6h8l - Revision history

OCA at 09:28, 1 April 2020

OCA — Wed, 01 Apr 2020 09:28:02 GMT

←Older revision		Revision as of 09:28, 1 April 2020
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/PDAC_BACSU PDAC_BACSU]] Catalyzes the deacetylation of N-acetylmuramic acid (MurNAc) residues in peptidoglycan, a modification that confers resistance to lysosyme. Is not able to deacetylate N-acetylglucosamine (GlcNAc) residues in peptidoglycan, but can deacylate chitin oligomers such as GlcNAc4 and GlcNAc5. Is essentially not active toward chitosan (partially deacetylated GlcNAc polymer) and has very low activity toward chitin (GlcNAc polymer). Does not deacetylate GlcNAc.<ref>PMID:22277649</ref>		[[http://www.uniprot.org/uniprot/PDAC_BACSU PDAC_BACSU]] Catalyzes the deacetylation of N-acetylmuramic acid (MurNAc) residues in peptidoglycan, a modification that confers resistance to lysosyme. Is not able to deacetylate N-acetylglucosamine (GlcNAc) residues in peptidoglycan, but can deacylate chitin oligomers such as GlcNAc4 and GlcNAc5. Is essentially not active toward chitosan (partially deacetylated GlcNAc polymer) and has very low activity toward chitin (GlcNAc polymer). Does not deacetylate GlcNAc.<ref>PMID:22277649</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacillus subtilis PdaC (BsPdaC) is a membrane-bound, multidomain peptidoglycan N-deacetylase acting on N-acetylmuramic acid (MurNAc) residues and conferring lysozyme resistance to modified cell wall peptidoglycans. BsPdaC contains a C-terminal family 4 carbohydrate esterase (CE4) catalytic domain, but unlike other MurNAc deacetylases, BsPdaC also has GlcNAc deacetylase activity on chitooligosaccharides (COSs), characteristic of chitin deacetylases. To uncover the molecular basis of this dual activity, here we determined the X-ray structure of the BsPdaC CE4 domain at 1.54 A resolution and analyzed its mode of action on COS substrates. We found that the minimal substrate is GlcNAc3 and that activity increases with the degree of glycan polymerization. COS deacetylation kinetics revealed that BsPdaC operates by a multiple-chain mechanism starting at the internal GlcNAc units and leading to deacetylation of all but the reducing-end GlcNAc residues. Interestingly, BsPdaC shares higher sequence similarity with the peptidoglycan GlcNAc deacetylase SpPgdaA than with other MurNAc deacetylases. Therefore, we used ligand-docking simulations to analyze the dual GlcNAc- and MurNAc-binding specificities of BsPdaC and compared them with those of SpPgdA and BsPdaA, representing peptidoglycan deacetylases highly specific for GlcNAc or MurNAc residues, respectively. BsPdaC retains the conserved Asp-His-His metal-binding triad characteristic of CE4 enzymes acting on GlcNAc residues, differing from MurNAc deacetylases that lack the metal-coordinating Asp residue. BsPdaC contains short loops similar to those in SpPgdA, resulting in an open binding cleft that can accommodate polymeric substrates. We propose that PdaC is the first member of a new subclass of peptidoglycan MurNAc deacetylases.
		+
		+	Structure-function relationships underlying the dual N-acetylmuramic and N-acetylglucosamine specificities of the bacterial peptidoglycan deacetylase PdaC.,Grifoll-Romero L, Sainz-Polo MA, Albesa-Jove D, Guerin ME, Biarnes X, Planas A J Biol Chem. 2019 Dec 13;294(50):19066-19080. doi: 10.1074/jbc.RA119.009510. Epub, 2019 Nov 5. PMID:31690626<ref>PMID:31690626</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6h8l" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:29, 27 March 2020

OCA — Fri, 27 Mar 2020 10:29:42 GMT

←Older revision		Revision as of 10:29, 27 March 2020
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	<StructureSection load='6h8l' size='340' side='right'caption='[[6h8l]], [[Resolution\|resolution]] 1.54Å' scene=''>		<StructureSection load='6h8l' size='340' side='right'caption='[[6h8l]], [[Resolution\|resolution]] 1.54Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6h8l]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6H8L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6H8L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6h8l]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6H8L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6H8L FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pdaC, yjeA, BSU12100 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=6h8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6h8l OCA], [http://pdbe.org/6h8l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6h8l RCSB], [http://www.ebi.ac.uk/pdbsum/6h8l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6h8l 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=6h8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6h8l OCA], [http://pdbe.org/6h8l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6h8l RCSB], [http://www.ebi.ac.uk/pdbsum/6h8l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6h8l ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacsu]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Albesa-Jove, D]]		[[Category: Albesa-Jove, D]]

OCA at 10:56, 13 November 2019

OCA — Wed, 13 Nov 2019 10:56:26 GMT

←Older revision		Revision as of 10:56, 13 November 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6h8l is ~~ON HOLD until Paper Publication~~	+	==Structure of peptidoglycan deacetylase PdaC from Bacillus subtilis==
-		+	<StructureSection load='6h8l' size='340' side='right'caption='[[6h8l]], [[Resolution\|resolution]] 1.54Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6h8l]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6H8L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6H8L FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6h8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6h8l OCA], [http://pdbe.org/6h8l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6h8l RCSB], [http://www.ebi.ac.uk/pdbsum/6h8l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6h8l ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PDAC_BACSU PDAC_BACSU]] Catalyzes the deacetylation of N-acetylmuramic acid (MurNAc) residues in peptidoglycan, a modification that confers resistance to lysosyme. Is not able to deacetylate N-acetylglucosamine (GlcNAc) residues in peptidoglycan, but can deacylate chitin oligomers such as GlcNAc4 and GlcNAc5. Is essentially not active toward chitosan (partially deacetylated GlcNAc polymer) and has very low activity toward chitin (GlcNAc polymer). Does not deacetylate GlcNAc.<ref>PMID:22277649</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Albesa-Jove, D]]
		+	[[Category: Grifoll-Romero, L]]
		+	[[Category: Guerin, M E]]
		+	[[Category: Planas, A]]
		+	[[Category: Sainz-Polo, M A]]
		+	[[Category: Deacetylase]]
		+	[[Category: Hydrolase]]

OCA: Protected "6h8l" [edit=sysop:move=sysop]

OCA — Thu, 09 Aug 2018 20:10:23 GMT

Protected "6h8l" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:10, 9 August 2018

OCA: New page: '''Unreleased structure''' The entry 6h8l is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Thu, 09 Aug 2018 20:10:22 GMT

New page: '''Unreleased structure''' The entry 6h8l is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6h8l is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]