5b3r - Revision history

OCA at 09:07, 20 March 2024

OCA — Wed, 20 Mar 2024 09:07:14 GMT

←Older revision		Revision as of 09:07, 20 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5b3r]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B3R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B3R FirstGlance]. <br>		<table><tr><td colspan='2'>[[5b3r]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B3R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B3R FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5b3r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b3r OCA], [https://pdbe.org/5b3r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b3r RCSB], [https://www.ebi.ac.uk/pdbsum/5b3r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b3r ProSAT]</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=5b3r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b3r OCA], [https://pdbe.org/5b3r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b3r RCSB], [https://www.ebi.ac.uk/pdbsum/5b3r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b3r ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q5U807_PSEAI Q5U807_PSEAI]		[https://www.uniprot.org/uniprot/Q5U807_PSEAI Q5U807_PSEAI]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	IMP-type metallo-beta-lactamases (MBLs) are exogenous zinc metalloenzymes that hydrolyze a broad range of beta-lactams, including carbapenems. Here we report the crystal structure of IMP-18, an MBL cloned from Pseudomonas aeruginosa, at 2.0-A resolution. The overall structure of IMP-18 resembles that of IMP-1, with an alphabeta/betaalpha "folded sandwich" configuration, but the loop that covers the active site has a distinct conformation. The relationship between IMP-18's loop conformation and its kinetic properties was investigated by replacing the amino acid residues that can affect the loop conformation (Lys44, Thr50, and Ile69) in IMP-18 with those occupying the corresponding positions in the well-described enzyme IMP-1. The replacement of Thr50 with Pro considerably modified IMP-18's kinetic properties, specifically those pertaining to meropenem, with the kcat/Km value increased by an order of magnitude. The results indicate that this is a key residue that defines the kinetic properties of IMP-type beta-lactamases.
-
-	Structural and Mutagenic Analysis of Metallo-beta-Lactamase IMP-18.,Furuyama T, Nonomura H, Ishii Y, Hanson ND, Shimizu-Ibuka A Antimicrob Agents Chemother. 2016 Aug 22;60(9):5521-6. doi: 10.1128/AAC.00985-16., Print 2016 Sep. PMID:27381398<ref>PMID:27381398</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5b3r" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]		*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:37, 31 May 2023

OCA — Wed, 31 May 2023 06:37:52 GMT

←Older revision		Revision as of 06:37, 31 May 2023
Line 3:		Line 3:
	<StructureSection load='5b3r' size='340' side='right'caption='[[5b3r]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5b3r' size='340' side='right'caption='[[5b3r]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5b3r]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B3R OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5B3R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5b3r]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B3R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B3R FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IMP-18, blaIMP-18, blaimp-18, imp-18 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</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=5b3r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b3r OCA], [https://pdbe.org/5b3r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b3r RCSB], [https://www.ebi.ac.uk/pdbsum/5b3r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b3r 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=5b3r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b3r OCA], [~~http~~://pdbe.org/5b3r PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5b3r RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5b3r PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5b3r ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5U807_PSEAI Q5U807_PSEAI]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Beta-lactamase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ishii, Y~~]]	+	[[Category: Pseudomonas aeruginosa]]
-	[[Category: ~~Shimizu-Ibuka, A~~]]	+	[[Category: Ishii Y]]
-	[[Category: ~~Antibiotic resistance]]~~	+	[[Category: Shimizu-Ibuka A]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Metallo~~-~~beta-lactamase~~]]	+

OCA at 10:02, 26 February 2020

OCA — Wed, 26 Feb 2020 10:02:54 GMT

←Older revision		Revision as of 10:02, 26 February 2020
Line 1:		Line 1:

	==Crystal structure of metallo-beta-lactamase IMP-18 from Pseudomonas aeruginosa==		==Crystal structure of metallo-beta-lactamase IMP-18 from Pseudomonas aeruginosa==
-	<StructureSection load='5b3r' size='340' side='right' caption='[[5b3r]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5b3r' size='340' side='right'caption='[[5b3r]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5b3r]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B3R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B3R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5b3r]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B3R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B3R FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IMP-18, blaIMP-18, blaimp-18, imp-18 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</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=5b3r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b3r OCA], [http://pdbe.org/5b3r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b3r RCSB], [http://www.ebi.ac.uk/pdbsum/5b3r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b3r 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=5b3r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b3r OCA], [http://pdbe.org/5b3r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b3r RCSB], [http://www.ebi.ac.uk/pdbsum/5b3r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b3r ProSAT]</span></td></tr>
Line 17:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5b3r" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5b3r" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 22:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
		+	[[Category: Large Structures]]
	[[Category: Ishii, Y]]		[[Category: Ishii, Y]]
	[[Category: Shimizu-Ibuka, A]]		[[Category: Shimizu-Ibuka, A]]

