5onl - Revision history

OCA at 16:55, 13 December 2023

OCA — Wed, 13 Dec 2023 16:55:40 GMT

←Older revision		Revision as of 16:55, 13 December 2023
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	<StructureSection load='5onl' size='340' side='right'caption='[[5onl]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5onl' size='340' side='right'caption='[[5onl]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5onl]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"vibrio_subtilis"_ehrenberg_1835 "vibrio~~ subtilis~~" ehrenberg 1835~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ONL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ONL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5onl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ONL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ONL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=010:PHENYLMETHANOL'>010</scene>, <scene name='pdbligand=FAH:FLUOROACETIC+ACID'>FAH</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.7Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">B4417_0239 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=010:PHENYLMETHANOL'>010</scene>, <scene name='pdbligand=FAH:FLUOROACETIC+ACID'>FAH</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5onl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5onl OCA], [~~http~~://pdbe.org/5onl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5onl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5onl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5onl 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=5onl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5onl OCA], [https://pdbe.org/5onl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5onl RCSB], [https://www.ebi.ac.uk/pdbsum/5onl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5onl ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/YNDL_BACSU YNDL_BACSU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Vibrio~~ subtilis ~~ehrenberg 1835~~]]	+	[[Category: Bacillus subtilis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Calvio, C]]	+	[[Category: Calvio C]]
-	[[Category: Morelli, C]]	+	[[Category: Morelli C]]
-	[[Category: Pastore, A]]	+	[[Category: Pastore A]]
-	[[Category: Ramaswamy, S]]	+	[[Category: Ramaswamy S]]
-	[[Category: Rasheed, M]]	+	[[Category: Rasheed M]]
-	[[Category: Sutton, B]]	+	[[Category: Sutton B]]
-	~~[[Category: Gamma-pga-hydrolase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:04, 4 March 2020

OCA — Wed, 04 Mar 2020 07:04:11 GMT

←Older revision		Revision as of 07:04, 4 March 2020
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	<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=5onl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5onl OCA], [http://pdbe.org/5onl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5onl RCSB], [http://www.ebi.ac.uk/pdbsum/5onl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5onl 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=5onl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5onl OCA], [http://pdbe.org/5onl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5onl RCSB], [http://www.ebi.ac.uk/pdbsum/5onl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5onl ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The identification of new strategies to fight bacterial infections in view of the spread of multiple resistance to antibiotics has become mandatory. It has been demonstrated that several bacteria develop poly-gamma-glutamic acid (gamma-PGA) capsules as a protection from external insults and/or host defence systems. Among the pathogens that shield themselves in these capsules are Bacillus anthracis, Francisella tularensis and several Staphylococcus strains. These are important pathogens with a profound influence on human health. The recently characterised gamma-PGA hydrolases, which can dismantle the gamma-PGA-capsules, are an attractive new direction that can offer real hope for the development of alternatives to antibiotics, particularly in cases of multidrug resistant bacteria. We have characterised in detail the cleaving mechanism and stereospecificity of the enzyme PghL (previously named YndL) from Bacillus subtilis encoded by a gene of phagic origin and dramatically efficient in degrading the long polymeric chains of gamma-PGA. We used X-ray crystallography to solve the three-dimensional structures of the enzyme in its zinc-free, zinc-bound and complexed forms. The protein crystallised with a gamma-PGA hexapeptide substrate and thus reveals details of the interaction which could explain the stereospecificity observed and give hints on the catalytic mechanism of this class of hydrolytic enzymes.
		+
		+	The structure of PghL hydrolase bound to its substrate poly-gamma-glutamate.,Ramaswamy S, Rasheed M, Morelli CF, Calvio C, Sutton BJ, Pastore A FEBS J. 2018 Dec;285(24):4575-4589. doi: 10.1111/febs.14688. Epub 2018 Nov 19. PMID:30387270<ref>PMID:30387270</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5onl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:56, 16 October 2019

