6k4t - Revision history

OCA at 10:26, 22 November 2023

OCA — Wed, 22 Nov 2023 10:26:36 GMT

←Older revision		Revision as of 10:26, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='6k4t' size='340' side='right'caption='[[6k4t]], [[Resolution\|resolution]] 1.39Å' scene=''>		<StructureSection load='6k4t' size='340' side='right'caption='[[6k4t]], [[Resolution\|resolution]] 1.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6k4t]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_marcescens"_(bizio_1823)_trevisan_in_de_toni_and_trevisan_1889 "bacillus~~ marcescens~~" (bizio 1823) trevisan in de toni and trevisan 1889~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K4T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6K4T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k4t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K4T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K4T FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=JKE:2-SULFANYLBENZOIC+ACID'>JKE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 1.39Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SMB-1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=615 "Bacillus marcescens" (Bizio 1823) Trevisan in de Toni and Trevisan 1889])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JKE:2-SULFANYLBENZOIC+ACID'>JKE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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'>[https://proteopedia.org/fgij/fg.htm?mol=6k4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k4t OCA], [https://pdbe.org/6k4t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k4t RCSB], [https://www.ebi.ac.uk/pdbsum/6k4t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k4t 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=6k4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k4t OCA], [~~http~~://pdbe.org/6k4t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6k4t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6k4t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6k4t ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/G5ELM3_SERMA G5ELM3_SERMA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6k4t" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6k4t" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Beta-lactamase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Wachino, J~~]]	+	[[Category: Serratia marcescens]]
-	[[Category: ~~Hydrolase]]~~	+	[[Category: Wachino J]]
-	~~[[Category: Metallo-beta-lactamase~~]]	+

OCA at 07:23, 19 February 2020

OCA — Wed, 19 Feb 2020 07:23:04 GMT

←Older revision		Revision as of 07:23, 19 February 2020
Line 3:		Line 3:
	<StructureSection load='6k4t' size='340' side='right'caption='[[6k4t]], [[Resolution\|resolution]] 1.39Å' scene=''>		<StructureSection load='6k4t' size='340' side='right'caption='[[6k4t]], [[Resolution\|resolution]] 1.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6k4t]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K4T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K4T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k4t]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_marcescens"_(bizio_1823)_trevisan_in_de_toni_and_trevisan_1889 "bacillus marcescens" (bizio 1823) trevisan in de toni and trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K4T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K4T FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=JKE:2-SULFANYLBENZOIC+ACID'>JKE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=JKE:2-SULFANYLBENZOIC+ACID'>JKE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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">SMB-1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=615 "Bacillus marcescens" (Bizio 1823) Trevisan in de Toni and Trevisan 1889])</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=6k4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k4t OCA], [http://pdbe.org/6k4t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k4t RCSB], [http://www.ebi.ac.uk/pdbsum/6k4t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k4t 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=6k4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k4t OCA], [http://pdbe.org/6k4t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k4t RCSB], [http://www.ebi.ac.uk/pdbsum/6k4t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k4t ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The number of cases of infection with carbapenem-resistant Enterobacteriaceae (CRE) has been increasing and has become a major clinical and public health concern. Production of metallo-beta-lactamases (MBLs) is one of the principal carbapenem resistance mechanisms in CRE. Therefore, developing MBL inhibitors is a promising strategy to overcome the problems of carbapenem resistance conferred by MBLs. To date, the development and evaluation of MBL inhibitors have focused on subclass B1 MBLs but not on B3 MBLs. In the present study, we searched for B3 MBL (specifically, SMB-1) inhibitors and found thiosalicylic acid (TSA) to be a potent inhibitor of B3 SMB-1 MBL (50% inhibitory concentration [IC50], 0.95 muM). TSA inhibited the purified SMB-1 to a considerable degree but was not active against Escherichia coli cells producing SMB-1, as the meropenem (MEM) MIC for the SMB-1 producer was only slightly reduced with TSA. We then introduced a primary amine to TSA and synthesized 4-amino-2-sulfanylbenzoic acid (ASB), which substantially reduced the MEM MICs for SMB-1 producers. X-ray crystallographic analyses revealed that ASB binds to the two zinc ions, Ser221, and Thr223 at the active site of SMB-1. These are ubiquitously conserved residues across clinically relevant B3 MBLs. ASB also significantly inhibited other B3 MBLs, including AIM-1, LMB-1, and L1. Therefore, the characterization of ASB provides a starting point for the development of optimum B3 MBL inhibitors.
		+
		+	4-Amino-2-Sulfanylbenzoic Acid as a Potent Subclass B3 Metallo-beta-Lactamase-Specific Inhibitor Applicable for Distinguishing Metallo-beta-Lactamase Subclasses.,Wachino JI, Kanechi R, Nishino E, Mochizuki M, Jin W, Kimura K, Kurosaki H, Arakawa Y Antimicrob Agents Chemother. 2019 Sep 23;63(10). pii: AAC.01197-19. doi:, 10.1128/AAC.01197-19. Print 2019 Oct. PMID:31405855<ref>PMID:31405855</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6k4t" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 05:52, 7 August 2019

OCA — Wed, 07 Aug 2019 05:52:14 GMT

←Older revision		Revision as of 05:52, 7 August 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6k4t is ON HOLD until May 27 2021~~	+	==Crystal structure of SMB-1 metallo-beta-lactamase in a complex with TSA==
-		+	<StructureSection load='6k4t' size='340' side='right'caption='[[6k4t]], [[Resolution\|resolution]] 1.39Å' scene=''>
-	~~Authors: Wachino, J.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6k4t]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K4T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K4T FirstGlance]. <br>
-	~~Description:~~ Crystal structure of SMB-1 metallo-beta-lactamase in a complex with TSA	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=JKE:2-SULFANYLBENZOIC+ACID'>JKE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6k4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k4t OCA], [http://pdbe.org/6k4t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k4t RCSB], [http://www.ebi.ac.uk/pdbsum/6k4t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k4t ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-lactamase]]
		+	[[Category: Large Structures]]
	[[Category: Wachino, J]]		[[Category: Wachino, J]]
		+	[[Category: Hydrolase]]
		+	[[Category: Metallo-beta-lactamase]]

OCA at 03:51, 12 June 2019

OCA — Wed, 12 Jun 2019 03:51:38 GMT

←Older revision		Revision as of 03:51, 12 June 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6k4t is ON HOLD	+	The entry 6k4t is ON HOLD until May 27 2021

	Authors: Wachino, J.		Authors: Wachino, J.

OCA: Protected "6k4t" [edit=sysop:move=sysop]

OCA — Wed, 05 Jun 2019 20:59:22 GMT

Protected "6k4t" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:59, 5 June 2019

OCA: New page: '''Unreleased structure''' The entry 6k4t is ON HOLD Authors: Wachino, J. Description: Crystal structure of SMB-1 metallo-beta-lactamase in a complex with TSA [[Category: Unreleased St...

OCA — Wed, 05 Jun 2019 20:59:20 GMT

New page: '''Unreleased structure''' The entry 6k4t is ON HOLD Authors: Wachino, J. Description: Crystal structure of SMB-1 metallo-beta-lactamase in a complex with TSA [[Category: Unreleased St...

New page

'''Unreleased structure'''

The entry 6k4t is ON HOLD

Authors: Wachino, J.

Description: Crystal structure of SMB-1 metallo-beta-lactamase in a complex with TSA
[[Category: Unreleased Structures]]
[[Category: Wachino, J]]