6n6y - Revision history

OCA at 06:47, 11 October 2023

OCA — Wed, 11 Oct 2023 06:47:12 GMT

←Older revision		Revision as of 06:47, 11 October 2023
Line 1:		Line 1:

	==OXA-23 mutant F110A/M221A neutral pH form meropenem complex==		==OXA-23 mutant F110A/M221A neutral pH form meropenem complex==
-	<StructureSection load='6n6y' size='340' side='right' caption='[[6n6y]], [[Resolution\|resolution]] 3.50Å' scene=''>	+	<StructureSection load='6n6y' size='340' side='right'caption='[[6n6y]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n6y]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Aciba Aciba~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N6Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6N6Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n6y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baumannii Acinetobacter baumannii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N6Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N6Y FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=KE1:meropenem~~,~~+bound+form'>KE1</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]] 3.501Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene><~~/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=KE1:meropenem,+bound+form'>KE1</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">ari-1~~, bla(OXA-23), bla-OXA-23, bla-oxa-23, bla_1, bla_2, bla_3, blaOXA, blaOXA-23, blaOXA23, OXA-23, oxa-23, oxa23, A7M90_19440, AB719_18095, ABUW_0563, AZE33_05050, AZE33_05100, AZE33_05150, AZE33_05250, C7G90_19950, CAS83_19595, CBE85_20255, CBI29_04474, CEJ63_03230, DV997_16620, DVA79_19285, IX87_16825, IX87_21860, LV38_03424, NG19_0098, SAMEA104305208_04008, SAMEA104305242_04084, SAMEA104305271_04290, SAMEA104305299_06196, SAMEA104305318_04148, SAMEA104305341_03854, SAMEA104305343_03919, SAMEA104305351_03822, SAMEA104305385_00775 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=470 ACIBA])</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=6n6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n6y OCA], [https://pdbe.org/6n6y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n6y RCSB], [https://www.ebi.ac.uk/pdbsum/6n6y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n6y 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~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6n6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n6y OCA], [~~http~~://pdbe.org/6n6y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6n6y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6n6y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6n6y ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9L4P2_ACIBA Q9L4P2_ACIBA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6n6y" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6n6y" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aciba~~]]	+	[[Category: Acinetobacter baumannii]]
-	[[Category: ~~Beta-lactamase~~]]	+	[[Category: Large Structures]]
-	[[Category: Smith~~, C A~~]]	+	[[Category: Smith CA]]
-	[[Category: Vakulenko~~, S B]]~~	+	[[Category: Vakulenko SB]]
-	~~[[Category: Antibiotic resistance]]~~	+
-	~~[[Category: Carbapenemase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Mutant~~]]	+

