6es9 - Revision history

OCA at 06:18, 8 September 2022

OCA — Thu, 08 Sep 2022 06:18:52 GMT

←Older revision		Revision as of 06:18, 8 September 2022
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	<StructureSection load='6es9' size='340' side='right'caption='[[6es9]], [[Resolution\|resolution]] 1.37Å' scene=''>		<StructureSection load='6es9' size='340' side='right'caption='[[6es9]], [[Resolution\|resolution]] 1.37Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6es9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Pardp Pardp~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ES9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ES9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6es9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_denitrificans_PD1222 Paracoccus denitrificans PD1222]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ES9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ES9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pden_2840 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318586 PARDP])</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=6es9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6es9 OCA], [https://pdbe.org/6es9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6es9 RCSB], [https://www.ebi.ac.uk/pdbsum/6es9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6es9 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=6es9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6es9 OCA], [https://pdbe.org/6es9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6es9 RCSB], [https://www.ebi.ac.uk/pdbsum/6es9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6es9 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/A1B5Y0_PARDP A1B5Y0_PARDP]]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pardp~~]]	+	[[Category: Paracoccus denitrificans PD1222]]
-	[[Category: Erb~~, T J~~]]	+	[[Category: Erb TJ]]
-	[[Category: Schwander, T]]	+	[[Category: Schwander T]]
-	[[Category: Zarzycki, J]]	+	[[Category: Zarzycki J]]
-	~~[[Category: Acyl-coa dehydrogenase]]~~	+
-	~~[[Category: Ethylmalonyl-coa pathway]]~~	+
-	~~[[Category: Flavin adenine dinucleotide]]~~	+
-	~~[[Category: Flavoprotein]]~~	+
-	~~[[Category: Methylsuccinyl-coa~~]]	+

OCA at 05:21, 13 July 2022

OCA — Wed, 13 Jul 2022 05:21:29 GMT

←Older revision		Revision as of 05:21, 13 July 2022
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	==Methylsuccinyl-CoA dehydrogenase of Paracoccus denitrificans with bound flavin adenine dinucleotide==		==Methylsuccinyl-CoA dehydrogenase of Paracoccus denitrificans with bound flavin adenine dinucleotide==
-	<StructureSection load='6es9' size='340' side='right' caption='[[6es9]], [[Resolution\|resolution]] 1.37Å' scene=''>	+	<StructureSection load='6es9' size='340' side='right'caption='[[6es9]], [[Resolution\|resolution]] 1.37Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6es9]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pardp Pardp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ES9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6ES9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6es9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pardp Pardp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ES9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ES9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pden_2840 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318586 PARDP])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pden_2840 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318586 PARDP])</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=6es9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6es9 OCA], [~~http~~://pdbe.org/6es9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6es9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6es9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6es9 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=6es9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6es9 OCA], [https://pdbe.org/6es9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6es9 RCSB], [https://www.ebi.ac.uk/pdbsum/6es9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6es9 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 6es9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6es9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Acyl-CoA dehydrogenase 3D structures\|Acyl-CoA dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pardp]]		[[Category: Pardp]]
	[[Category: Erb, T J]]		[[Category: Erb, T J]]
	[[Category: Schwander, T]]		[[Category: Schwander, T]]
-	[[Category: Zarzycki, j]]	+	[[Category: Zarzycki, J]]
	[[Category: Acyl-coa dehydrogenase]]		[[Category: Acyl-coa dehydrogenase]]
	[[Category: Ethylmalonyl-coa pathway]]		[[Category: Ethylmalonyl-coa pathway]]

OCA at 07:09, 15 February 2018

OCA — Thu, 15 Feb 2018 07:09:59 GMT

←Older revision		Revision as of 07:09, 15 February 2018
Line 3:		Line 3:
	<StructureSection load='6es9' size='340' side='right' caption='[[6es9]], [[Resolution\|resolution]] 1.37Å' scene=''>		<StructureSection load='6es9' size='340' side='right' caption='[[6es9]], [[Resolution\|resolution]] 1.37Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6es9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ES9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ES9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6es9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pardp Pardp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ES9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ES9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pden_2840 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318586 PARDP])</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=6es9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6es9 OCA], [http://pdbe.org/6es9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6es9 RCSB], [http://www.ebi.ac.uk/pdbsum/6es9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6es9 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=6es9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6es9 OCA], [http://pdbe.org/6es9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6es9 RCSB], [http://www.ebi.ac.uk/pdbsum/6es9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6es9 ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Pardp]]
	[[Category: Erb, T J]]		[[Category: Erb, T J]]
	[[Category: Schwander, T]]		[[Category: Schwander, T]]

