7q4t - Revision history

OCA at 13:13, 1 February 2024

OCA — Thu, 01 Feb 2024 13:13:57 GMT

←Older revision		Revision as of 13:13, 1 February 2024
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-	====	+	==Structure of the Pseudomonas aeruginosa bacteriophage JG004 endolysin Pae87 bound to a peptidoglycan fragment.==
-	<StructureSection load='7q4t' size='340' side='right'caption='[[7q4t]]' scene=''>	+	<StructureSection load='7q4t' size='340' side='right'caption='[[7q4t]], [[Resolution\|resolution]] 1.27Å' 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= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7q4t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1] and [https://en.wikipedia.org/wiki/Pseudomonas_phage_JG004 Pseudomonas phage JG004]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Q4T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Q4T 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=7q4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7q4t OCA], [https://pdbe.org/7q4t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7q4t RCSB], [https://www.ebi.ac.uk/pdbsum/7q4t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7q4t 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]] 1.27Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGL:D-GLUTAMIC+ACID'>DGL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MUB:N-ACETYLMURAMIC+ACID'>MUB</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=7q4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7q4t OCA], [https://pdbe.org/7q4t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7q4t RCSB], [https://www.ebi.ac.uk/pdbsum/7q4t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7q4t ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/F4YDQ3_9CAUD F4YDQ3_9CAUD]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Phage lysins are a source of novel antimicrobials to tackle the bacterial antibiotic-resistance crisis. The engineering of phage lysins is being explored as a game-changing technological strategy to introduce a more precise approach in the way in which antimicrobial therapy is applied. Such engineering efforts will benefit from a better understanding of lysin structure and function. In this work, the antimicrobial activity of the endolysin from Pseudomonas aeruginosa phage JG004, termed Pae87, has been characterized. This lysin had previously been identified as an antimicrobial agent candidate that is able to interact with the Gram-negative surface and disrupt it. Further evidence is provided here based on a structural and biochemical study. A high-resolution crystal structure of Pae87 complexed with a peptidoglycan fragment showed a separate substrate-binding region within the catalytic domain, 18 A away from the catalytic site and located on the opposite side of the lysin molecule. This substrate-binding region was conserved among phylogenetically related lysins lacking an additional cell-wall-binding domain, but not among those containing such a module. Two glutamic acids were identified to be relevant for the peptidoglycan-degradation activity, although the antimicrobial activity of Pae87 was seemingly unrelated. In contrast, an antimicrobial peptide-like region within the Pae87 C-terminus, named P87, was found to be able to actively disturb the outer membrane and display antibacterial activity by itself. Therefore, an antimicrobial mechanism for Pae87 is proposed in which the P87 peptide plays the role of binding to the outer membrane and disrupting the cell-wall function, either with or without the participation of the catalytic activity of Pae87.
		+
		+	Monomodular Pseudomonas aeruginosa phage JG004 lysozyme (Pae87) contains a bacterial surface-active antimicrobial peptide-like region and a possible substrate-binding subdomain.,Vazquez R, Seoane-Blanco M, Rivero-Buceta V, Ruiz S, van Raaij MJ, Garcia P Acta Crystallogr D Struct Biol. 2022 Apr 1;78(Pt 4):435-454. doi:, 10.1107/S2059798322000936. Epub 2022 Mar 4. PMID:35362467<ref>PMID:35362467</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7q4t" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Z-~~disk~~]]	+	[[Category: Pseudomonas aeruginosa PAO1]]
		+	[[Category: Pseudomonas phage JG004]]
		+	[[Category: Seoane-Blanco M]]
		+	[[Category: Van Raaij MJ]]

OCA at 07:43, 23 February 2022

OCA — Wed, 23 Feb 2022 07:43:28 GMT

←Older revision		Revision as of 07:43, 23 February 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7q4t ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7q4t' size='340' side='right'caption='[[7q4t]]' scene=''>
-	~~Authors~~: ~~Seoane~~-~~Blanco, M~~.~~, van Raaij, M~~.J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~: ~~Structure of the Pseudomonas aeruginosa bacteriophage JG004 endolysin Pae87~~, ~~apo form~~.	+	</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=7q4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7q4t OCA], [https://pdbe.org/7q4t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7q4t RCSB], [https://www.ebi.ac.uk/pdbsum/7q4t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7q4t ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: ~~Van Raaij, M.J~~]]	+	__TOC__
-	[[Category: ~~Seoane~~-~~Blanco, M~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 15:30, 15 December 2021

OCA — Wed, 15 Dec 2021 15:30:05 GMT

←Older revision		Revision as of 15:30, 15 December 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7q4t is ON HOLD	+	The entry 7q4t is ON HOLD until Paper Publication

	Authors: Seoane-Blanco, M., van Raaij, M.J.		Authors: Seoane-Blanco, M., van Raaij, M.J.
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	Description: Structure of the Pseudomonas aeruginosa bacteriophage JG004 endolysin Pae87, apo form.		Description: Structure of the Pseudomonas aeruginosa bacteriophage JG004 endolysin Pae87, apo form.
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Seoane-Blanco, M]]
	[[Category: Van Raaij, M.J]]		[[Category: Van Raaij, M.J]]
		+	[[Category: Seoane-Blanco, M]]

OCA: Protected "7q4t" [edit=sysop:move=sysop]

OCA — Wed, 10 Nov 2021 05:11:16 GMT

Protected "7q4t" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:11, 10 November 2021

OCA: New page: '''Unreleased structure''' The entry 7q4t is ON HOLD Authors: Seoane-Blanco, M., van Raaij, M.J. Description: Structure of the Pseudomonas aeruginosa bacteriophage JG004 endolysin Pae8...

OCA — Wed, 10 Nov 2021 05:11:15 GMT

New page: '''Unreleased structure''' The entry 7q4t is ON HOLD Authors: Seoane-Blanco, M., van Raaij, M.J. Description: Structure of the Pseudomonas aeruginosa bacteriophage JG004 endolysin Pae8...

New page

'''Unreleased structure'''

The entry 7q4t is ON HOLD

Authors: Seoane-Blanco, M., van Raaij, M.J.

Description: Structure of the Pseudomonas aeruginosa bacteriophage JG004 endolysin Pae87, apo form.
[[Category: Unreleased Structures]]
[[Category: Seoane-Blanco, M]]
[[Category: Van Raaij, M.J]]