6lc8 - Revision history

OCA at 11:45, 23 March 2022

2022-03-23T11:45:26Z

←Older revision		Revision as of 11:45, 23 March 2022
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	<StructureSection load='6lc8' size='340' side='right'caption='[[6lc8]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='6lc8' size='340' side='right'caption='[[6lc8]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6lc8]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"aerobacter_cloacae"_(jordan_1890)_bergey_et_al._1923 "aerobacter cloacae" (jordan 1890) bergey et al. 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LC8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6LC8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6lc8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"aerobacter_cloacae"_(jordan_1890)_bergey_et_al._1923 "aerobacter cloacae" (jordan 1890) bergey et al. 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LC8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LC8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=NXL:(2S,5R)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE'>NXL</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" id="ligandDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=NXL:(2S,5R)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE'>NXL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6lc7\|6lc7]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6lc7\|6lc7]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CKO00_24250 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=550 "Aerobacter cloacae" (Jordan 1890) Bergey et al. 1923])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CKO00_24250 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=550 "Aerobacter cloacae" (Jordan 1890) Bergey et al. 1923])</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'>[https://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [https://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=6lc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lc8 OCA], [~~http~~://pdbe.org/6lc8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6lc8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6lc8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6lc8 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=6lc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lc8 OCA], [https://pdbe.org/6lc8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lc8 RCSB], [https://www.ebi.ac.uk/pdbsum/6lc8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lc8 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 14:31, 8 July 2020

2020-07-08T14:31:29Z

←Older revision		Revision as of 14:31, 8 July 2020
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6lc8" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6lc8" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:59, 29 April 2020

2020-04-29T06:59:06Z

←Older revision		Revision as of 06:59, 29 April 2020
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	==Crystal structure of AmpC Ent385 complex form with avibactam==		==Crystal structure of AmpC Ent385 complex form with avibactam==
-	<StructureSection load='6lc8' size='340' side='right'caption='[[6lc8]]' scene=''>	+	<StructureSection load='6lc8' size='340' side='right'caption='[[6lc8]], [[Resolution\|resolution]] 1.60Å' 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=6LC8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LC8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6lc8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"aerobacter_cloacae"_(jordan_1890)_bergey_et_al._1923 "aerobacter cloacae" (jordan 1890) bergey et al. 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LC8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LC8 FirstGlance]. <br>
-	</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=6lc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lc8 OCA], [http://pdbe.org/6lc8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lc8 RCSB], [http://www.ebi.ac.uk/pdbsum/6lc8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lc8 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=NXL:(2S,5R)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE'>NXL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6lc7\|6lc7]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CKO00_24250 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=550 "Aerobacter cloacae" (Jordan 1890) Bergey et al. 1923])</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=6lc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lc8 OCA], [http://pdbe.org/6lc8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lc8 RCSB], [http://www.ebi.ac.uk/pdbsum/6lc8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lc8 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ceftazidime-avibactam and cefiderocol are two of the latest generation beta-lactam agents that possess expanded activity against highly drug-resistant bacteria, including carbapenem-resistant Enterobacterales Here we show that structural changes in AmpC beta-lactamases can confer reduced susceptibility to both agents. A multidrug-resistant Enterobacter cloacae clinical strain (Ent385) was found to be resistant to ceftazidime-avibactam and cefiderocol without prior exposure to either agent. The AmpC beta-lactamase of Ent385 (AmpC(Ent385)) contained an alanine-proline deletion at positions 294-295 (A294_P295del) in the R2 loop. AmpC(Ent385) conferred reduced susceptibility to ceftazidime-avibactam and cefiderocol when cloned into Escherichia coli TOP10. Purified AmpC(Ent385) showed increased hydrolysis of ceftazidime and cefiderocol compared with AmpC(Ent385Rev), in which the deletion was reverted. Comparisons of crystal structures of AmpC(Ent385) and AmpC(P99), the canonical AmpC of E. cloacae, revealed that the two-residue deletion in AmpC(Ent385) induced drastic structural changes of the H-9 and H-10 helices and the R2 loop, which accounted for the increased hydrolysis of ceftazidime and cefiderocol. The potential for a single mutation in ampC to confer reduced susceptibility to both ceftazidime-avibactam and cefiderocol requires close monitoring.Importance Ceftazidime-avibactam and cefiderocol are newly approved beta-lactam agents that possess broad spectrum activity against multidrug-resistant (MDR) Gram-negative bacteria. We show here that a two amino-acid deletion in the chromosomal AmpC beta-lactamase, identified in a clinical strain of Enterobacter cloacae, confers reduced susceptibility to both agents. By crystallographic studies of free and drug-bound forms of enzyme, we demonstrate that this deletion in AmpC induces slanting of the H-9 helix that is directly connected with the R2 loop, and disappearance of the H-10 helix, is directly responsible for increased hydrolysis of ceftazidime and cefiderocol. These findings provide novel insights into how MDR Gram-negative bacteria may evolve their beta-lactamases to survive selective pressure from these newly developed beta-lactam agents.
		+
		+	Structural basis of reduced susceptibility to ceftazidime-avibactam and cefiderocol in Enterobacter cloacae due to AmpC R2 loop deletion.,Kawai A, McElheny CL, Iovleva A, Kline EG, Sluis-Cremer N, Shields RK, Doi Y Antimicrob Agents Chemother. 2020 Apr 13. pii: AAC.00198-20. doi:, 10.1128/AAC.00198-20. PMID:32284381<ref>PMID:32284381</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6lc8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Beta-lactamase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Doi Y]]	+	[[Category: Doi, Y]]
-	[[Category: Kawai A]]	+	[[Category: Kawai, A]]
		+	[[Category: Ampc]]
		+	[[Category: Avibactam]]
		+	[[Category: Class c]]
		+	[[Category: Hydrolase]]

