4yfm - Revision history

OCA at 10:55, 10 January 2024

OCA — Wed, 10 Jan 2024 10:55:04 GMT

←Older revision		Revision as of 10:55, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4yfm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacteroides_abscessus Mycobacteroides abscessus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YFM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YFM FirstGlance]. <br>		<table><tr><td colspan='2'>[[4yfm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacteroides_abscessus Mycobacteroides abscessus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YFM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YFM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <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]] 1.4Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=4yfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yfm OCA], [https://pdbe.org/4yfm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yfm RCSB], [https://www.ebi.ac.uk/pdbsum/4yfm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yfm 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=4yfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yfm OCA], [https://pdbe.org/4yfm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yfm RCSB], [https://www.ebi.ac.uk/pdbsum/4yfm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yfm ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:12, 3 May 2023

OCA — Wed, 03 May 2023 08:12:15 GMT

←Older revision		Revision as of 08:12, 3 May 2023
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	<StructureSection load='4yfm' size='340' side='right'caption='[[4yfm]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='4yfm' size='340' side='right'caption='[[4yfm]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yfm]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"mycobacterium_abcessus"_moore_and_frerichs_1953 "mycobacterium abcessus" moore and frerichs 1953~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YFM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4YFM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yfm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacteroides_abscessus Mycobacteroides abscessus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YFM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YFM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <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" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LA62_14585 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36809 "Mycobacterium abcessus" Moore and Frerichs 1953])</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=4yfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yfm OCA], [https://pdbe.org/4yfm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yfm RCSB], [https://www.ebi.ac.uk/pdbsum/4yfm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yfm 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=4yfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yfm OCA], [~~http~~://pdbe.org/4yfm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4yfm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4yfm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4yfm ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B1MCI3_MYCA9 B1MCI3_MYCA9]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Mycobacterium abcessus moore and frerichs 1953]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arthur, M]]	+	[[Category: Mycobacteroides abscessus]]
-	[[Category: Dubee, V]]	+	[[Category: Arthur M]]
-	[[Category: Sierra-Gallay, I ~~Li de la~~]]	+	[[Category: Dubee V]]
-	[[Category: Soroka, D]]	+	[[Category: Li de la Sierra-Gallay I]]
-	[[Category: Tilbeurgh, H ~~van]]~~	+	[[Category: Soroka D]]
-	~~[[Category: Beta-lactamase]]~~	+	[[Category: Van Tilbeurgh H]]
-	~~[[Category: Carbapenem]]~~	+
-	~~[[Category: Clavulanate]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Mycobacterium tuberculosis~~]]	+

OCA at 06:38, 12 June 2019

OCA — Wed, 12 Jun 2019 06:38:38 GMT

←Older revision		Revision as of 06:38, 12 June 2019
Line 1:		Line 1:
		+
	==Class A beta-lactamase from Mycobacterium abscessus==		==Class A beta-lactamase from Mycobacterium abscessus==
-	<StructureSection load='4yfm' size='340' side='right' caption='[[4yfm]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='4yfm' size='340' side='right'caption='[[4yfm]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yfm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YFM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YFM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yfm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"mycobacterium_abcessus"_moore_and_frerichs_1953 "mycobacterium abcessus" moore and frerichs 1953]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YFM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YFM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=4yfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yfm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4yfm RCSB], [http://www.ebi.ac.uk/pdbsum/4yfm PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LA62_14585 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36809 "Mycobacterium abcessus" Moore and Frerichs 1953])</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=4yfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yfm OCA], [http://pdbe.org/4yfm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yfm RCSB], [http://www.ebi.ac.uk/pdbsum/4yfm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yfm ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 16:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4yfm" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Mycobacterium abcessus moore and frerichs 1953]]
		+	[[Category: Large Structures]]
	[[Category: Arthur, M]]		[[Category: Arthur, M]]
	[[Category: Dubee, V]]		[[Category: Dubee, V]]

