7me9 - Revision history

OCA at 16:09, 18 October 2023

2023-10-18T16:09:58Z

←Older revision		Revision as of 16:09, 18 October 2023
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	==CDD-1 beta-lactamase in imidazole/MPD 30 seconds avibactam complex==		==CDD-1 beta-lactamase in imidazole/MPD 30 seconds avibactam complex==
-	<StructureSection load='7me9' size='340' side='right'caption='[[7me9]]' scene=''>	+	<StructureSection load='7me9' size='340' side='right'caption='[[7me9]], [[Resolution\|resolution]] 1.70Å' 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=7ME9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ME9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7me9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridioides_difficile Clostridioides difficile]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ME9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ME9 FirstGlance]. <br>
-	</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=7me9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7me9 OCA], [https://pdbe.org/7me9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7me9 RCSB], [https://www.ebi.ac.uk/pdbsum/7me9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7me9 ProSAT]</span></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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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'>[https://proteopedia.org/fgij/fg.htm?mol=7me9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7me9 OCA], [https://pdbe.org/7me9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7me9 RCSB], [https://www.ebi.ac.uk/pdbsum/7me9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7me9 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A160YKM3_CLODI A0A160YKM3_CLODI]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Class D beta-lactamases have risen to notoriety due to their wide spread in bacterial pathogens, propensity to inactivate clinically important beta-lactam antibiotics, and ability to withstand inhibition by the majority of classical beta-lactamase inhibitors. Understanding the catalytic mechanism of these enzymes is thus vitally important for the development of novel antibiotics and inhibitors active against infections caused by antibiotic-resistant bacteria. Here we report an in crystallo time-resolved study of the interaction of the class D beta-lactamase CDD-1 from Clostridioides difficile with the diazobicyclooctane inhibitor, avibactam. We show that the catalytic carboxylated lysine, a residue that is essential for both acylation and deacylation of beta-lactams, is sequestered within an internal sealed pocket of the enzyme. Time-resolved snapshots generated in this study allowed us to observe decarboxylation of the lysine and movement of CO2 and water molecules through a transient channel formed between the lysine pocket and the substrate binding site facilitated by rotation of the side chain of a conserved leucine residue. These studies provide novel insights on avibactam binding to CDD-1 and into the catalytic mechanism of class D beta-lactamases in general.
		+
		+	In Crystallo Time-Resolved Interaction of the Clostridioides difficile CDD-1 enzyme with Avibactam Provides New Insights into the Catalytic Mechanism of Class D beta-lactamases.,Stewart NK, Toth M, Stasyuk A, Vakulenko SB, Smith CA ACS Infect Dis. 2021 Apr 28. doi: 10.1021/acsinfecdis.1c00094. PMID:33908775<ref>PMID:33908775</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7me9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Clostridioides difficile]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Smith CA]]		[[Category: Smith CA]]
	[[Category: Vakulenko SB]]		[[Category: Vakulenko SB]]

OCA at 10:16, 16 February 2022

2022-02-16T10:16:07Z

←Older revision		Revision as of 10:16, 16 February 2022
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-	'''Unreleased structure'''

-	~~The entry 7me9 is ON HOLD until Paper Publication~~	+	==CDD-1 beta-lactamase in imidazole/MPD 30 seconds avibactam complex==
-		+	<StructureSection load='7me9' size='340' side='right'caption='[[7me9]]' scene=''>
-	~~Authors: Smith, C.A., Vakulenko, S.B.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ME9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ME9 FirstGlance]. <br>
-	~~Description:~~ CDD-1 beta-lactamase in imidazole/MPD 30 seconds avibactam complex	+	</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=7me9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7me9 OCA], [https://pdbe.org/7me9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7me9 RCSB], [https://www.ebi.ac.uk/pdbsum/7me9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7me9 ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Vakulenko~~, S.B]]	+	__TOC__
-	[[Category: Smith~~, C.A~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Smith CA]]
		+	[[Category: Vakulenko SB]]

OCA at 08:08, 12 May 2021

2021-05-12T08:08:59Z

←Older revision		Revision as of 08:08, 12 May 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7me9 is ON HOLD	+	The entry 7me9 is ON HOLD until Paper Publication

	Authors: Smith, C.A., Vakulenko, S.B.		Authors: Smith, C.A., Vakulenko, S.B.
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	Description: CDD-1 beta-lactamase in imidazole/MPD 30 seconds avibactam complex		Description: CDD-1 beta-lactamase in imidazole/MPD 30 seconds avibactam complex
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Smith, C.A]]
	[[Category: Vakulenko, S.B]]		[[Category: Vakulenko, S.B]]
		+	[[Category: Smith, C.A]]

OCA at 06:18, 21 April 2021

2021-04-21T06:18:11Z

←Older revision		Revision as of 06:18, 21 April 2021
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	The entry 7me9 is ON HOLD		The entry 7me9 is ON HOLD

-	Authors: Smith, C.A., ~~Vakullenko~~, S.B.	+	Authors: Smith, C.A., Vakulenko, S.B.

	Description: CDD-1 beta-lactamase in imidazole/MPD 30 seconds avibactam complex		Description: CDD-1 beta-lactamase in imidazole/MPD 30 seconds avibactam complex
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Vakullenko, S.B]]
	[[Category: Smith, C.A]]		[[Category: Smith, C.A]]
		+	[[Category: Vakulenko, S.B]]

OCA: Protected "7me9" [edit=sysop:move=sysop]

2021-04-14T05:43:39Z

Protected "7me9" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:43, 14 April 2021

OCA: New page: '''Unreleased structure''' The entry 7me9 is ON HOLD Authors: Smith, C.A., Vakullenko, S.B. Description: CDD-1 beta-lactamase in imidazole/MPD 30 seconds avibactam complex [[Category: ...

2021-04-14T05:43:38Z

New page: '''Unreleased structure''' The entry 7me9 is ON HOLD Authors: Smith, C.A., Vakullenko, S.B. Description: CDD-1 beta-lactamase in imidazole/MPD 30 seconds avibactam complex [[Category: ...

New page

'''Unreleased structure'''

The entry 7me9 is ON HOLD

Authors: Smith, C.A., Vakullenko, S.B.

Description: CDD-1 beta-lactamase in imidazole/MPD 30 seconds avibactam complex
[[Category: Unreleased Structures]]
[[Category: Vakullenko, S.B]]
[[Category: Smith, C.A]]