5iy2 - Revision history

OCA at 10:37, 6 September 2023

OCA — Wed, 06 Sep 2023 10:37:42 GMT

←Older revision		Revision as of 10:37, 6 September 2023
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	<StructureSection load='5iy2' size='340' side='right'caption='[[5iy2]], [[Resolution\|resolution]] 1.15Å' scene=''>		<StructureSection load='5iy2' size='340' side='right'caption='[[5iy2]], [[Resolution\|resolution]] 1.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5iy2]] is a 2 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=5IY2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5IY2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5iy2]] is a 2 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=5IY2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IY2 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GOL:GLYCEROL'>GOL</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]] 1.15Å</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=GOL:GLYCEROL'>GOL</scene>, <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">bla-OXA-143 ([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=5iy2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iy2 OCA], [https://pdbe.org/5iy2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5iy2 RCSB], [https://www.ebi.ac.uk/pdbsum/5iy2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5iy2 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=5iy2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iy2 OCA], [~~http~~://pdbe.org/5iy2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5iy2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5iy2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5iy2 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D0UHC8_ACIBA D0UHC8_ACIBA]
	<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: ~~Aciba~~]]	+	[[Category: Acinetobacter baumannii]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Smith~~, C A~~]]	+	[[Category: Smith CA]]
-	[[Category: Vakulenko~~, S B]]~~	+	[[Category: Vakulenko SB]]
-	~~[[Category: Antibiotic resistance]]~~	+
-	~~[[Category: Carbapenemase]]~~	+
-	~~[[Category: Enzyme kinetic]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Mechanism of resistance~~]]	+

OCA at 16:19, 11 December 2019

OCA — Wed, 11 Dec 2019 16:19:43 GMT

←Older revision		Revision as of 16:19, 11 December 2019
Line 1:		Line 1:

	==Structure of apo OXA-143 carbapenemase==		==Structure of apo OXA-143 carbapenemase==
-	<StructureSection load='5iy2' size='340' side='right' caption='[[5iy2]], [[Resolution\|resolution]] 1.15Å' scene=''>	+	<StructureSection load='5iy2' size='340' side='right'caption='[[5iy2]], [[Resolution\|resolution]] 1.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5iy2]] is a 2 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=5IY2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IY2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5iy2]] is a 2 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=5IY2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IY2 FirstGlance]. <br>
Line 20:		Line 20:

	==See Also==		==See Also==
-	*[[Beta-lactamase\|Beta-lactamase]]	+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 26:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Aciba]]		[[Category: Aciba]]
		+	[[Category: Large Structures]]
	[[Category: Smith, C A]]		[[Category: Smith, C A]]
	[[Category: Vakulenko, S B]]		[[Category: Vakulenko, S B]]

