsible for biosynthesis of a cellulose exopolysaccharide. The data we present here allowed us to propose a model for Clostridial cellulose synthesis and serves as an entry point to an understanding of cellulose biofilm formation among class Clostridia.
		+
		+	Identification of the Clostridial cellulose synthase and characterization of the cognate glycosyl hydrolase, CcsZ.,Scott W, Lowrance B, Anderson AC, Weadge JT PLoS One. 2020 Dec 2;15(12):e0242686. doi: 10.1371/journal.pone.0242686., eCollection 2020. PMID:33264329<ref>PMID:33264329</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ujf" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus difficilis hall and o'toole 1935]]
		+	[[Category: Cellulase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Anderson AC]]	+	[[Category: Anderson, A C]]
-	[[Category: Lowrance B]]	+	[[Category: Lowrance, B]]
-	[[Category: Scott W]]	+	[[Category: Scott, W]]
-	[[Category: Weadge JT]]	+	[[Category: Weadge, J T]]
		+	[[Category: Biofilm]]
		+	[[Category: Cellulose]]
		+	[[Category: Gh8]]
		+	[[Category: Glycosyl]]
		+	[[Category: Hydrolase]]

OCA at 05:47, 14 October 2020

2020-10-14T05:47:37Z

←Older revision		Revision as of 05:47, 14 October 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6ujf is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of the Clostridial cellulose synthase subunit Z (CcsZ) from Clostridioides difficile==
-		+	<StructureSection load='6ujf' size='340' side='right'caption='[[6ujf]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UJF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6UJF FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6ujf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ujf OCA], [http://pdbe.org/6ujf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ujf RCSB], [http://www.ebi.ac.uk/pdbsum/6ujf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ujf ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Anderson AC]]
		+	[[Category: Lowrance B]]
		+	[[Category: Scott W]]
		+	[[Category: Weadge JT]]

OCA at 07:36, 30 October 2019

2019-10-30T07:36:09Z

←Older revision		Revision as of 07:36, 30 October 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

2019-10-10T04:02:17Z

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

←Older revision

Revision as of 04:02, 10 October 2019

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

2019-10-10T04:02:16Z

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

New page

'''Unreleased structure'''

The entry 6ujf is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]