6n9i - Revision history

OCA at 06:48, 11 October 2023

2023-10-11T06:48:11Z

←Older revision		Revision as of 06:48, 11 October 2023
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	<StructureSection load='6n9i' size='340' side='right'caption='[[6n9i]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='6n9i' size='340' side='right'caption='[[6n9i]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n9i]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Geobacillus_caldoxylosilyticus_nbrc_107762 Geobacillus~~ caldoxylosilyticus ~~nbrc~~ 107762]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N9I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6N9I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n9i]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Parageobacillus_caldoxylosilyticus_NBRC_107762 Parageobacillus caldoxylosilyticus NBRC 107762]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N9I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N9I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 1.6Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GCA01S_030_00190 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1220594 Geobacillus caldoxylosilyticus NBRC 107762])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=6n9i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n9i OCA], [~~http~~://pdbe.org/6n9i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6n9i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6n9i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6n9i 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=6n9i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n9i OCA], [https://pdbe.org/6n9i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n9i RCSB], [https://www.ebi.ac.uk/pdbsum/6n9i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n9i ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A023DFE8_9BACI A0A023DFE8_9BACI]
	<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: Geobacillus caldoxylosilyticus nbrc 107762]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Bergonzi, C~~]]	+	[[Category: Parageobacillus caldoxylosilyticus NBRC 107762]]
-	[[Category: ~~Elias, M~~]]	+	[[Category: Bergonzi C]]
-	[[Category: ~~Schwab,~~ M]]	+	[[Category: Elias M]]
-	[[Category: ~~Ahl]]~~	+	[[Category: Schwab M]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Lactonase]]~~	+
-	~~[[Category: Mll]]~~	+
-	~~[[Category: Quorum quenching]]~~	+
-	~~[[Category: Quorum sensing]]~~	+
-	~~[[Category: Thermophile~~]]	+

OCA at 09:19, 1 May 2019

2019-05-01T09:19:40Z

←Older revision		Revision as of 09:19, 1 May 2019
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	<StructureSection load='6n9i' size='340' side='right'caption='[[6n9i]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='6n9i' size='340' side='right'caption='[[6n9i]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n9i]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N9I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N9I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n9i]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_caldoxylosilyticus_nbrc_107762 Geobacillus caldoxylosilyticus nbrc 107762]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N9I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N9I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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">GCA01S_030_00190 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1220594 Geobacillus caldoxylosilyticus NBRC 107762])</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=6n9i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n9i OCA], [http://pdbe.org/6n9i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n9i RCSB], [http://www.ebi.ac.uk/pdbsum/6n9i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n9i 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=6n9i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n9i OCA], [http://pdbe.org/6n9i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n9i RCSB], [http://www.ebi.ac.uk/pdbsum/6n9i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n9i ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Geobacillus caldoxylosilyticus nbrc 107762]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bergonzi, C]]		[[Category: Bergonzi, C]]

OCA at 07:08, 3 April 2019

2019-04-03T07:08:31Z

←Older revision		Revision as of 07:08, 3 April 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6n9i is ~~ON HOLD~~	+	==Structure of the Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus - free==
		+	<StructureSection load='6n9i' size='340' side='right'caption='[[6n9i]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6n9i]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N9I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N9I FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=6n9i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n9i OCA], [http://pdbe.org/6n9i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n9i RCSB], [http://www.ebi.ac.uk/pdbsum/6n9i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n9i ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Quorum quenching lactonases are enzymes capable of hydrolyzing lactones, including N-acyl homoserine lactones (AHLs). AHLs are molecules known as signals in bacterial communication dubbed quorum sensing. Bacterial signal disruption by lactonases was previously reported to inhibit behaviors regulated by quorum sensing such as the expression of virulence factors and the formation of biofilms. Here, we report the enzymatic and structural characterization of a novel lactonase representative from the metallo-beta-lactamase superfamily, dubbed GcL. GcL is both a broad spectrum and a highly proficient lactonase, with kcat/KM values in the range of 104 to 106 M-1.s-1. Analysis of GcL structures obtained free, and in complex with AHL substrates of different acyl chain length, namely C4-AHL and 3-oxo-C12-AHL allowed us to elucidate their respective binding modes. Structures reveal three sub-sites in the binding crevice: (i) the small sub-site where chemistry is performed on the lactone ring; (ii) a hydrophobic ring that accommodates the amide group of AHLs and small acyl chains; and (iii) the outer, hydrophilic sub-site that extends to the protein surface. Unexpectedly, the absence of structural accommodation for long substrate acyl chains seem to relate to the enzyme's broad substrate specificity.