OCA at 08:48, 26 December 2018

OCA — Wed, 26 Dec 2018 08:48:22 GMT

←Older revision		Revision as of 08:48, 26 December 2018
Line 3:		Line 3:
	<StructureSection load='6n6y' size='340' side='right' caption='[[6n6y]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='6n6y' size='340' side='right' caption='[[6n6y]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n6y]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N6Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N6Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n6y]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aciba Aciba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N6Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N6Y FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=KE1:meropenem,+bound+form'>KE1</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=KE1:meropenem,+bound+form'>KE1</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ari-1, bla(OXA-23), bla-OXA-23, bla-oxa-23, bla_1, bla_2, bla_3, blaOXA, blaOXA-23, blaOXA23, OXA-23, oxa-23, oxa23, A7M90_19440, AB719_18095, ABUW_0563, AZE33_05050, AZE33_05100, AZE33_05150, AZE33_05250, C7G90_19950, CAS83_19595, CBE85_20255, CBI29_04474, CEJ63_03230, DV997_16620, DVA79_19285, IX87_16825, IX87_21860, LV38_03424, NG19_0098, SAMEA104305208_04008, SAMEA104305242_04084, SAMEA104305271_04290, SAMEA104305299_06196, SAMEA104305318_04148, SAMEA104305341_03854, SAMEA104305343_03919, SAMEA104305351_03822, SAMEA104305385_00775 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=470 ACIBA])</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=6n6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n6y OCA], [http://pdbe.org/6n6y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n6y RCSB], [http://www.ebi.ac.uk/pdbsum/6n6y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n6y 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=6n6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n6y OCA], [http://pdbe.org/6n6y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n6y RCSB], [http://www.ebi.ac.uk/pdbsum/6n6y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n6y ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Class D carbapenemases are enzymes of utmost clinical importance due to their ability to confer resistance to the last resort carbapenem antibiotics. We investigated the role of the conserved hydrophobic bridge in the carbapenemase activity of OXA-23, the major carbapenemase of the important pathogen, Acinetobacter baumannii We show that substitution of the bridge residue Phe110 affects resistance to meropenem and doripenem and has little effect on MICs of imipenem. The opposite effect was observed upon substitution of the other bridge residue, Met221. Complete disruption of the bridge by the F110A/M221A substitution resulted in a significant loss of affinity for doripenem and meropenem, and to a lesser extent, for imipenem, which is reflected in the reduced MICs of these antibiotics. In the wild-type OXA-23, the pyrrolidine ring of the meropenem tail forms a hydrophobic interaction with Phe110 of the bridge. Similar interactions would ensue with ring-containing doripenem but not with imipenem, which lacks this ring. Our structural studies showed that this interaction with the meropenem tail is missing in the F110A/M221A mutant. These data explain why disruption of the interaction between the enzyme and the carbapenem substrate impacts the affinity and MICs of meropenem and doripenem to a larger degree than those of imipenem. Our structures also show that the bridge directs the acylated carbapenem into a specific tautomeric conformation. However, it is not this conformation, but rather the stabilizing interaction between the tail of the antibiotic and the hydrophobic bridge that contributes to the carbapenemase activity of class D beta-lactamases.
		+
		+	Role of the Hydrophobic Bridge in the Carbapenemase Activity of Class D beta-Lactamases.,Stewart NK, Smith CA, Antunes NT, Toth M, Vakulenko SB Antimicrob Agents Chemother. 2018 Dec 10. pii: AAC.02191-18. doi:, 10.1128/AAC.02191-18. PMID:30530607<ref>PMID:30530607</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6n6y" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aciba]]
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
	[[Category: Smith, C A]]		[[Category: Smith, C A]]

OCA at 08:36, 19 December 2018

OCA — Wed, 19 Dec 2018 08:36:44 GMT

←Older revision		Revision as of 08:36, 19 December 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6n6y is ~~ON HOLD~~	+	==OXA-23 mutant F110A/M221A neutral pH form meropenem complex==
-		+	<StructureSection load='6n6y' size='340' side='right' caption='[[6n6y]], [[Resolution\|resolution]] 3.50Å' scene=''>
-	~~Authors~~: ~~Smith~~, C.A., ~~Vakulenko~~, S.B.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6n6y]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N6Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N6Y FirstGlance]. <br>
-	~~Description~~: ~~OXA~~-~~23 mutant F110A/M221A neutral pH form meropenem complex~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=KE1:meropenem,+bound+form'>KE1</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
-	[[Category: Vakulenko, S.B]]	+	<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>
-	[[Category: ~~Smith, C.A~~]]	+	<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=6n6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n6y OCA], [http://pdbe.org/6n6y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n6y RCSB], [http://www.ebi.ac.uk/pdbsum/6n6y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n6y ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-lactamase]]
		+	[[Category: Smith, C A]]
		+	[[Category: Vakulenko, S B]]
		+	[[Category: Antibiotic resistance]]
		+	[[Category: Carbapenemase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Mutant]]

OCA: Protected "6n6y" [edit=sysop:move=sysop]

OCA — Wed, 05 Dec 2018 05:18:02 GMT

Protected "6n6y" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:18, 5 December 2018

OCA: New page: '''Unreleased structure''' The entry 6n6y is ON HOLD Authors: Smith, C.A., Vakulenko, S.B. Description: OXA-23 mutant F110A/M221A neutral pH form meropenem complex [[Category: Unreleas...

OCA — Wed, 05 Dec 2018 05:18:00 GMT

New page: '''Unreleased structure''' The entry 6n6y is ON HOLD Authors: Smith, C.A., Vakulenko, S.B. Description: OXA-23 mutant F110A/M221A neutral pH form meropenem complex [[Category: Unreleas...

New page

'''Unreleased structure'''

The entry 6n6y is ON HOLD

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

Description: OXA-23 mutant F110A/M221A neutral pH form meropenem complex
[[Category: Unreleased Structures]]
[[Category: Vakulenko, S.B]]
[[Category: Smith, C.A]]