6n2o - Revision history

OCA at 06:43, 11 October 2023

OCA — Wed, 11 Oct 2023 06:43:57 GMT

←Older revision		Revision as of 06:43, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6n2o' size='340' side='right'caption='[[6n2o]], [[Resolution\|resolution]] 2.82Å' scene=''>		<StructureSection load='6n2o' size='340' side='right'caption='[[6n2o]], [[Resolution\|resolution]] 2.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n2o]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Magmm Magmm~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N2O OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6N2O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n2o]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Magnetococcus_marinus_MC-1 Magnetococcus marinus MC-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N2O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N2O FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SCA:SUCCINYL-COENZYME+A'>SCA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</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]] 2.824Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6n2n\|6n2n]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SCA:SUCCINYL-COENZYME+A'>SCA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Mmc1_1749 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=156889 MAGMM]), Mmc1_1750 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=156889 MAGMM])</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=6n2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n2o OCA], [https://pdbe.org/6n2o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n2o RCSB], [https://www.ebi.ac.uk/pdbsum/6n2o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n2o 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=6n2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n2o OCA], [~~http~~://pdbe.org/6n2o PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6n2o RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6n2o PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6n2o ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0L8G4_MAGMM A0L8G4_MAGMM]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Magmm~~]]	+	[[Category: Magnetococcus marinus MC-1]]
-	[[Category: Chen~~, P Y.~~T]]	+	[[Category: Chen PY-T]]
-	[[Category: Drennan~~, C L]]~~	+	[[Category: Drennan CL]]
-	~~[[Category: 2-oxoglutarate:ferredoxin oxidoreductase]]~~	+
-	~~[[Category: Carbon fixation]]~~	+
-	~~[[Category: Electron transfer]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Reductive tricarboxylic acid cycle]]~~	+
-	~~[[Category: Rtca]]~~	+
-	~~[[Category: Thiamine pyrophosphate~~]]	+

OCA at 11:40, 13 November 2019

OCA — Wed, 13 Nov 2019 11:40:47 GMT

←Older revision		Revision as of 11:40, 13 November 2019
Line 3:		Line 3:
	<StructureSection load='6n2o' size='340' side='right'caption='[[6n2o]], [[Resolution\|resolution]] 2.82Å' scene=''>		<StructureSection load='6n2o' size='340' side='right'caption='[[6n2o]], [[Resolution\|resolution]] 2.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n2o]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N2O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N2O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n2o]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Magmm Magmm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N2O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N2O FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SCA:SUCCINYL-COENZYME+A'>SCA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SCA:SUCCINYL-COENZYME+A'>SCA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6n2n\|6n2n]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6n2n\|6n2n]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Mmc1_1749 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=156889 MAGMM]), Mmc1_1750 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=156889 MAGMM])</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=6n2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n2o OCA], [http://pdbe.org/6n2o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n2o RCSB], [http://www.ebi.ac.uk/pdbsum/6n2o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n2o 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=6n2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n2o OCA], [http://pdbe.org/6n2o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n2o RCSB], [http://www.ebi.ac.uk/pdbsum/6n2o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n2o ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	2-oxoglutarate:ferredoxin oxidoreductase (OGOR) is a thiamine pyrophosphate (TPP) and [4Fe-4S] cluster-dependent enzyme from the reductive tricarboxylic acid (rTCA) cycle that fixes CO2 to succinyl-CoA, forming 2-oxoglutarate and CoA. Here we report an OGOR from the rTCA cycle of Magnetococcus marinus MC-1, along with all three potential ferredoxin (Fd) redox partners. We demonstrate MmOGOR operates bidirectionally (both CO2-fixing and 2-oxoglutarate oxidizing), and that only one Fd (MmFd1) supports efficient catalysis. Our 1.94-A and 2.80-A resolution crystal structures of native and substrate-bound forms of MmOGOR reveal the determinants of substrate specificity and CoA-binding in an OGOR, and illuminate the [4Fe-4S] cluster environment, portraying the electronic conduit allowing MmFd1 to be wired to the bound-TPP. Structural and biochemical data further identify Glu45alpha as a mobile residue that impacts catalytic bias toward CO2-fixation although it makes no direct contact with TPP-bound intermediates, indicating that reaction directionality can be tuned by second layer interactions. (149 of 150 words limit).
		+
		+	A reverse TCA cycle 2-oxoacid:ferredoxin oxidoreductase that makes C-C bonds from CO2.,Chen PY, Li B, Drennan CL, Elliott SJ Joule. 2019 Feb 20;3(2):595-611. doi: 10.1016/j.joule.2018.12.006. Epub 2019 Jan , 4. PMID:31080943<ref>PMID:31080943</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6n2o" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Magmm]]
	[[Category: Chen, P Y.T]]		[[Category: Chen, P Y.T]]
	[[Category: Drennan, C L]]		[[Category: Drennan, C L]]