-	~~Authors: Bergonzi~~, C., Schwab, M., ~~Elias~~, M.	+	The Structural Determinants Accounting for the Broad Substrate Specificity of the Quorum Quenching Lactonase GcL.,Bergonzi C, Schwab M, Naik T, Elias M Chembiochem. 2019 Mar 12. doi: 10.1002/cbic.201900024. PMID:30864300<ref>PMID:30864300</ref>

-	~~Description: Structure~~ of the ~~Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus~~ -~~free~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6n9i" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Bergonzi, C]]		[[Category: Bergonzi, C]]
	[[Category: Elias, M]]		[[Category: Elias, M]]
	[[Category: Schwab, M]]		[[Category: Schwab, M]]
		+	[[Category: Ahl]]
		+	[[Category: Hydrolase]]
		+	[[Category: Lactonase]]
		+	[[Category: Mll]]
		+	[[Category: Quorum quenching]]
		+	[[Category: Quorum sensing]]
		+	[[Category: Thermophile]]

OCA at 05:53, 20 March 2019

2019-03-20T05:53:56Z

←Older revision		Revision as of 05:53, 20 March 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6n9i is ON HOLD ~~until Paper Publication~~	+	The entry 6n9i is ON HOLD

	Authors: Bergonzi, C., Schwab, M., Elias, M.		Authors: Bergonzi, C., Schwab, M., Elias, M.
Line 7:		Line 7:
	Description: Structure of the Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus -free		Description: Structure of the Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus -free
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Elias, M]]
	[[Category: Bergonzi, C]]		[[Category: Bergonzi, C]]
		+	[[Category: Elias, M]]
	[[Category: Schwab, M]]		[[Category: Schwab, M]]

OCA at 06:27, 30 January 2019

2019-01-30T06:27:33Z

←Older revision		Revision as of 06:27, 30 January 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6n9i is ON HOLD	+	The entry 6n9i is ON HOLD until Paper Publication

	Authors: Bergonzi, C., Schwab, M., Elias, M.		Authors: Bergonzi, C., Schwab, M., Elias, M.
Line 7:		Line 7:
	Description: Structure of the Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus -free		Description: Structure of the Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus -free
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Bergonzi, C]]
	[[Category: Elias, M]]		[[Category: Elias, M]]
		+	[[Category: Bergonzi, C]]
	[[Category: Schwab, M]]		[[Category: Schwab, M]]

OCA: Protected "6n9i" [edit=sysop:move=sysop]

2018-12-12T05:22:55Z

Protected "6n9i" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:22, 12 December 2018

OCA: New page: '''Unreleased structure''' The entry 6n9i is ON HOLD Authors: Bergonzi, C., Schwab, M., Elias, M. Description: Structure of the Quorum Quenching lactonase from Parageobacillus caldoxyl...

2018-12-12T05:22:54Z

New page: '''Unreleased structure''' The entry 6n9i is ON HOLD Authors: Bergonzi, C., Schwab, M., Elias, M. Description: Structure of the Quorum Quenching lactonase from Parageobacillus caldoxyl...

New page

'''Unreleased structure'''

The entry 6n9i is ON HOLD

Authors: Bergonzi, C., Schwab, M., Elias, M.

Description: Structure of the Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus -free
[[Category: Unreleased Structures]]
[[Category: Bergonzi, C]]
[[Category: Elias, M]]
[[Category: Schwab, M]]