OCA at 17:34, 10 March 2017

OCA — Fri, 10 Mar 2017 17:34:07 GMT

←Older revision		Revision as of 17:34, 10 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5b3r is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of metallo-beta-lactamase IMP-18 from Pseudomonas aeruginosa==
		+	<StructureSection load='5b3r' size='340' side='right' caption='[[5b3r]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5b3r]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B3R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B3R FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5b3r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b3r OCA], [http://pdbe.org/5b3r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b3r RCSB], [http://www.ebi.ac.uk/pdbsum/5b3r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b3r ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	IMP-type metallo-beta-lactamases (MBLs) are exogenous zinc metalloenzymes that hydrolyze a broad range of beta-lactams, including carbapenems. Here we report the crystal structure of IMP-18, an MBL cloned from Pseudomonas aeruginosa, at 2.0-A resolution. The overall structure of IMP-18 resembles that of IMP-1, with an alphabeta/betaalpha "folded sandwich" configuration, but the loop that covers the active site has a distinct conformation. The relationship between IMP-18's loop conformation and its kinetic properties was investigated by replacing the amino acid residues that can affect the loop conformation (Lys44, Thr50, and Ile69) in IMP-18 with those occupying the corresponding positions in the well-described enzyme IMP-1. The replacement of Thr50 with Pro considerably modified IMP-18's kinetic properties, specifically those pertaining to meropenem, with the kcat/Km value increased by an order of magnitude. The results indicate that this is a key residue that defines the kinetic properties of IMP-type beta-lactamases.

-	~~Authors~~:	+	Structural and Mutagenic Analysis of Metallo-beta-Lactamase IMP-18.,Furuyama T, Nonomura H, Ishii Y, Hanson ND, Shimizu-Ibuka A Antimicrob Agents Chemother. 2016 Aug 22;60(9):5521-6. doi: 10.1128/AAC.00985-16., Print 2016 Sep. PMID:27381398<ref>PMID:27381398</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5b3r" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-lactamase]]
		+	[[Category: Ishii, Y]]
		+	[[Category: Shimizu-Ibuka, A]]
		+	[[Category: Antibiotic resistance]]
		+	[[Category: Hydrolase]]
		+	[[Category: Metallo-beta-lactamase]]

OCA at 11:07, 15 May 2016

OCA — Sun, 15 May 2016 11:07:08 GMT

←Older revision		Revision as of 11:07, 15 May 2016
Line 3:		Line 3:
	The entry 5b3r is ON HOLD until Paper Publication		The entry 5b3r is ON HOLD until Paper Publication

-	Authors: ~~Shimizu-Ibuka, A., Ishii, Y.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Shimizu-Ibuka, A]]
-	[[Category: Ishii, Y]]

OCA: Protected "5b3r" [edit=sysop:move=sysop]

OCA — Tue, 10 May 2016 20:56:29 GMT

Protected "5b3r" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:56, 10 May 2016

OCA: New page: '''Unreleased structure''' The entry 5b3r is ON HOLD until Paper Publication Authors: Shimizu-Ibuka, A., Ishii, Y. Description: Category: Unreleased Structures [[Category: Shimizu...

OCA — Tue, 10 May 2016 20:56:28 GMT

New page: '''Unreleased structure''' The entry 5b3r is ON HOLD until Paper Publication Authors: Shimizu-Ibuka, A., Ishii, Y. Description: Category: Unreleased Structures [[Category: Shimizu...

New page

'''Unreleased structure'''

The entry 5b3r is ON HOLD until Paper Publication

Authors: Shimizu-Ibuka, A., Ishii, Y.

Description:
[[Category: Unreleased Structures]]
[[Category: Shimizu-Ibuka, A]]
[[Category: Ishii, Y]]