7cfl - Revision history

OCA at 16:07, 29 November 2023

2023-11-29T16:07:21Z

←Older revision		Revision as of 16:07, 29 November 2023
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	<StructureSection load='7cfl' size='340' side='right'caption='[[7cfl]], [[Resolution\|resolution]] 1.56Å' scene=''>		<StructureSection load='7cfl' size='340' side='right'caption='[[7cfl]], [[Resolution\|resolution]] 1.56Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7cfl]] is a 4 chain structure with sequence from [https://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=7CFL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CFL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7cfl]] is a 4 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=7CFL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CFL FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FLC:CITRATE+ANION'>FLC</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]] 1.56Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>CD630_24020 ([https://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=FLC:CITRATE+ANION'>FLC</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=7cfl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cfl OCA], [https://pdbe.org/7cfl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cfl RCSB], [https://www.ebi.ac.uk/pdbsum/7cfl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cfl 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=7cfl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cfl OCA], [https://pdbe.org/7cfl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cfl RCSB], [https://www.ebi.ac.uk/pdbsum/7cfl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cfl ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q181Y8_CLOD6 Q181Y8_CLOD6]
	<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: ~~Bacillus difficilis hall and o'toole 1935~~]]	+	[[Category: Clostridioides difficile]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kamitori, S]]	+	[[Category: Kamitori S]]
-	[[Category: Tamai, E]]	+	[[Category: Tamai E]]
-	~~[[Category: Autolysin]]~~	+
-	~~[[Category: Endopeptidase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 09:38, 12 May 2021

2021-05-12T09:38:36Z

←Older revision		Revision as of 09:38, 12 May 2021
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	==X-ray structure of autolysin Acd24020 catalytic domain from Clostridium difficile==		==X-ray structure of autolysin Acd24020 catalytic domain from Clostridium difficile==
-	<StructureSection load='7cfl' size='340' side='right'caption='[[7cfl]]' scene=''>	+	<StructureSection load='7cfl' size='340' side='right'caption='[[7cfl]], [[Resolution\|resolution]] 1.56Å' 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=7CFL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7CFL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7cfl]] is a 4 chain structure with sequence from [https://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=7CFL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CFL 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=7cfl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cfl OCA], [~~http~~://pdbe.org/7cfl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7cfl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7cfl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7cfl 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=FLC:CITRATE+ANION'>FLC</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CD630_24020 ([https://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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7cfl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cfl OCA], [https://pdbe.org/7cfl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cfl RCSB], [https://www.ebi.ac.uk/pdbsum/7cfl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cfl ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Autolysin is a lytic enzyme that hydrolyzes peptidoglycans of the bacterial cell wall, with a catalytic domain and cell wall-binding (CWB) domains, to be involved in different physiological functions that require bacterial cell wall remodeling. We identified a novel autolysin, Acd24020, from Clostridioides (Clostridium) difficile (C. difficile), with an endopeptidase catalytic domain belonging to the NlpC/P60 family and three bacterial Src-homology 3 domains as CWB domains. The catalytic domain of Acd24020 (Acd24020-CD) exhibited C. difficile-specific lytic activity equivalent to Acd24020, indicating that Acd24020-CD has full-function as a lytic enzyme by itself. To elucidate the specific peptidoglycan-recognition and catalytic reaction mechanisms of Acd24020-CD, biochemical characterization, X-ray structure determination, a modeling study of the enzyme/substrate complex, and mutagenesis analysis were performed. Acd24020-CD has an hourglass-shaped substrate-binding groove across the molecule, which is responsible for recognizing the direct 3-4 cross-linking structure unique to C. difficile peptidoglycan. Based on the X-ray structure and modeling study, we propose a dynamic Cys/His catalyzing mechanism, in which the catalytic Cys299 and His354 residues dynamically change their conformations to complement each step of the enzyme catalytic reaction.
		+
		+	Structural and biochemical characterizations of the novel autolysin Acd24020 from Clostridioides difficile and its full-function catalytic domain as a lytic enzyme.,Sekiya H, Tamai E, Kawasaki J, Murakami K, Kamitori S Mol Microbiol. 2020 Nov 2. doi: 10.1111/mmi.14636. PMID:33140473<ref>PMID:33140473</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7cfl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus difficilis hall and o'toole 1935]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kamitori S]]	+	[[Category: Kamitori, S]]
-	[[Category: Tamai E]]	+	[[Category: Tamai, E]]
		+	[[Category: Autolysin]]
		+	[[Category: Endopeptidase]]
		+	[[Category: Hydrolase]]

OCA at 06:58, 25 November 2020

2020-11-25T06:58:51Z

←Older revision		Revision as of 06:58, 25 November 2020
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-	'''Unreleased structure'''

-	~~The entry 7cfl is ON HOLD until Paper Publication~~	+	==X-ray structure of autolysin Acd24020 catalytic domain from Clostridium difficile==
-		+	<StructureSection load='7cfl' size='340' side='right'caption='[[7cfl]]' scene=''>
-	~~Authors: Kamitori, S., Tamai, E.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CFL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7CFL FirstGlance]. <br>
-	~~Description:~~ X-ray structure of autolysin Acd24020 catalytic domain from Clostridium difficile	+	</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=7cfl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cfl OCA], [http://pdbe.org/7cfl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7cfl RCSB], [http://www.ebi.ac.uk/pdbsum/7cfl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7cfl ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Tamai~~, E]]	+	__TOC__
-	[[Category: Kamitori, S]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Kamitori S]]
		+	[[Category: Tamai E]]

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

2020-07-08T11:30:21Z

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

←Older revision

Revision as of 11:30, 8 July 2020

OCA: New page: '''Unreleased structure''' The entry 7cfl is ON HOLD until Paper Publication Authors: Kamitori, S., Tamai, E. Description: X-ray structure of autolysin Acd24020 catalytic domain from C...

2020-07-08T11:30:19Z

New page: '''Unreleased structure''' The entry 7cfl is ON HOLD until Paper Publication Authors: Kamitori, S., Tamai, E. Description: X-ray structure of autolysin Acd24020 catalytic domain from C...

New page

'''Unreleased structure'''

The entry 7cfl is ON HOLD until Paper Publication

Authors: Kamitori, S., Tamai, E.

Description: X-ray structure of autolysin Acd24020 catalytic domain from Clostridium difficile
[[Category: Unreleased Structures]]
[[Category: Tamai, E]]
[[Category: Kamitori, S]]