5ghz - Revision history

OCA at 11:32, 2 August 2023

2023-08-02T11:32:03Z

←Older revision		Revision as of 11:32, 2 August 2023
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	<StructureSection load='5ghz' size='340' side='right'caption='[[5ghz]], [[Resolution\|resolution]] 1.93Å' scene=''>		<StructureSection load='5ghz' size='340' side='right'caption='[[5ghz]], [[Resolution\|resolution]] 1.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ghz]] 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=5GHZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5GHZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ghz]] 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=5GHZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GHZ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CED:5~~-~~METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-3~~,~~6-DIHYDRO-2H-~~[~~1,3]THIAZINE-4-CARBOXYLIC+ACID'>CED</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]] 1.93Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[~~[Related_structure~~\|~~Related:]]</b></td><td class="sblockDat">[[5ghx\|5ghx]], [[5ghy\|5ghy~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CED:5-METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC+ACID'>CED</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5ghz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ghz OCA], [https://pdbe.org/5ghz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ghz RCSB], [https://www.ebi.ac.uk/pdbsum/5ghz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ghz ProSAT]</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~~://proteopedia.org/fgij/fg.htm?mol=5ghz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ghz OCA], [~~http~~://pdbe.org/5ghz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ghz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ghz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ghz 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: Hydrolase~~]]	+

OCA at 06:43, 13 May 2020

2020-05-13T06:43:24Z

←Older revision		Revision as of 06:43, 13 May 2020
Line 1:		Line 1:

	==Crystal structure of beta-lactamase PenP mutant-E166H in complex with cephaloridine as "pre-deacylation" intermediate==		==Crystal structure of beta-lactamase PenP mutant-E166H in complex with cephaloridine as "pre-deacylation" intermediate==
-	<StructureSection load='5ghz' size='340' side='right' caption='[[5ghz]], [[Resolution\|resolution]] 1.93Å' scene=''>	+	<StructureSection load='5ghz' size='340' side='right'caption='[[5ghz]], [[Resolution\|resolution]] 1.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ghz]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GHZ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5GHZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ghz]] 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=5GHZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5GHZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CED:5-METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC+ACID'>CED</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CED:5-METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC+ACID'>CED</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ghx\|5ghx]], [[5ghy\|5ghy]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ghx\|5ghx]], [[5ghy\|5ghy]]</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=5ghz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ghz OCA], [http://pdbe.org/5ghz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ghz RCSB], [http://www.ebi.ac.uk/pdbsum/5ghz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ghz 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=5ghz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ghz OCA], [http://pdbe.org/5ghz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ghz RCSB], [http://www.ebi.ac.uk/pdbsum/5ghz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ghz ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5ghz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ghz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Clostridium licheniforme weigmann 1898]]
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
		+	[[Category: Large Structures]]
	[[Category: Pan, X]]		[[Category: Pan, X]]
	[[Category: Zhao, Y]]		[[Category: Zhao, Y]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 09:49, 22 March 2017

