6pqi - Revision history

OCA at 07:33, 11 October 2023

OCA — Wed, 11 Oct 2023 07:33:50 GMT

←Older revision		Revision as of 07:33, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6pqi' size='340' side='right'caption='[[6pqi]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='6pqi' size='340' side='right'caption='[[6pqi]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pqi]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_pneumoniae"_(schroeter_1886)_flugge_1886 "bacillus~~ pneumoniae~~" (schroeter 1886) flugge 1886~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PQI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6PQI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pqi]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PQI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PQI FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>~~, ~~<scene name='pdbligand=CEF:CEFOTAXIME,+C3+CLEAVED,+OPEN,+BOUND+FORM'>CEF</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 2.05Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>blaOXA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~573~~ "~~Bacillus pneumoniae~~" ~~(Schroeter 1886) Flugge 1886])~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CEF:CEFOTAXIME,+C3+CLEAVED,+OPEN,+BOUND+FORM'>CEF</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=6pqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pqi OCA], [https://pdbe.org/6pqi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pqi RCSB], [https://www.ebi.ac.uk/pdbsum/6pqi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pqi 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=6pqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pqi OCA], [~~http~~://pdbe.org/6pqi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6pqi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6pqi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6pqi ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q6XEC0_KLEPN Q6XEC0_KLEPN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Beta-lactamase~~]]	+	[[Category: Klebsiella pneumoniae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Akhtar, A]]	+	[[Category: Akhtar A]]
-	[[Category: Chen, Y]]	+	[[Category: Chen Y]]
-	~~[[Category: Carbapenem]]~~	+
-	~~[[Category: Carbapenemase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolyzed product]]~~	+
-	~~[[Category: Substrate~~]]	+

OCA at 05:47, 5 August 2020

OCA — Wed, 05 Aug 2020 05:47:24 GMT

←Older revision		Revision as of 05:47, 5 August 2020
Line 3:		Line 3:
	<StructureSection load='6pqi' size='340' side='right'caption='[[6pqi]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='6pqi' size='340' side='right'caption='[[6pqi]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pqi]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PQI OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6PQI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pqi]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pneumoniae"_(schroeter_1886)_flugge_1886 "bacillus pneumoniae" (schroeter 1886) flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PQI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PQI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CEF:CEFOTAXIME,+C3+CLEAVED,+OPEN,+BOUND+FORM'>CEF</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CEF:CEFOTAXIME,+C3+CLEAVED,+OPEN,+BOUND+FORM'>CEF</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">blaOXA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=573 "Bacillus pneumoniae" (Schroeter 1886) Flugge 1886])</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=6pqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pqi OCA], [http://pdbe.org/6pqi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pqi RCSB], [http://www.ebi.ac.uk/pdbsum/6pqi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pqi 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=6pqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pqi OCA], [http://pdbe.org/6pqi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pqi RCSB], [http://www.ebi.ac.uk/pdbsum/6pqi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pqi ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Carbapenem-hydrolyzing class D beta-lactamases (CHDLs) are a diverse family of enzymes that are rapidly becoming the predominant cause of bacterial resistance against beta-lactam antibiotics in many regions of the world. OXA-48, an atypical member of CHDLs, is one of the most frequently observed in the clinic and exhibits a unique substrate profile. We applied X-ray crystallography to OXA-48 complexes with multiple beta-lactam antibiotics to elucidate this enzyme's carbapenemase activity and its preference of imipenem over meropenem and other substrates such as cefotaxime. In particular, we obtained acyl-enzyme complexes of OXA-48 with imipenem, meropenem, faropenem, cefotaxime, and cefoxitin, and a product complex with imipenem. Importantly, the product complex captures a key reaction milestone with the newly generated carboxylate group still in the oxyanion hole, and represents the first such complex with a wild-type serine beta-lactamase. A potential hydrogen bond is observed between the two carboxylate groups from the product and the carbamylated Lys73, representing the stage immediately after the breakage of the acyl-enzyme bond where the product carboxylate would be neutral. The placement of the product carboxylate also illustrates the approximate transient location of the deacylation water that has long eluded structural characterization in class D beta-lactamases. Additionally, comparing the product complex with the acyl-enzyme intermediates provides new insights into the various mechanisms by which specific side chain groups hinder the access of the deacylation water to the acyl-enzyme linkage, especially in meropenem. Taken together, these data offer valuable information on the substrate specificity of OXA-48 and the catalytic mechanism of CHDLs.
		+
		+	Structural Basis for Substrate Specificity and Carbapenemase Activity of OXA-48 Class D beta-Lactamase.,Akhtar A, Pemberton OA, Chen Y ACS Infect Dis. 2020 Feb 14;6(2):261-271. doi: 10.1021/acsinfecdis.9b00304. Epub , 2020 Jan 7. PMID:31872762<ref>PMID:31872762</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6pqi" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:13, 22 January 2020