OCA at 14:08, 22 July 2015

OCA — Wed, 22 Jul 2015 14:08:31 GMT

←Older revision		Revision as of 14:08, 22 July 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Class A beta-lactamase from Mycobacterium abscessus==
		+	<StructureSection load='4yfm' size='340' side='right' caption='[[4yfm]], [[Resolution\|resolution]] 1.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4yfm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YFM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YFM FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=4yfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yfm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4yfm RCSB], [http://www.ebi.ac.uk/pdbsum/4yfm PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Combinations of beta-lactams with clavulanate are currently investigated for tuberculosis treatment. Since Mycobacterium tuberculosis produces a broad spectrum beta-lactamase, BlaC, the success of this approach could be compromised by the emergence of clavulanate-resistant variants, as observed for inhibitor resistant TEM variants in enterobacteria. Previous analyses based on site-directed mutagenesis of BlaC have led to the conclusion that this risk was limited. Here, we used a different approach based on determination of the crystal structure of beta-lactamase BlaMab of Mycobacterium abscessus, which efficiently hydrolyses clavulanate. Comparison of BlaMab and BlaC allowed for structure-assisted site-directed mutagenesis of BlaC and identification of the G132N substitution that was sufficient to switch interaction of BlaC with clavulanate from irreversible inactivation to efficient hydrolysis. The substitution, which restored the canonical SDN motif (SDG-->SDN), allowed for efficient hydrolysis of clavulanate, with a more than 104 increase in kcat (0.41 s-1), without affecting hydrolysis of other beta-lactams. Mass spectrometry revealed that acylation of BlaC and of its G132N variant by clavulanate follows similar paths involving sequential formation of two acylenzymes. Decarboxylation of the first acylenzyme results in a stable secondary acylenzyme in BlaC, whereas hydrolysis occurs in the G132N variant. The SDN/SDG polymorphism defines two mycobacterial lineages comprising rapidly and slowly growing species, respectively. Together, these results suggest that the efficacy of beta-lactam-clavulanate combinations may be limited by emergence of resistance. beta-lactams active without clavulanate, such as faropenem, should be prioritized for development of new therapies.

-	~~The entry 4yfm is ON HOLD until Paper Publication~~	+	Hydrolysis of clavulanate by Mycobacterium tuberculosis beta-lactamase BlaC harboring a canonic SDN motif.,Soroka D, Li de la Sierra-Gallay I, Dubee V, Triboulet S, van Tilbeurgh H, Compain F, Ballell L, Barros D, Mainardi JL, Hugonnet JE, Arthur M Antimicrob Agents Chemother. 2015 Jul 6. pii: AAC.00598-15. PMID:26149997<ref>PMID:26149997</ref>

-	~~Authors: Soroka~~, D.~~, Li de la Sierra-Gallay, I~~.~~, Dubee, V., van Tilbeurgh, H., Arthur, M~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Class A beta-lactamase from Mycobacterium abscessus~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Arthur, M]]
	[[Category: Dubee, V]]		[[Category: Dubee, V]]
		+	[[Category: Sierra-Gallay, I Li de la]]
	[[Category: Soroka, D]]		[[Category: Soroka, D]]
-	[[Category: ~~Van~~ Tilbeurgh, H]]	+	[[Category: Tilbeurgh, H van]]
-	[[Category: ~~Arthur, M~~]]	+	[[Category: Beta-lactamase]]
-	[[Category: ~~Li De La Sierra-Gallay, I~~]]	+	[[Category: Carbapenem]]
		+	[[Category: Clavulanate]]
		+	[[Category: Hydrolase]]
		+	[[Category: Mycobacterium tuberculosis]]

OCA: Protected "4yfm" [edit=sysop:move=sysop]

OCA — Wed, 04 Mar 2015 10:25:32 GMT

Protected "4yfm" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:25, 4 March 2015

OCA: New page: '''Unreleased structure''' The entry 4yfm is ON HOLD until Paper Publication Authors: Soroka, D., Li de la Sierra-Gallay, I., Dubee, V., van Tilbeurgh, H., Arthur, M. Description: Clas...

OCA — Wed, 04 Mar 2015 10:25:31 GMT

New page: '''Unreleased structure''' The entry 4yfm is ON HOLD until Paper Publication Authors: Soroka, D., Li de la Sierra-Gallay, I., Dubee, V., van Tilbeurgh, H., Arthur, M. Description: Clas...

New page

'''Unreleased structure'''

The entry 4yfm is ON HOLD until Paper Publication

Authors: Soroka, D., Li de la Sierra-Gallay, I., Dubee, V., van Tilbeurgh, H., Arthur, M.

Description: Class A beta-lactamase from Mycobacterium abscessus
[[Category: Unreleased Structures]]
[[Category: Dubee, V]]
[[Category: Soroka, D]]
[[Category: Van Tilbeurgh, H]]
[[Category: Arthur, M]]
[[Category: Li De La Sierra-Gallay, I]]