4y0t - Revision history

OCA at 18:01, 26 April 2023

OCA — Wed, 26 Apr 2023 18:01:45 GMT

←Older revision		Revision as of 18:01, 26 April 2023
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	<StructureSection load='4y0t' size='340' side='right'caption='[[4y0t]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4y0t' size='340' side='right'caption='[[4y0t]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4y0t]] is a 4 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=4Y0T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4Y0T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4y0t]] is a 4 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=4Y0T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y0T FirstGlance]. <br>
-	</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>~~	+	</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></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4y0o\|4y0o]], [[4y0u\|4y0u]]</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=4y0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y0t OCA], [https://pdbe.org/4y0t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y0t RCSB], [https://www.ebi.ac.uk/pdbsum/4y0t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y0t ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">blaOXA-58, bla-oxa-58, bla-oxa58 ([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='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=4y0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y0t OCA], [~~http~~://pdbe.org/4y0t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4y0t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4y0t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4y0t ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q2TR58_ACIBA Q2TR58_ACIBA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aciba]]~~	+	[[Category: Acinetobacter baumannii]]
-	~~[[Category: Beta-lactamase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gill, P]]	+	[[Category: Gill P]]
-	[[Category: Golemi-Kotra, D]]	+	[[Category: Golemi-Kotra D]]
-	[[Category: Katiki, M]]	+	[[Category: Katiki M]]
-	[[Category: Kumar, P]]	+	[[Category: Kumar P]]
-	[[Category: Pratap, S]]	+	[[Category: Pratap S]]
-	~~[[Category: 4mol/asu]]~~	+
-	~~[[Category: Class d beta-lactamase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Oxa-58~~]]	+

OCA at 00:17, 6 June 2019

OCA — Thu, 06 Jun 2019 00:17:07 GMT

←Older revision		Revision as of 00:17, 6 June 2019
Line 1:		Line 1:
		+
	==Crystal structure of apo form of OXA-58, a Carbapenem hydrolyzing Class D beta-lactamase from Acinetobacter baumanii (P21, 4mol/ASU)==		==Crystal structure of apo form of OXA-58, a Carbapenem hydrolyzing Class D beta-lactamase from Acinetobacter baumanii (P21, 4mol/ASU)==
-	<StructureSection load='4y0t' size='340' side='right' caption='[[4y0t]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='4y0t' size='340' side='right'caption='[[4y0t]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4y0t]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y0T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y0T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4y0t]] is a 4 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=4Y0T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y0T FirstGlance]. <br>
	</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>		</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4y0o\|4y0o]], [[4y0u\|4y0u]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4y0o\|4y0o]], [[4y0u\|4y0u]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">blaOXA-58, bla-oxa-58, bla-oxa58 ([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=4y0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y0t OCA], [http://pdbe.org/4y0t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y0t RCSB], [http://www.ebi.ac.uk/pdbsum/4y0t PDBsum]</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=4y0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y0t OCA], [http://pdbe.org/4y0t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y0t RCSB], [http://www.ebi.ac.uk/pdbsum/4y0t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4y0t ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 4y0t" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4y0t" 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: Beta-lactamase]]		[[Category: Beta-lactamase]]
		+	[[Category: Large Structures]]
	[[Category: Gill, P]]		[[Category: Gill, P]]
	[[Category: Golemi-Kotra, D]]		[[Category: Golemi-Kotra, D]]