OCA — Wed, 22 Jan 2020 16:13:49 GMT

←Older revision		Revision as of 16:13, 22 January 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6pqi is ~~ON HOLD~~	+	==Crystal Structure of Class D Beta-lactamase OXA-48 with Cefotaxime==
-		+	<StructureSection load='6pqi' size='340' side='right'caption='[[6pqi]], [[Resolution\|resolution]] 2.05Å' scene=''>
-	~~Authors~~: ~~Akhtar~~, A., ~~Chen~~, Y.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6pqi]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PQI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PQI FirstGlance]. <br>
-	~~Description~~: ~~Crystal Structure of Class D~~ Beta-lactamase ~~OXA-48 with Cefotaxime~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CEF:CEFOTAXIME,+C3+CLEAVED,+OPEN,+BOUND+FORM'>CEF</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=6pqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pqi OCA], [http://pdbe.org/6pqi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pqi RCSB], [http://www.ebi.ac.uk/pdbsum/6pqi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pqi ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-lactamase]]
		+	[[Category: Large Structures]]
	[[Category: Akhtar, A]]		[[Category: Akhtar, A]]
	[[Category: Chen, Y]]		[[Category: Chen, Y]]
		+	[[Category: Carbapenem]]
		+	[[Category: Carbapenemase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolyzed product]]
		+	[[Category: Substrate]]

OCA at 06:21, 4 December 2019

OCA — Wed, 04 Dec 2019 06:21:52 GMT

←Older revision		Revision as of 06:21, 4 December 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6pqi is ON HOLD ~~until Paper Publication~~	+	The entry 6pqi is ON HOLD

	Authors: Akhtar, A., Chen, Y.		Authors: Akhtar, A., Chen, Y.

OCA at 04:12, 21 August 2019

OCA — Wed, 21 Aug 2019 04:12:57 GMT

←Older revision		Revision as of 04:12, 21 August 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Akhtar, A., Chen, Y.		Authors: Akhtar, A., Chen, Y.

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

OCA — Wed, 17 Jul 2019 09:07:30 GMT

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

←Older revision

Revision as of 09:07, 17 July 2019

OCA: New page: '''Unreleased structure''' The entry 6pqi is ON HOLD Authors: Akhtar, A., Chen, Y. Description: Crystal Structure of Class D Beta-lactamase OXA-48 with Cefotaxime [[Category: Unrelease...

OCA — Wed, 17 Jul 2019 09:07:28 GMT

New page: '''Unreleased structure''' The entry 6pqi is ON HOLD Authors: Akhtar, A., Chen, Y. Description: Crystal Structure of Class D Beta-lactamase OXA-48 with Cefotaxime [[Category: Unrelease...

New page

'''Unreleased structure'''

The entry 6pqi is ON HOLD

Authors: Akhtar, A., Chen, Y.

Description: Crystal Structure of Class D Beta-lactamase OXA-48 with Cefotaxime
[[Category: Unreleased Structures]]
[[Category: Akhtar, A]]
[[Category: Chen, Y]]