OCA at 05:52, 3 January 2018

OCA — Wed, 03 Jan 2018 05:52:51 GMT

←Older revision		Revision as of 05:52, 3 January 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6es9 is ~~ON HOLD until Paper~~ Publication	+	==Methylsuccinyl-CoA dehydrogenase of Paracoccus denitrificans with bound flavin adenine dinucleotide==
		+	<StructureSection load='6es9' size='340' side='right' caption='[[6es9]], [[Resolution\|resolution]] 1.37Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6es9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ES9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ES9 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6es9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6es9 OCA], [http://pdbe.org/6es9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6es9 RCSB], [http://www.ebi.ac.uk/pdbsum/6es9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6es9 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	(2S)-methylsuccinyl-CoA dehydrogenase (MCD) belongs to the family of FAD-dependent acyl-CoA dehydrogenase (ACD) and is a key enzyme of the ethylmalonyl-CoA pathway for acetate assimilation. It catalyzes the oxidation of (2S)-methylsuccinyl-CoA to alpha,beta-unsaturated mesaconyl-CoA and shows only about 0.5% activity with succinyl-CoA. Here we report the crystal structure of MCD at a resolution of 1.37 A. The enzyme forms a homodimer of two 60 kDa subunits. Compared to other ACDs, MCD contains a ~170 residue long N-terminal extension that structurally mimics a dimer-dimer interface of these enzymes that are canonically organized as tetramers. MCD catalyzes the unprecedented oxidation of an alpha-methyl branched dicarboxylic acid CoA thioester. Substrate specificity is achieved by a cluster of three arginines that accommodates the terminal carboxyl group and a dedicated cavity that facilitates binding of the C2 methyl branch. MCD apparently evolved towards preventing the unspecific oxidation of succinyl-CoA, a close structural homolog of (2S)-methylsuccinyl-CoA, and an essential intermediate in central carbon metabolism. For different metabolic engineering and biotechnological applications, however, an enzyme that can oxidize succinyl-CoA to fumaryl-CoA is sought after. Based on the MCD structure, we were able to shift substrate specificity of MCD towards succinyl-CoA through active site mutagenesis.

-	~~Authors~~: ~~Zarzycki, j~~., Schwander, T., ~~Erb~~, T.J.	+	Structural basis for substrate specificity of methylsuccinyl-CoA dehydrogenase: an unusual member of the acyl-CoA dehydrogenase family.,Schwander T, McLean R, Zarzycki J, Erb TJ J Biol Chem. 2017 Dec 22. pii: RA117.000764. doi: 10.1074/jbc.RA117.000764. PMID:29275330<ref>PMID:29275330</ref>

-	~~Description: Methylsuccinyl-CoA dehydrogenase~~ of ~~Paracoccus denitrificans with bound flavin adenine dinucleotide~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6es9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Erb, T J]]
	[[Category: Schwander, T]]		[[Category: Schwander, T]]
-	[[Category: ~~Erb~~, ~~T.J~~]]	+	[[Category: Zarzycki, j]]
-	[[Category: ~~Zarzycki, J~~]]	+	[[Category: Acyl-coa dehydrogenase]]
		+	[[Category: Ethylmalonyl-coa pathway]]
		+	[[Category: Flavin adenine dinucleotide]]
		+	[[Category: Flavoprotein]]
		+	[[Category: Methylsuccinyl-coa]]

OCA at 05:04, 1 November 2017

OCA — Wed, 01 Nov 2017 05:04:33 GMT

←Older revision		Revision as of 05:04, 1 November 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6es9 is ON HOLD	+	The entry 6es9 is ON HOLD until Paper Publication

	Authors: Zarzycki, j., Schwander, T., Erb, T.J.		Authors: Zarzycki, j., Schwander, T., Erb, T.J.

-	Description: Methylsuccinyl-CoA dehydrogenase with bound flavin adenine dinucleotide	+	Description: Methylsuccinyl-CoA dehydrogenase of Paracoccus denitrificans with bound flavin adenine dinucleotide
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Schwander, T]]
	[[Category: Erb, T.J]]		[[Category: Erb, T.J]]
	[[Category: Zarzycki, J]]		[[Category: Zarzycki, J]]
-	[[Category: Schwander, T]]

OCA: Protected "6es9" [edit=sysop:move=sysop]

OCA — Wed, 25 Oct 2017 06:07:59 GMT

Protected "6es9" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:07, 25 October 2017

OCA: New page: '''Unreleased structure''' The entry 6es9 is ON HOLD Authors: Zarzycki, j., Schwander, T., Erb, T.J. Description: Methylsuccinyl-CoA dehydrogenase with bound flavin adenine dinucleotid...

OCA — Wed, 25 Oct 2017 06:07:58 GMT

New page: '''Unreleased structure''' The entry 6es9 is ON HOLD Authors: Zarzycki, j., Schwander, T., Erb, T.J. Description: Methylsuccinyl-CoA dehydrogenase with bound flavin adenine dinucleotid...

New page

'''Unreleased structure'''

The entry 6es9 is ON HOLD

Authors: Zarzycki, j., Schwander, T., Erb, T.J.

Description: Methylsuccinyl-CoA dehydrogenase with bound flavin adenine dinucleotide
[[Category: Unreleased Structures]]
[[Category: Erb, T.J]]
[[Category: Zarzycki, J]]
[[Category: Schwander, T]]