OCA at 05:40, 22 April 2020

2020-04-22T05:40:19Z

←Older revision		Revision as of 05:40, 22 April 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6lc8 ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of AmpC Ent385 complex form with avibactam==
-		+	<StructureSection load='6lc8' size='340' side='right'caption='[[6lc8]]' scene=''>
-	~~Authors~~: ~~Kawai~~, A., ~~Doi~~, Y.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LC8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LC8 FirstGlance]. <br>
-	~~Description: Crystal structure of AmpC Ent385 complex form with avibactam~~	+	</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=6lc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lc8 OCA], [http://pdbe.org/6lc8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lc8 RCSB], [http://www.ebi.ac.uk/pdbsum/6lc8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lc8 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Doi, Y]]	+	__TOC__
-	[[Category: Kawai, A]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Doi Y]]
		+	[[Category: Kawai A]]

OCA at 13:23, 11 December 2019

2019-12-11T13:23:42Z

←Older revision		Revision as of 13:23, 11 December 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6lc8 is ON HOLD	+	The entry 6lc8 is ON HOLD until Paper Publication

	Authors: Kawai, A., Doi, Y.		Authors: Kawai, A., Doi, Y.

OCA: Protected "6lc8" [edit=sysop:move=sysop]

2019-11-27T05:05:37Z

Protected "6lc8" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:05, 27 November 2019

OCA: New page: '''Unreleased structure''' The entry 6lc8 is ON HOLD Authors: Kawai, A., Doi, Y. Description: Crystal structure of AmpC Ent385 complex form with avibactam [[Category: Unreleased Struct...

2019-11-27T05:05:36Z

New page: '''Unreleased structure''' The entry 6lc8 is ON HOLD Authors: Kawai, A., Doi, Y. Description: Crystal structure of AmpC Ent385 complex form with avibactam [[Category: Unreleased Struct...

New page

'''Unreleased structure'''

The entry 6lc8 is ON HOLD

Authors: Kawai, A., Doi, Y.

Description: Crystal structure of AmpC Ent385 complex form with avibactam
[[Category: Unreleased Structures]]
[[Category: Doi, Y]]
[[Category: Kawai, A]]