6k4x - Revision history

OCA at 10:26, 22 November 2023

2023-11-22T10:26:39Z

←Older revision		Revision as of 10:26, 22 November 2023
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	<StructureSection load='6k4x' size='340' side='right'caption='[[6k4x]], [[Resolution\|resolution]] 1.17Å' scene=''>		<StructureSection load='6k4x' size='340' side='right'caption='[[6k4x]], [[Resolution\|resolution]] 1.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6k4x]] 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=6K4X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6K4X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k4x]] 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=6K4X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K4X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D0U:4-azanyl-2-sulfanyl-benzoic+acid'>D0U</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]] 1.17Å</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=D0U:4-azanyl-2-sulfanyl-benzoic+acid'>D0U</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=6k4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k4x OCA], [https://pdbe.org/6k4x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k4x RCSB], [https://www.ebi.ac.uk/pdbsum/6k4x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k4x 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=6k4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k4x OCA], [~~http~~://pdbe.org/6k4x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6k4x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6k4x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6k4x 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 ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6k4x" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6k4x" 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

2020-02-19T07:23:11Z

←Older revision		Revision as of 07:23, 19 February 2020
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	<StructureSection load='6k4x' size='340' side='right'caption='[[6k4x]], [[Resolution\|resolution]] 1.17Å' scene=''>		<StructureSection load='6k4x' size='340' side='right'caption='[[6k4x]], [[Resolution\|resolution]] 1.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6k4x]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K4X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K4X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k4x]] 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=6K4X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K4X FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D0U:4-azanyl-2-sulfanyl-benzoic+acid'>D0U</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=D0U:4-azanyl-2-sulfanyl-benzoic+acid'>D0U</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=6k4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k4x OCA], [http://pdbe.org/6k4x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k4x RCSB], [http://www.ebi.ac.uk/pdbsum/6k4x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k4x 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=6k4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k4x OCA], [http://pdbe.org/6k4x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k4x RCSB], [http://www.ebi.ac.uk/pdbsum/6k4x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k4x 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 6k4x" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 05:52, 7 August 2019

2019-08-07T05:52:23Z

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

-	~~The entry 6k4x is ON HOLD until May 27 2021~~	+	==Crystal structure of SMB-1 metallo-beta-lactamase in a complex with ASB==
-		+	<StructureSection load='6k4x' size='340' side='right'caption='[[6k4x]], [[Resolution\|resolution]] 1.17Å' scene=''>
-	~~Authors: Wachino, J.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6k4x]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K4X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K4X FirstGlance]. <br>
-	~~Description:~~ Crystal structure of SMB-1 metallo-beta-lactamase in a complex with ASB	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D0U:4-azanyl-2-sulfanyl-benzoic+acid'>D0U</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=6k4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k4x OCA], [http://pdbe.org/6k4x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k4x RCSB], [http://www.ebi.ac.uk/pdbsum/6k4x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k4x 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 05:03, 26 June 2019

2019-06-26T05:03:29Z

←Older revision		Revision as of 05:03, 26 June 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6k4x is ON HOLD	+	The entry 6k4x is ON HOLD until May 27 2021

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

OCA: Protected "6k4x" [edit=sysop:move=sysop]

2019-06-05T20:59:37Z

Protected "6k4x" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:59, 5 June 2019

OCA: New page: '''Unreleased structure''' The entry 6k4x is ON HOLD Authors: Wachino, J. Description: Crystal structure of SMB-1 metallo-beta-lactamase in a complex with ASB [[Category: Unreleased St...

2019-06-05T20:59:35Z

New page: '''Unreleased structure''' The entry 6k4x is ON HOLD Authors: Wachino, J. Description: Crystal structure of SMB-1 metallo-beta-lactamase in a complex with ASB [[Category: Unreleased St...

New page

'''Unreleased structure'''

The entry 6k4x is ON HOLD

Authors: Wachino, J.

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