OCA at 08:02, 20 March 2019

OCA — Wed, 20 Mar 2019 08:02:47 GMT

←Older revision		Revision as of 08:02, 20 March 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6n2o is ON HOLD until Nov 13 2020~~	+	==2-oxoglutarate:ferredoxin oxidoreductase from Magnetococcus marinus with 2-oxoglutarate, coenzyme A and succinyl-CoA bound==
-		+	<StructureSection load='6n2o' size='340' side='right'caption='[[6n2o]], [[Resolution\|resolution]] 2.82Å' scene=''>
-	~~Authors: Chen, P.Y.-T., Drennan, C.L.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6n2o]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N2O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N2O FirstGlance]. <br>
-	~~Description:~~ 2-oxoglutarate:ferredoxin oxidoreductase from Magnetococcus marinus with 2-oxoglutarate, coenzyme A and succinyl-CoA bound	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SCA:SUCCINYL-COENZYME+A'>SCA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6n2n\|6n2n]]</td></tr>
-	[[~~Category~~: ~~Drennan~~, C.L]]	+	<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=6n2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n2o OCA], [http://pdbe.org/6n2o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n2o RCSB], [http://www.ebi.ac.uk/pdbsum/6n2o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n2o ProSAT]</span></td></tr>
-	[[Category: Chen, P.Y.-T]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Chen, P Y.T]]
		+	[[Category: Drennan, C L]]
		+	[[Category: 2-oxoglutarate:ferredoxin oxidoreductase]]
		+	[[Category: Carbon fixation]]
		+	[[Category: Electron transfer]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Reductive tricarboxylic acid cycle]]
		+	[[Category: Rtca]]
		+	[[Category: Thiamine pyrophosphate]]

OCA: Protected "6n2o" [edit=sysop:move=sysop]

OCA — Sun, 02 Dec 2018 19:10:14 GMT

Protected "6n2o" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:10, 2 December 2018

OCA: New page: '''Unreleased structure''' The entry 6n2o is ON HOLD until Nov 13 2020 Authors: Chen, P.Y.-T., Drennan, C.L. Description: 2-oxoglutarate:ferredoxin oxidoreductase from Magnetococcus ma...

OCA — Sun, 02 Dec 2018 19:10:13 GMT

New page: '''Unreleased structure''' The entry 6n2o is ON HOLD until Nov 13 2020 Authors: Chen, P.Y.-T., Drennan, C.L. Description: 2-oxoglutarate:ferredoxin oxidoreductase from Magnetococcus ma...

New page

'''Unreleased structure'''

The entry 6n2o is ON HOLD until Nov 13 2020

Authors: Chen, P.Y.-T., Drennan, C.L.

Description: 2-oxoglutarate:ferredoxin oxidoreductase from Magnetococcus marinus with 2-oxoglutarate, coenzyme A and succinyl-CoA bound
[[Category: Unreleased Structures]]
[[Category: Drennan, C.L]]
[[Category: Chen, P.Y.-T]]