OCA — Wed, 16 Oct 2019 06:56:09 GMT

←Older revision		Revision as of 06:56, 16 October 2019
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	==YNDL-apo (Zinc-free)==		==YNDL-apo (Zinc-free)==
-	<StructureSection load='5onl' size='340' side='right' caption='[[5onl]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5onl' size='340' side='right'caption='[[5onl]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5onl]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ONL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ONL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5onl]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ONL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ONL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=010:PHENYLMETHANOL'>010</scene>, <scene name='pdbligand=FAH:FLUOROACETIC+ACID'>FAH</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=010:PHENYLMETHANOL'>010</scene>, <scene name='pdbligand=FAH:FLUOROACETIC+ACID'>FAH</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">B4417_0239 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=5onl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5onl OCA], [http://pdbe.org/5onl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5onl RCSB], [http://www.ebi.ac.uk/pdbsum/5onl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5onl 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=5onl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5onl OCA], [http://pdbe.org/5onl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5onl RCSB], [http://www.ebi.ac.uk/pdbsum/5onl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5onl ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Vibrio subtilis ehrenberg 1835]]
		+	[[Category: Large Structures]]
	[[Category: Calvio, C]]		[[Category: Calvio, C]]
	[[Category: Morelli, C]]		[[Category: Morelli, C]]

OCA at 07:16, 29 August 2018

OCA — Wed, 29 Aug 2018 07:16:09 GMT

←Older revision		Revision as of 07:16, 29 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5onl ~~is ON HOLD~~	+	==YNDL-apo (Zinc-free)==
-		+	<StructureSection load='5onl' size='340' side='right' caption='[[5onl]], [[Resolution\|resolution]] 1.70Å' scene=''>
-	~~Authors~~: ~~Ramaswamy, S~~.~~, Rasheed, M~~.~~, Morelli, C~~.~~, Calvio, C~~.~~, Sutton, B~~., ~~Pastore~~, A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5onl]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ONL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ONL FirstGlance]. <br>
-	~~Description~~: ~~YNDL~~-~~apo (Zinc~~-~~free)~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=010:PHENYLMETHANOL'>010</scene>, <scene name='pdbligand=FAH:FLUOROACETIC+ACID'>FAH</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5onl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5onl OCA], [http://pdbe.org/5onl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5onl RCSB], [http://www.ebi.ac.uk/pdbsum/5onl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5onl ProSAT]</span></td></tr>
-	[[Category: ~~Ramaswamy~~, S]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Calvio, C]]
	[[Category: Morelli, C]]		[[Category: Morelli, C]]
	[[Category: Pastore, A]]		[[Category: Pastore, A]]
		+	[[Category: Ramaswamy, S]]
	[[Category: Rasheed, M]]		[[Category: Rasheed, M]]
	[[Category: Sutton, B]]		[[Category: Sutton, B]]
-	[[Category: ~~Calvio, C~~]]	+	[[Category: Gamma-pga-hydrolase]]
		+	[[Category: Hydrolase]]

OCA: Protected "5onl" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 12:37:45 GMT

Protected "5onl" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:37, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5onl is ON HOLD Authors: Ramaswamy, S., Rasheed, M., Morelli, C., Calvio, C., Sutton, B., Pastore, A. Description: YNDL-apo (Zinc-free) [[Category:...

OCA — Wed, 27 Sep 2017 12:37:44 GMT

New page: '''Unreleased structure''' The entry 5onl is ON HOLD Authors: Ramaswamy, S., Rasheed, M., Morelli, C., Calvio, C., Sutton, B., Pastore, A. Description: YNDL-apo (Zinc-free) [[Category:...

New page

'''Unreleased structure'''

The entry 5onl is ON HOLD

Authors: Ramaswamy, S., Rasheed, M., Morelli, C., Calvio, C., Sutton, B., Pastore, A.

Description: YNDL-apo (Zinc-free)
[[Category: Unreleased Structures]]
[[Category: Ramaswamy, S]]
[[Category: Morelli, C]]
[[Category: Pastore, A]]
[[Category: Rasheed, M]]
[[Category: Sutton, B]]
[[Category: Calvio, C]]