OCA at 20:07, 13 January 2016

OCA — Wed, 13 Jan 2016 20:07:31 GMT

←Older revision		Revision as of 20:07, 13 January 2016
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of apo form of OXA-58, a Carbapenem hydrolyzing Class D beta-lactamase from Acinetobacter baumanii (P21, 4mol/ASU)==
		+	<StructureSection load='4y0t' size='340' side='right' caption='[[4y0t]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4y0t]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y0T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y0T FirstGlance]. <br>
		+	</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4y0o\|4y0o]], [[4y0u\|4y0u]]</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=4y0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y0t OCA], [http://pdbe.org/4y0t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y0t RCSB], [http://www.ebi.ac.uk/pdbsum/4y0t PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Carbapenem-hydrolyzing class D beta-lactamases (CHDLs) are a subgroup of class D beta-lactamases, which are enzymes that hydrolyze beta-lactams. They have attracted interest due to the emergence of multidrug-resistant Acinetobacter baumannii, which is not responsive to treatment with carbapenems, the usual antibiotics of choice for this bacterium. Unlike other class D beta-lactamases, these enzymes efficiently hydrolyze carbapenem antibiotics. To explore the structural requirements for the catalysis of carbapenems by these enzymes, we determined the crystal structure of the OXA-58 CHDL of A. baumannii following acylation of its active-site serine by a 6alpha-hydroxymethyl penicillin derivative that is a structural mimetic for a carbapenem. In addition, several point mutation variants of the active site of OXA-58, as identified by the crystal structure analysis, were characterized kinetically. These combined studies confirm the mechanistic relevance of a hydrophobic bridge formed over the active site. This structural feature is suggested to stabilize the hydrolysis-productive acyl-enzyme species formed from the carbapenem substrates of this enzyme. Furthermore, our structural studies provide strong evidence that the hydroxyethyl group of carbapenems samples different orientations in the active sites of CHDLs, and the optimum orientation for catalysis depends on the topology of the active site allowing proper closure of the active site. We propose that CHDLs use the plasticity of the active site to drive the mechanism of carbapenem hydrolysis toward efficiency.

-	~~The entry 4y0t is ON HOLD until Paper Publication~~	+	Active-Site Plasticity Is Essential to Carbapenem Hydrolysis by OXA-58 Class D beta-Lactamase of Acinetobacter baumannii.,Pratap S, Katiki M, Gill P, Kumar P, Golemi-Kotra D Antimicrob Agents Chemother. 2015 Oct 12;60(1):75-86. doi: 10.1128/AAC.01393-15. PMID:26459904<ref>PMID:26459904</ref>

-	~~Authors: Pratap~~, S.~~, Katiki, M., Gill, P., Golemi-Kotra, D., Kumar, P~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Crystal structure of apo form of OXA~~-~~58, a Carbapenem hydrolyzing Class D beta~~-~~lactamase from Acinetobacter baumanii (P21, 4mol~~/~~ASU)~~	+	<div class="pdbe-citations 4y0t" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
-	[[Category: ~~Pratap~~, S]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-lactamase]]
		+	[[Category: Gill, P]]
	[[Category: Golemi-Kotra, D]]		[[Category: Golemi-Kotra, D]]
		+	[[Category: Katiki, M]]
	[[Category: Kumar, P]]		[[Category: Kumar, P]]
-	[[Category: ~~Katiki~~, M]]	+	[[Category: Pratap, S]]
-	[[Category: ~~Gill, P~~]]	+	[[Category: 4mol/asu]]
		+	[[Category: Class d beta-lactamase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Oxa-58]]

OCA at 23:23, 30 November 2015

OCA — Mon, 30 Nov 2015 23:23:49 GMT

←Older revision		Revision as of 23:23, 30 November 2015
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Pratap, S]]		[[Category: Pratap, S]]
-	[[Category: Kumar, P]]
	[[Category: Golemi-Kotra, D]]		[[Category: Golemi-Kotra, D]]
		+	[[Category: Kumar, P]]
	[[Category: Katiki, M]]		[[Category: Katiki, M]]
	[[Category: Gill, P]]		[[Category: Gill, P]]

OCA at 09:00, 30 April 2015

OCA — Thu, 30 Apr 2015 09:00:23 GMT

←Older revision		Revision as of 09:00, 30 April 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4y0t is ON HOLD	+	The entry 4y0t is ON HOLD until Paper Publication

	Authors: Pratap, S., Katiki, M., Gill, P., Golemi-Kotra, D., Kumar, P.		Authors: Pratap, S., Katiki, M., Gill, P., Golemi-Kotra, D., Kumar, P.

