6sqx - Revision history

OCA at 12:46, 24 January 2024

OCA — Wed, 24 Jan 2024 12:46:11 GMT

←Older revision		Revision as of 12:46, 24 January 2024
Line 1:		Line 1:

-	==Insights into a novel NlpC/P60 Endopeptidase from Photobacterium damselae subsp. ~~piscisida~~==	+	==Insights into a novel NlpC/P60 Endopeptidase from Photobacterium damselae subsp. piscicida==
-	<StructureSection load='6sqx' size='340' side='right'caption='[[6sqx]]' scene=''>	+	<StructureSection load='6sqx' size='340' side='right'caption='[[6sqx]], [[Resolution\|resolution]] 1.40Å' 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=6SQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6SQX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6sqx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Photobacterium_damselae_subsp._piscicida Photobacterium damselae subsp. piscicida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6SQX 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=6sqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sqx OCA], [https://pdbe.org/6sqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6sqx RCSB], [https://www.ebi.ac.uk/pdbsum/6sqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6sqx ProSAT]</span></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]] 1.4Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=6sqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sqx OCA], [https://pdbe.org/6sqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6sqx RCSB], [https://www.ebi.ac.uk/pdbsum/6sqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6sqx ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A1V1VDL8_PHODP A0A1V1VDL8_PHODP]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Peptidoglycan (PG) is a major component of the bacterial cell wall, forming a mesh-like structure enwrapping the bacteria that is essential for maintaining structural integrity and providing support for anchoring other components of the cell envelope. PG biogenesis is highly dynamic and requires multiple enzymes, including several hydrolases that cleave glycosidic or amide bonds in the PG. This work describes the structural and functional characterization of an NlpC/P60-containing peptidase from Photobacterium damselae subsp. piscicida (Phdp), a Gram-negative bacterium that causes high mortality of warm-water marine fish with great impact for the aquaculture industry. PnpA ( PhotobacteriumNlpC-like protein A) has a four-domain structure with a hydrophobic and narrow access to the catalytic center and specificity for the gamma-d-glutamyl-meso-diaminopimelic acid bond. However, PnpA does not cleave the PG of Phdp or PG of several Gram-negative and Gram-positive bacterial species. Interestingly, it is secreted by the Phdp type II secretion system and degrades the PG of Vibrio anguillarum and Vibrio vulnificus This suggests that PnpA is used by Phdp to gain an advantage over bacteria that compete for the same resources or to obtain nutrients in nutrient-scarce environments. Comparison of the muropeptide composition of PG susceptible and resistant to the catalytic activity of PnpA showed that the global content of muropeptides is similar, suggesting that susceptibility to PnpA is determined by the three-dimensional organization of the muropeptides in the PG.IMPORTANCE Peptidoglycan (PG) is a major component of the bacterial cell wall formed by long chains of two alternating sugars interconnected by short peptides, generating a mesh-like structure that enwraps the bacterial cell. Although PG provides structural integrity and support for anchoring other components of the cell envelope, it is constantly being remodeled through the action of specific enzymes that cleave or join its components. Here, it is shown that Photobacterium damselae subsp. piscicida, a bacterium that causes high mortality in warm-water marine fish, produces PnpA, an enzyme that is secreted into the environment and is able to cleave the PG of potentially competing bacteria, either to gain a competitive advantage and/or to obtain nutrients. The specificity of PnpA for the PG of some bacteria and its inability to cleave others may be explained by differences in the structure of the PG mesh and not by different muropeptide composition.
		+
		+	A Secreted NlpC/P60 Endopeptidase from Photobacterium damselae subsp. piscicida Cleaves the Peptidoglycan of Potentially Competing Bacteria.,Lisboa J, Pereira C, Rifflet A, Ayala J, Terceti MS, Barca AV, Rodrigues I, Pereira PJB, Osorio CR, Garcia-Del Portillo F, Gomperts Boneca I, do Vale A, Dos Santos NMS mSphere. 2021 Feb 3;6(1):e00736-20. doi: 10.1128/mSphere.00736-20. PMID:33536321<ref>PMID:33536321</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6sqx" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Photobacterium damselae subsp. piscicida]]
	[[Category: Lisboa J]]		[[Category: Lisboa J]]
	[[Category: Pereira PJB]]		[[Category: Pereira PJB]]
	[[Category: Dos Santos NMS]]		[[Category: Dos Santos NMS]]

OCA at 06:45, 24 February 2021

OCA — Wed, 24 Feb 2021 06:45:41 GMT

←Older revision		Revision as of 06:45, 24 February 2021
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	<StructureSection load='6sqx' size='340' side='right'caption='[[6sqx]]' scene=''>		<StructureSection load='6sqx' size='340' side='right'caption='[[6sqx]]' 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=6SQX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6SQX FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6SQX 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=6sqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sqx OCA], [~~http~~://pdbe.org/6sqx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6sqx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6sqx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6sqx ProSAT]</span></td></tr>	+	</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=6sqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sqx OCA], [https://pdbe.org/6sqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6sqx RCSB], [https://www.ebi.ac.uk/pdbsum/6sqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6sqx ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 07:06, 30 September 2020

OCA — Wed, 30 Sep 2020 07:06:09 GMT

←Older revision		Revision as of 07:06, 30 September 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6sqx is ~~ON HOLD until Paper Publication~~	+	==Insights into a novel NlpC/P60 Endopeptidase from Photobacterium damselae subsp. piscisida==
-		+	<StructureSection load='6sqx' size='340' side='right'caption='[[6sqx]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SQX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6SQX 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=6sqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sqx OCA], [http://pdbe.org/6sqx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6sqx RCSB], [http://www.ebi.ac.uk/pdbsum/6sqx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6sqx ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Lisboa J]]
		+	[[Category: Pereira PJB]]
		+	[[Category: Dos Santos NMS]]

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

OCA — Wed, 02 Oct 2019 07:37:27 GMT

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

←Older revision

Revision as of 07:37, 2 October 2019

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

OCA — Wed, 02 Oct 2019 07:37:26 GMT

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

New page

'''Unreleased structure'''

The entry 6sqx is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]