OCA at 06:22, 18 April 2018

OCA — Wed, 18 Apr 2018 06:22:51 GMT

←Older revision		Revision as of 06:22, 18 April 2018
Line 3:		Line 3:
	<StructureSection load='5iy2' size='340' side='right' caption='[[5iy2]], [[Resolution\|resolution]] 1.15Å' scene=''>		<StructureSection load='5iy2' size='340' side='right' caption='[[5iy2]], [[Resolution\|resolution]] 1.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5iy2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IY2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IY2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5iy2]] is a 2 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=5IY2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IY2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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">bla-OXA-143 ([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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5iy2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iy2 OCA], [http://pdbe.org/5iy2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iy2 RCSB], [http://www.ebi.ac.uk/pdbsum/5iy2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iy2 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=5iy2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iy2 OCA], [http://pdbe.org/5iy2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iy2 RCSB], [http://www.ebi.ac.uk/pdbsum/5iy2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iy2 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Carbapenem-hydrolyzing class D beta-lactamases (CHDLs) produce resistance to the last-resort carbapenem antibiotics and render these drugs ineffective for the treatment of life-threatening infections. Here, it is shown that among the clinically important CHDLs, OXA-143 produces the highest levels of resistance to carbapenems and has the highest catalytic efficiency against these substrates. Structural data demonstrate that acylated carbapenems entirely fill the active site of CHDLs, leaving no space for water molecules, including the deacylating water. Since the entrance to the active site is obstructed by the acylated antibiotic, the deacylating water molecule must take a different route for entry. It is shown that in OXA-143 the movement of a conserved hydrophobic valine residue on the surface opens a channel to the active site of the enzyme, which would not only allow the exchange of water molecules between the active site and the milieu, but would also create extra space for a water molecule to position itself in the vicinity of the scissile bond of the acyl-enzyme intermediate to perform deacylation. Structural analysis of the OXA-23 carbapenemase shows that in this enzyme movement of the conserved leucine residue, juxtaposed to the valine on the molecular surface, creates a similar channel to the active site. These data strongly suggest that all CHDLs may employ a mechanism whereupon the movement of highly conserved valine or leucine residues would allow a water molecule to access the active site to promote deacylation. It is further demonstrated that the 6alpha-hydroxyethyl group of the bound carbapenem plays an important role in the stabilization of this channel. The recognition of a universal deacylation mechanism for CHDLs suggests a direction for the future development of inhibitors and novel antibiotics for these enzymes of utmost clinical importance.
		+
		+	The role of conserved surface hydrophobic residues in the carbapenemase activity of the class D beta-lactamases.,Toth M, Smith CA, Antunes NT, Stewart NK, Maltz L, Vakulenko SB Acta Crystallogr D Struct Biol. 2017 Aug 1;73(Pt 8):692-701. doi:, 10.1107/S2059798317008671. Epub 2017 Jul 28. PMID:28777084<ref>PMID:28777084</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5iy2" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase\|Beta-lactamase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aciba]]
	[[Category: Smith, C A]]		[[Category: Smith, C A]]
	[[Category: Vakulenko, S B]]		[[Category: Vakulenko, S B]]

OCA at 07:11, 6 October 2017

OCA — Fri, 06 Oct 2017 07:11:06 GMT

←Older revision		Revision as of 07:11, 6 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5iy2 ~~is ON HOLD until Paper Publication~~	+	==Structure of apo OXA-143 carbapenemase==
-		+	<StructureSection load='5iy2' size='340' side='right' caption='[[5iy2]], [[Resolution\|resolution]] 1.15Å' scene=''>
-	~~Authors~~: ~~Smith, C~~.A.~~, Vakulenko, S~~.B.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5iy2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IY2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IY2 FirstGlance]. <br>
-	~~Description~~: ~~Structure of apo OXA~~-~~143 carbapenemase~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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: 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=5iy2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iy2 OCA], [http://pdbe.org/5iy2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iy2 RCSB], [http://www.ebi.ac.uk/pdbsum/5iy2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iy2 ProSAT]</span></td></tr>
-	[[Category: Vakulenko, S.B]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Smith, C A]]
		+	[[Category: Vakulenko, S B]]
		+	[[Category: Antibiotic resistance]]
		+	[[Category: Carbapenemase]]
		+	[[Category: Enzyme kinetic]]
		+	[[Category: Hydrolase]]
		+	[[Category: Mechanism of resistance]]

OCA: Protected "5iy2" [edit=sysop:move=sysop]

OCA — Wed, 11 May 2016 01:09:22 GMT

Protected "5iy2" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:09, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5iy2 is ON HOLD until Paper Publication Authors: Smith, C.A., Vakulenko, S.B. Description: Structure of apo OXA-143 carbapenemase [[Category: Unrel...

OCA — Wed, 11 May 2016 01:09:21 GMT

New page: '''Unreleased structure''' The entry 5iy2 is ON HOLD until Paper Publication Authors: Smith, C.A., Vakulenko, S.B. Description: Structure of apo OXA-143 carbapenemase [[Category: Unrel...

New page

'''Unreleased structure'''

The entry 5iy2 is ON HOLD until Paper Publication

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

Description: Structure of apo OXA-143 carbapenemase
[[Category: Unreleased Structures]]
[[Category: Smith, C.A]]
[[Category: Vakulenko, S.B]]