5zfl - Revision history

OCA at 08:53, 22 November 2023

2023-11-22T08:53:09Z

←Older revision		Revision as of 08:53, 22 November 2023
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	<StructureSection load='5zfl' size='340' side='right'caption='[[5zfl]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='5zfl' size='340' side='right'caption='[[5zfl]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zfl]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"clostridium_licheniforme"_weigmann_1898 "clostridium licheniforme" weigmann 1898~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZFL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5ZFL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zfl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_licheniformis Bacillus licheniformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZFL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZFL FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDO:1,2~~-~~ETHANEDIOL'>EDO</scene>~~, ~~<scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-~~1~~-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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]] 1.5Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>penP, blaP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1402~~ "~~Clostridium licheniforme~~" ~~Weigmann 1898])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Beta~~-~~lactamase Beta~~-~~lactamase], with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6]~~ </~~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=5zfl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zfl OCA], [https://pdbe.org/5zfl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zfl RCSB], [https://www.ebi.ac.uk/pdbsum/5zfl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zfl ProSAT]</span></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=5zfl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zfl OCA], [~~http~~://pdbe.org/5zfl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zfl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zfl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zfl ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/BLAC_BACLI BLAC_BACLI]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Clostridium licheniforme weigmann 1898]]~~	+	[[Category: Bacillus licheniformis]]
-	~~[[Category: Beta-lactamase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Pan, X]]	+	[[Category: Pan X]]
-	[[Category: Zhao, Y]]	+	[[Category: Zhao Y]]
-	~~[[Category: Antibiotic resistance]]~~	+
-	~~[[Category: Class a beta-lactamase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 14:26, 8 July 2020

2020-07-08T14:26:56Z

←Older revision		Revision as of 14:26, 8 July 2020
Line 3:		Line 3:
	<StructureSection load='5zfl' size='340' side='right'caption='[[5zfl]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='5zfl' size='340' side='right'caption='[[5zfl]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zfl]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZFL OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZFL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zfl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"clostridium_licheniforme"_weigmann_1898 "clostridium licheniforme" weigmann 1898]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZFL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ZFL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">penP, blaP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1402 "Clostridium licheniforme" Weigmann 1898])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </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=5zfl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zfl OCA], [http://pdbe.org/5zfl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zfl RCSB], [http://www.ebi.ac.uk/pdbsum/5zfl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zfl ProSAT]</span></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=5zfl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zfl OCA], [http://pdbe.org/5zfl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zfl RCSB], [http://www.ebi.ac.uk/pdbsum/5zfl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zfl ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Serine-based beta-lactamases of Class A, C and D all rely on a key water molecule to hydrolyze and inactivate beta-lactam antibiotics. This process involves two conserved catalytic steps. In the first acylation step, the beta-lactam antibiotic forms an acyl-enzyme intermediate (ES) with the catalytic serine residue. In the second deacylation step, an activated water molecule serves as nucleophile (WAT_Nu) to attack ES and release the inactivated beta-lactam. The coordination and activation of WAT_Nu is not fully understood. Using time-resolved x-ray crystallography and QM/MM simulations, we analyzed three intermediate structures of Class A beta-lactamase PenP as it slowly hydrolyzed cephaloridine. WAT_Nu is centrally located in the apo structure but becomes slightly displaced away by ES* in the post-acylation structure. In the deacylation structure, WAT_Nu moves back and is positioned along the Burgi-Dunitz trajectory with favorable energetic profile to attack ES. Unexpectedly, WAT_Nu is also found to adopt a catalytically incompetent conformation in the deacylation structure forming a hydrogen bond with ES. Our results reveal that ES* plays a significant role in coordinating and activating WAT_Nu through subtle yet distinct interactions at different stages of the catalytic process. These interactions may serve as potential targets to circumvent beta-lactamase-mediated antibiotic resistance.
		+
		+	The hydrolytic water molecule of Class A beta-lactamase relies on the acyl-enzyme intermediate ES* for proper coordination and catalysis.,He Y, Lei J, Pan X, Huang X, Zhao Y Sci Rep. 2020 Jun 23;10(1):10205. doi: 10.1038/s41598-020-66431-w. PMID:32576842<ref>PMID:32576842</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5zfl" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Clostridium licheniforme weigmann 1898]]
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 07:40, 20 March 2019

2019-03-20T07:40:31Z

←Older revision		Revision as of 07:40, 20 March 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zfl is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of beta-lactamase PenP mutant E166Y==
-		+	<StructureSection load='5zfl' size='340' side='right'caption='[[5zfl]], [[Resolution\|resolution]] 1.50Å' scene=''>
-	~~Authors~~: ~~Pan~~, X., ~~Zhao~~, Y.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5zfl]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZFL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZFL FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of beta~~-lactamase ~~PenP mutant E166Y~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </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=5zfl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zfl OCA], [http://pdbe.org/5zfl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zfl RCSB], [http://www.ebi.ac.uk/pdbsum/5zfl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zfl ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-lactamase]]
		+	[[Category: Large Structures]]
	[[Category: Pan, X]]		[[Category: Pan, X]]
	[[Category: Zhao, Y]]		[[Category: Zhao, Y]]
		+	[[Category: Antibiotic resistance]]
		+	[[Category: Class a beta-lactamase]]
		+	[[Category: Hydrolase]]

OCA at 04:45, 2 January 2019

2019-01-02T04:45:52Z

←Older revision		Revision as of 04:45, 2 January 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zfl is ON HOLD	+	The entry 5zfl is ON HOLD until Paper Publication

	Authors: Pan, X., Zhao, Y.		Authors: Pan, X., Zhao, Y.

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

2018-03-14T05:00:29Z

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

←Older revision

Revision as of 05:00, 14 March 2018

OCA: New page: '''Unreleased structure''' The entry 5zfl is ON HOLD Authors: Pan, X., Zhao, Y. Description: Crystal structure of beta-lactamase PenP mutant E166Y Category: Unreleased Structures [...

2018-03-14T05:00:28Z

New page: '''Unreleased structure''' The entry 5zfl is ON HOLD Authors: Pan, X., Zhao, Y. Description: Crystal structure of beta-lactamase PenP mutant E166Y Category: Unreleased Structures [...

New page

'''Unreleased structure'''

The entry 5zfl is ON HOLD

Authors: Pan, X., Zhao, Y.

Description: Crystal structure of beta-lactamase PenP mutant E166Y
[[Category: Unreleased Structures]]
[[Category: Pan, X]]
[[Category: Zhao, Y]]