5wib - Revision history

OCA at 14:13, 4 October 2023

OCA — Wed, 04 Oct 2023 14:13:49 GMT

←Older revision		Revision as of 14:13, 4 October 2023
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	<StructureSection load='5wib' size='340' side='right'caption='[[5wib]], [[Resolution\|resolution]] 1.87Å' scene=''>		<StructureSection load='5wib' size='340' side='right'caption='[[5wib]], [[Resolution\|resolution]] 1.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wib]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Acinetobacter_sp._enrichment_culture_clone_8407 Acinetobacter sp. enrichment culture clone 8407]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WIB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5WIB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wib]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_sp._enrichment_culture_clone_8407 Acinetobacter sp. enrichment culture clone 8407]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WIB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WIB FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=ID1:IMIPENEM'>ID1</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]] 1.87Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">OXA-239 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=1182652 Acinetobacter sp. enrichment culture clone 8407])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ID1:IMIPENEM'>ID1</scene></td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http://en.wikipedia.org/wiki/Barbiturase Barbiturase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.1 3.5.2.1]~~ </~~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=5wib FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wib OCA], [https://pdbe.org/5wib PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wib RCSB], [https://www.ebi.ac.uk/pdbsum/5wib PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wib 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=5wib FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wib OCA], [~~http~~://pdbe.org/5wib PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5wib RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5wib PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5wib ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/I6YCI1_9GAMM I6YCI1_9GAMM]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Acinetobacter sp. enrichment culture clone 8407]]		[[Category: Acinetobacter sp. enrichment culture clone 8407]]
-	[[Category: Barbiturase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Harper~~, T M~~]]	+	[[Category: Harper TM]]
-	[[Category: June~~, C M~~]]	+	[[Category: June CM]]
-	[[Category: Leonard~~, D A~~]]	+	[[Category: Leonard DA]]
-	[[Category: Powers~~, R A]]~~	+	[[Category: Powers RA]]
-	~~[[Category: Antibiotic resistance]]~~	+
-	~~[[Category: Beta-lactamase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 17:35, 11 December 2019

OCA — Wed, 11 Dec 2019 17:35:38 GMT

←Older revision		Revision as of 17:35, 11 December 2019
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	==Structure of Acinetobacter baumannii carbapenemase OXA-239 K82D bound to imipenem==		==Structure of Acinetobacter baumannii carbapenemase OXA-239 K82D bound to imipenem==
-	<StructureSection load='5wib' size='340' side='right' caption='[[5wib]], [[Resolution\|resolution]] 1.87Å' scene=''>	+	<StructureSection load='5wib' size='340' side='right'caption='[[5wib]], [[Resolution\|resolution]] 1.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5wib]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_sp._enrichment_culture_clone_8407 Acinetobacter sp. enrichment culture clone 8407]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WIB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WIB FirstGlance]. <br>		<table><tr><td colspan='2'>[[5wib]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_sp._enrichment_culture_clone_8407 Acinetobacter sp. enrichment culture clone 8407]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WIB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WIB FirstGlance]. <br>
Line 24:		Line 24:
	[[Category: Acinetobacter sp. enrichment culture clone 8407]]		[[Category: Acinetobacter sp. enrichment culture clone 8407]]
	[[Category: Barbiturase]]		[[Category: Barbiturase]]
		+	[[Category: Large Structures]]
	[[Category: Harper, T M]]		[[Category: Harper, T M]]
	[[Category: June, C M]]		[[Category: June, C M]]

OCA at 20:50, 24 January 2018

OCA — Wed, 24 Jan 2018 20:50:03 GMT

←Older revision		Revision as of 20:50, 24 January 2018
Line 3:		Line 3:
	<StructureSection load='5wib' size='340' side='right' caption='[[5wib]], [[Resolution\|resolution]] 1.87Å' scene=''>		<StructureSection load='5wib' size='340' side='right' caption='[[5wib]], [[Resolution\|resolution]] 1.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wib]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WIB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WIB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wib]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_sp._enrichment_culture_clone_8407 Acinetobacter sp. enrichment culture clone 8407]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WIB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WIB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ID1:IMIPENEM'>ID1</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ID1:IMIPENEM'>ID1</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">OXA-239 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1182652 Acinetobacter sp. enrichment culture clone 8407])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Barbiturase Barbiturase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.1 3.5.2.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Barbiturase Barbiturase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.1 3.5.2.1] </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=5wib FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wib OCA], [http://pdbe.org/5wib PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wib RCSB], [http://www.ebi.ac.uk/pdbsum/5wib PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wib 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=5wib FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wib OCA], [http://pdbe.org/5wib PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wib RCSB], [http://www.ebi.ac.uk/pdbsum/5wib PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wib ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Acinetobacter sp. enrichment culture clone 8407]]
	[[Category: Barbiturase]]		[[Category: Barbiturase]]
	[[Category: Harper, T M]]		[[Category: Harper, T M]]

