5t2u - Revision history

OCA at 15:35, 6 March 2024

OCA — Wed, 06 Mar 2024 15:35:42 GMT

←Older revision		Revision as of 15:35, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='5t2u' size='340' side='right'caption='[[5t2u]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5t2u' size='340' side='right'caption='[[5t2u]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5t2u]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Mycs2 Mycs2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T2U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5T2U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5t2u]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_MC2_155 Mycolicibacterium smegmatis MC2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T2U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T2U FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NAP:NADP+NICOTINAMIDE~~-~~ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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]] 2.2Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~MSMEG_6753, MSMEI_6571 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=246196 MYCS2])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5t2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t2u OCA], [~~http~~://pdbe.org/5t2u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5t2u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5t2u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5t2u 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=5t2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t2u OCA], [https://pdbe.org/5t2u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t2u RCSB], [https://www.ebi.ac.uk/pdbsum/5t2u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t2u ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A0R723_MYCS2 A0R723_MYCS2]
-	The ketoacyl-acyl carrier protein (ACP) reductase FabG catalyzes the NADPH/NADH dependent reduction of beta-ketoacyl-ACP substrates to beta-hydroxyacyl-ACP products, the first reductive step in the fatty acid biosynthesis elongation cycle. FabG proteins are ubiquitous in bacteria and are part of the type II fatty acid synthase system. Mining the Mycobacterium smegmatis genome uncovered several putative FabG-like proteins. Among them, we identified M. smegmatis MSMEG_6753 whose gene was found adjacent to MSMEG_6754, encoding a recently characterized enoyl-CoA dehydratase, and to MSMEG_6755, encoding another potential reductase. Recombinantly expressed and purified MSMEG_6753 exhibits ketoacyl reductase activity in the presence of acetoacetyl-CoA and NADPH. This activity was subsequently confirmed by functional complementation studies in a fabG thermosensitive Escherichia coli mutant. Furthermore, comparison of the apo and the NADP+-bound MSMEG_6753 crystal structures showed that cofactor binding induces a closed conformation of the protein. A DeltaMSMEG_6753 deletion mutant could be generated in M. smegmatis, indicating that this gene is dispensable for mycobacterial growth. Overall, these results showcase the diversity of FabG-like proteins in mycobacteria and new structural features regarding the catalytic mechanism of this important family of enzymes that may be of importance for the rational design of specific FabG inhibitors.	+
-		+
-	~~Binding of NADP+ triggers an open-to-closed transition in a mycobacterial FabG beta-ketoacyl-ACP reductase.,Blaise M, Van Wyk N, Baneres-Roquet F, Guerardel Y, Kremer L Biochem J. 2017 Mar 7;474(6)~~:~~907-921. doi: 10.1042~~/~~BCJ20161052. PMID:28126742<ref>PMID:28126742<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5t2u" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Mycs2~~]]	+	[[Category: Mycolicibacterium smegmatis MC2 155]]
-	[[Category: Baneres-Roquet, F]]	+	[[Category: Baneres-Roquet F]]
-	[[Category: Laurent, K]]	+	[[Category: Laurent K]]
-	[[Category: Mickael, B]]	+	[[Category: Mickael B]]
-	[[Category: Wyk, N ~~Van~~]]	+	[[Category: Van Wyk N]]
-	[[Category: Yann, G]]	+	[[Category: Yann G]]
-	~~[[Category: Fabg]]~~	+
-	~~[[Category: Fatty acid]]~~	+
-	~~[[Category: Mycobacterium]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 11:18, 16 September 2020

OCA — Wed, 16 Sep 2020 11:18:58 GMT

←Older revision		Revision as of 11:18, 16 September 2020
Line 1:		Line 1:

	==short chain dehydrogenase/reductase family protein==		==short chain dehydrogenase/reductase family protein==
-	<StructureSection load='5t2u' size='340' side='right' caption='[[5t2u]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5t2u' size='340' side='right'caption='[[5t2u]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5t2u]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T2U OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca.weizmann~~.~~ac.il/oca-docs~~/fgij/fg.htm?mol=5T2U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5t2u]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycs2 Mycs2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T2U OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5T2U FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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=5t2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t2u OCA], [http://pdbe.org/5t2u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t2u RCSB], [http://www.ebi.ac.uk/pdbsum/5t2u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t2u ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MSMEG_6753, MSMEI_6571 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5t2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t2u OCA], [http://pdbe.org/5t2u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t2u RCSB], [http://www.ebi.ac.uk/pdbsum/5t2u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t2u ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Mycs2]]
	[[Category: Baneres-Roquet, F]]		[[Category: Baneres-Roquet, F]]
	[[Category: Laurent, K]]		[[Category: Laurent, K]]