OCA at 10:32, 22 April 2015

OCA — Wed, 22 Apr 2015 10:32:11 GMT

←Older revision		Revision as of 10:32, 22 April 2015
Line 3:		Line 3:
	The entry 4y0t is ON HOLD		The entry 4y0t is ON HOLD

-	Authors: Pratap, S., Katiki, M., Gill, P., Golemi-Kotra, D.	+	Authors: Pratap, S., Katiki, M., Gill, P., Golemi-Kotra, D., Kumar, P.

-	Description: Crystal structure of apo form of Carbapenem hydrolyzing Class D beta-lactamase of Acinetobacter baumanii ~~OXA-58~~ (4mol/ASU)	+	Description: Crystal structure of apo form of OXA-58, a Carbapenem hydrolyzing Class D beta-lactamase from Acinetobacter baumanii (P21, 4mol/ASU)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Pratap, S]]		[[Category: Pratap, S]]
		+	[[Category: Kumar, P]]
	[[Category: Golemi-Kotra, D]]		[[Category: Golemi-Kotra, D]]
	[[Category: Katiki, M]]		[[Category: Katiki, M]]
	[[Category: Gill, P]]		[[Category: Gill, P]]

OCA at 12:34, 25 February 2015

OCA — Wed, 25 Feb 2015 12:34:08 GMT

←Older revision		Revision as of 12:34, 25 February 2015
Line 3:		Line 3:
	The entry 4y0t is ON HOLD		The entry 4y0t is ON HOLD

-	Authors: ~~Shivendra~~ Pratap, ~~Madhusudhnarao~~ Katiki, ~~Preet~~ Gill, ~~Dasantila~~ Golemi-Kotra	+	Authors: Pratap, S., Katiki, M., Gill, P., Golemi-Kotra, D.

	Description: Crystal structure of apo form of Carbapenem hydrolyzing Class D beta-lactamase of Acinetobacter baumanii OXA-58 (4mol/ASU)		Description: Crystal structure of apo form of Carbapenem hydrolyzing Class D beta-lactamase of Acinetobacter baumanii OXA-58 (4mol/ASU)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Shivendra~~ Pratap, ~~Madhusudhnarao~~ Katiki, ~~Preet~~ Gill, ~~Dasantila Golemi-Kotra~~]]	+	[[Category: Pratap, S]]
		+	[[Category: Golemi-Kotra, D]]
		+	[[Category: Katiki, M]]
		+	[[Category: Gill, P]]

OCA: Protected "4y0t" [edit=sysop:move=sysop]

OCA — Thu, 12 Feb 2015 10:58:42 GMT

Protected "4y0t" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:58, 12 February 2015

OCA: New page: '''Unreleased structure''' The entry 4y0t is ON HOLD Authors: Shivendra Pratap, Madhusudhnarao Katiki, Preet Gill, Dasantila Golemi-Kotra Description: Crystal structure of apo form of ...

OCA — Thu, 12 Feb 2015 10:58:41 GMT

New page: '''Unreleased structure''' The entry 4y0t is ON HOLD Authors: Shivendra Pratap, Madhusudhnarao Katiki, Preet Gill, Dasantila Golemi-Kotra Description: Crystal structure of apo form of ...

New page

'''Unreleased structure'''

The entry 4y0t is ON HOLD

Authors: Shivendra Pratap, Madhusudhnarao Katiki, Preet Gill, Dasantila Golemi-Kotra

Description: Crystal structure of apo form of Carbapenem hydrolyzing Class D beta-lactamase of Acinetobacter baumanii OXA-58 (4mol/ASU)
[[Category: Unreleased Structures]]
[[Category: Shivendra Pratap, Madhusudhnarao Katiki, Preet Gill, Dasantila Golemi-Kotra]]