OCA at 08:29, 27 December 2017

OCA — Wed, 27 Dec 2017 08:29:24 GMT

←Older revision		Revision as of 08:29, 27 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5wib is ~~ON HOLD until Paper~~ Publication	+	==Structure of Acinetobacter baumannii carbapenemase OXA-239 K82D bound to imipenem==
		+	<StructureSection load='5wib' size='340' side='right' caption='[[5wib]], [[Resolution\|resolution]] 1.87Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5wib]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WIB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WIB FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ID1:IMIPENEM'>ID1</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Barbiturase Barbiturase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.1 3.5.2.1] </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=5wib FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wib OCA], [http://pdbe.org/5wib PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wib RCSB], [http://www.ebi.ac.uk/pdbsum/5wib PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wib ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	OXA-239 is a class D carbapenemase isolated from an Acinetobacter baumannii strain found in Mexico. This enzyme is a variant of OXA-23 with three amino acid substitutions in or near the active site. These substitutions cause OXA-239 to hydrolyze late-generation cephalosporins and the monobactam aztreonam with greater efficiency than OXA-23. OXA-239 activity against the carbapenems doripenem and imipenem is reduced approximately 3-fold and 20-fold respectively. Further analysis demonstrated that two of the substitutions (P225S and D222N) are largely responsible for the observed alteration of kinetic parameters, while the third (S109L) may serve to stabilize the protein. Structures of OXA-239 with cefotaxime, doripenem and imipenem bound as acyl-intermediates were determined. These structures reveal that OXA-239 has increased flexibility in a loop that contains P225S and D222N. When carbapenems are bound, the conformation of this loop is essentially identical to that observed previously for OXA-23, with a narrow active site that makes extensive contacts to the ligand. When cefotaxime is bound, the loop can adopt a different conformation that widens the active site to allow binding of that bulky drug. This alternate conformation is made possible by P225S and further stabilized by D222N. Taken together, these results suggest that the three substitutions were selected to expand the substrate specificity profile of OXA-23 to cephalosporins and monobactams. The loss of activity against imipenem, however, suggests that there may be limits to the plasticity of class D enzymes with regard to evolving active sites that can effectively bind multiple classes of beta-lactam drugs.

-	~~Authors: Harper, T.M~~., June, ~~C.M.~~, Powers, R.A.~~, Leonard, D~~.A.	+	Multiple substitutions lead to increased loop flexibility and expanded specificity in Acinetobacter baumannii carbapenemase OXA-239.,Harper TM, June CM, Taracila MA, Bonomo RA, Powers RA, Leonard DA Biochem J. 2017 Dec 11. pii: BCJ20170702. doi: 10.1042/BCJ20170702. PMID:29229762<ref>PMID:29229762</ref>

-	~~Description: Structure~~ of ~~Acinetobacter baumannii carbapenemase OXA~~-~~239 K82D bound to imipenem~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Harper, T.M]]	+	<div class="pdbe-citations 5wib" style="background-color:#fffaf0;"></div>
-	[[Category: Leonard, D.A]]	+	== References ==
-	[[Category: Powers, R.A]]	+	<references/>
-	[[Category: ~~June, C.M~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Barbiturase]]
		+	[[Category: Harper, T M]]
		+	[[Category: June, C M]]
		+	[[Category: Leonard, D A]]
		+	[[Category: Powers, R A]]
		+	[[Category: Antibiotic resistance]]
		+	[[Category: Beta-lactamase]]
		+	[[Category: Hydrolase]]

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

OCA — Wed, 27 Sep 2017 14:51:09 GMT

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

←Older revision

Revision as of 14:51, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5wib is ON HOLD until Paper Publication Authors: Harper, T.M., June, C.M., Powers, R.A., Leonard, D.A. Description: Structure of Acinetobacter baum...

OCA — Wed, 27 Sep 2017 14:51:08 GMT

New page: '''Unreleased structure''' The entry 5wib is ON HOLD until Paper Publication Authors: Harper, T.M., June, C.M., Powers, R.A., Leonard, D.A. Description: Structure of Acinetobacter baum...

New page

'''Unreleased structure'''

The entry 5wib is ON HOLD until Paper Publication

Authors: Harper, T.M., June, C.M., Powers, R.A., Leonard, D.A.

Description: Structure of Acinetobacter baumannii carbapenemase OXA-239 K82D bound to imipenem
[[Category: Unreleased Structures]]
[[Category: Harper, T.M]]
[[Category: Leonard, D.A]]
[[Category: Powers, R.A]]
[[Category: June, C.M]]