OCA at 17:44, 10 March 2017

OCA — Fri, 10 Mar 2017 17:44:52 GMT

←Older revision		Revision as of 17:44, 10 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5t2u is ~~ON HOLD until Paper~~ Publication	+	==short chain dehydrogenase/reductase family protein==
		+	<StructureSection load='5t2u' size='340' side='right' caption='[[5t2u]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5t2u]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T2U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T2U FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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=5t2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t2u OCA], [http://pdbe.org/5t2u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t2u RCSB], [http://www.ebi.ac.uk/pdbsum/5t2u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t2u ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The ketoacyl-acyl carrier protein (ACP) reductase FabG catalyzes the NADPH/NADH dependent reduction of beta-ketoacyl-ACP substrates to beta-hydroxyacyl-ACP products, the first reductive step in the fatty acid biosynthesis elongation cycle. FabG proteins are ubiquitous in bacteria and are part of the type II fatty acid synthase system. Mining the Mycobacterium smegmatis genome uncovered several putative FabG-like proteins. Among them, we identified M. smegmatis MSMEG_6753 whose gene was found adjacent to MSMEG_6754, encoding a recently characterized enoyl-CoA dehydratase, and to MSMEG_6755, encoding another potential reductase. Recombinantly expressed and purified MSMEG_6753 exhibits ketoacyl reductase activity in the presence of acetoacetyl-CoA and NADPH. This activity was subsequently confirmed by functional complementation studies in a fabG thermosensitive Escherichia coli mutant. Furthermore, comparison of the apo and the NADP+-bound MSMEG_6753 crystal structures showed that cofactor binding induces a closed conformation of the protein. A DeltaMSMEG_6753 deletion mutant could be generated in M. smegmatis, indicating that this gene is dispensable for mycobacterial growth. Overall, these results showcase the diversity of FabG-like proteins in mycobacteria and new structural features regarding the catalytic mechanism of this important family of enzymes that may be of importance for the rational design of specific FabG inhibitors.

-	~~Authors: Mickael~~, B., Van Wyk, N., Baneres, F~~.R.~~, ~~Michel~~, D.~~, Yann, G~~.~~, Laurent, K~~.	+	Binding of NADP+ triggers an open-to-closed transition in a mycobacterial FabG beta-ketoacyl-ACP reductase.,Blaise M, Van Wyk N, Baneres-Roquet F, Guerardel Y, Kremer L Biochem J. 2017 Mar 7;474(6):907-921. doi: 10.1042/BCJ20161052. PMID:28126742<ref>PMID:28126742</ref>

-	~~Description: short chain dehydrogenase~~/~~reductase family protein~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Mickael~~, B]]	+	<div class="pdbe-citations 5t2u" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Baneres-Roquet, F]]
	[[Category: Laurent, K]]		[[Category: Laurent, K]]
		+	[[Category: Mickael, B]]
		+	[[Category: Wyk, N Van]]
	[[Category: Yann, G]]		[[Category: Yann, G]]
-	[[Category: ~~Michel, D~~]]	+	[[Category: Fabg]]
-	[[Category: ~~Baneres, F.R~~]]	+	[[Category: Fatty acid]]
-	[[Category: ~~Van Wyk, N~~]]	+	[[Category: Mycobacterium]]
		+	[[Category: Oxidoreductase]]

OCA: Protected "5t2u" [edit=sysop:move=sysop]

OCA — Fri, 09 Sep 2016 15:36:55 GMT

Protected "5t2u" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:36, 9 September 2016

OCA: New page: '''Unreleased structure''' The entry 5t2u is ON HOLD until Paper Publication Authors: Mickael, B., Van Wyk, N., Baneres, F.R., Michel, D., Yann, G., Laurent, K. Description: short chai...

OCA — Fri, 09 Sep 2016 15:36:54 GMT

New page: '''Unreleased structure''' The entry 5t2u is ON HOLD until Paper Publication Authors: Mickael, B., Van Wyk, N., Baneres, F.R., Michel, D., Yann, G., Laurent, K. Description: short chai...

New page

'''Unreleased structure'''

The entry 5t2u is ON HOLD until Paper Publication

Authors: Mickael, B., Van Wyk, N., Baneres, F.R., Michel, D., Yann, G., Laurent, K.

Description: short chain dehydrogenase/reductase family protein
[[Category: Unreleased Structures]]
[[Category: Mickael, B]]
[[Category: Laurent, K]]
[[Category: Yann, G]]
[[Category: Michel, D]]
[[Category: Baneres, F.R]]
[[Category: Van Wyk, N]]