2017-03-22T09:49:10Z

←Older revision		Revision as of 09:49, 22 March 2017
Line 9:		Line 9:
	<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=5ghz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ghz OCA], [http://pdbe.org/5ghz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ghz RCSB], [http://www.ebi.ac.uk/pdbsum/5ghz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ghz 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=5ghz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ghz OCA], [http://pdbe.org/5ghz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ghz RCSB], [http://www.ebi.ac.uk/pdbsum/5ghz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ghz ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	beta-Lactamases confer resistance to beta-lactam-based antibiotics. There is great interest in understanding their mechanisms to enable the development of beta-lactamase-specific inhibitors. The mechanism of class A beta-lactamases has been studied extensively, revealing Lys-73 and Glu-166 as general bases that assist the catalytic residue Ser-70. However, the specific roles of these two residues within the catalytic cycle remain not fully understood. To help resolve this, we first identified an E166H mutant that is functional but is kinetically slow. We then carried out time-resolved crystallographic study of a full cycle of the catalytic reaction. We obtained structures that represent apo, ES-acylation, and ES-deacylation states and analyzed the conformational changes of His-166. The "in" conformation in the apo structure allows His-166 to form a hydrogen bond with Lys-73. The unexpected "flipped-out" conformation of His-166 in the ES-acylation structure was further examined by molecular dynamics simulations, which suggested deprotonated Lys-73 serving as the general base for acylation. The "revert-in" conformation in the ES-deacylation structure aligns His-166 toward the water molecule that hydrolyzes the acyl adduct. Finally, when the acyl adduct is fully hydrolyzed, His-166 rotates back to the "in" conformation of the apo-state, restoring the Lys-73/His-166 interaction. Using His-166 as surrogate, our study identifies distinct conformational changes within the active site during catalysis. We suggest that the native Glu-166 executes similar changes in a less constricted way. Taken together, this structural series improves our understanding of beta-lactam hydrolysis in this important class of enzymes.
		+
		+	Crystallographic Snapshots of Class A beta-Lactamase Catalysis Reveal Structural Changes That Facilitate beta-Lactam Hydrolysis.,Pan X, He Y, Lei J, Huang X, Zhao Y J Biol Chem. 2017 Mar 10;292(10):4022-4033. doi: 10.1074/jbc.M116.764340. Epub, 2017 Jan 18. PMID:28100776<ref>PMID:28100776</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ghz" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 23:39, 25 January 2017

2017-01-25T23:39:29Z

←Older revision		Revision as of 23:39, 25 January 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5ghz is ON HOLD~~	+	==Crystal structure of beta-lactamase PenP mutant-E166H in complex with cephaloridine as "pre-deacylation" intermediate==
-		+	<StructureSection load='5ghz' size='340' side='right' caption='[[5ghz]], [[Resolution\|resolution]] 1.93Å' scene=''>
-	~~Authors: Pan, X., Zhao, Y.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ghz]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GHZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GHZ FirstGlance]. <br>
-	~~Description:~~ Crystal structure of beta-lactamase PenP mutant-E166H in complex with cephaloridine as ""pre-deacylation"" intermediate	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CED:5-METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC+ACID'>CED</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ghx\|5ghx]], [[5ghy\|5ghy]]</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=5ghz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ghz OCA], [http://pdbe.org/5ghz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ghz RCSB], [http://www.ebi.ac.uk/pdbsum/5ghz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ghz ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-lactamase]]
	[[Category: Pan, X]]		[[Category: Pan, X]]
	[[Category: Zhao, Y]]		[[Category: Zhao, Y]]
		+	[[Category: Hydrolase]]

OCA at 09:13, 18 January 2017

2017-01-18T09:13:04Z

←Older revision		Revision as of 09:13, 18 January 2017
Line 5:		Line 5:
	Authors: Pan, X., Zhao, Y.		Authors: Pan, X., Zhao, Y.

-	Description: Crystal structure of beta-lactamase PenP mutant-E166H	+	Description: Crystal structure of beta-lactamase PenP mutant-E166H in complex with cephaloridine as ""pre-deacylation"" intermediate
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Pan, X]]		[[Category: Pan, X]]
	[[Category: Zhao, Y]]		[[Category: Zhao, Y]]

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

2016-07-12T21:34:47Z

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

←Older revision

Revision as of 21:34, 12 July 2016

OCA: New page: '''Unreleased structure''' The entry 5ghz is ON HOLD Authors: Pan, X., Zhao, Y. Description: Crystal structure of beta-lactamase PenP mutant-E166H Category: Unreleased Structures [...

2016-07-12T21:34:46Z

New page: '''Unreleased structure''' The entry 5ghz is ON HOLD Authors: Pan, X., Zhao, Y. Description: Crystal structure of beta-lactamase PenP mutant-E166H Category: Unreleased Structures [...

New page

'''Unreleased structure'''

The entry 5ghz is ON HOLD

Authors: Pan, X., Zhao, Y.

Description: Crystal structure of beta-lactamase PenP mutant-E166H
[[Category: Unreleased Structures]]
[[Category: Pan, X]]
[[Category: Zhao, Y]]