OCA at 08:22, 11 October 2023

2023-10-11T08:22:19Z

←Older revision		Revision as of 08:22, 11 October 2023
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	==Crystal structure of air-exposed C45G/T50C D. vulgaris carbon monoxide dehydrogenase (2 day air exposure)==		==Crystal structure of air-exposed C45G/T50C D. vulgaris carbon monoxide dehydrogenase (2 day air exposure)==
-	<StructureSection load='6vx1' size='340' side='right'caption='[[6vx1]]' scene=''>	+	<StructureSection load='6vx1' size='340' side='right'caption='[[6vx1]], [[Resolution\|resolution]] 2.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VX1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6VX1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vx1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._Hildenborough Desulfovibrio vulgaris str. Hildenborough]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VX1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VX1 FirstGlance]. <br>
-	</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=6vx1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vx1 OCA], [~~http~~://pdbe.org/6vx1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6vx1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6vx1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6vx1 ProSAT]</span></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]] 2.78Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CUV:Fe(4)-Ni(1)-S(4)+cluster,+oxidized'>CUV</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=6vx1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vx1 OCA], [https://pdbe.org/6vx1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vx1 RCSB], [https://www.ebi.ac.uk/pdbsum/6vx1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vx1 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q72A99_DESVH Q72A99_DESVH]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ni-Fe CO-dehydrogenases (CODHs) catalyze the conversion between CO and CO2 using a chain of Fe-S clusters to mediate long-range electron transfer. One of these clusters, the D-cluster, is surface-exposed and serves to transfer electrons between CODH and external redox partners. These enzymes tend to be extremely O2-sensitive and are always manipulated under strictly anaerobic conditions. However, the CODH from Desulfovibrio vulgaris (Dv) appears unique: exposure to micromolar concentrations of O2 on the minutes-time scale only reversibly inhibits the enzyme, and full activity is recovered after reduction. Here, we examine whether this unusual property of Dv CODH results from the nature of its D-cluster, which is a [2Fe-2S] cluster, instead of the [4Fe-4S] cluster observed in all other characterized CODHs. To this aim, we produced and characterized a Dv CODH variant where the [2Fe-2S] D-cluster is replaced with a [4Fe-4S] D-cluster through mutagenesis of the D-cluster-binding sequence motif. We determined the crystal structure of this CODH variant to 1.83-A resolution and confirmed the incorporation of a [4Fe-4S] D-cluster. We show that upon long-term O2-exposure, the [4Fe-4S] D-cluster degrades, whereas the [2Fe-2S] D-cluster remains intact. Crystal structures of the Dv CODH variant exposed to O2 for increasing periods of time provide snapshots of [4Fe-4S] D-cluster degradation. We further show that the WT enzyme purified under aerobic conditions retains 30% activity relative to a fully anaerobic purification, compared to 10% for the variant, and the WT enzyme loses activity more slowly than the variant upon prolonged aerobic storage. The D-cluster is therefore a key site of irreversible oxidative damage in Dv CODH, and the presence of a [2Fe-2S] D-cluster contributes to the O2-tolerance of this enzyme. Together, these results relate O2-sensitivity with the details of the protein structure in this family of enzymes.
		+
		+	The Solvent-Exposed Fe-S D-Cluster Contributes to Oxygen-Resistance in Desulfovibrio vulgaris Ni-Fe Carbon Monoxide Dehydrogenase.,Wittenborn EC, Guendon C, Merrouch M, Benvenuti M, Fourmond V, Leger C, Drennan CL, Dementin S ACS Catal. 2020 Jul 2;10(13):7328-7335. doi: 10.1021/acscatal.0c00934. Epub 2020 , Jun 4. PMID:32655979<ref>PMID:32655979</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6vx1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Carbon monoxide dehydrogenase 3D structures\|Carbon monoxide dehydrogenase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Desulfovibrio vulgaris str. Hildenborough]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Drennan CL]]		[[Category: Drennan CL]]
	[[Category: Wittenborn EC]]		[[Category: Wittenborn EC]]

OCA at 11:10, 29 July 2020

2020-07-29T11:10:06Z

←Older revision		Revision as of 11:10, 29 July 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6vx1 ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of air-exposed C45G/T50C D. vulgaris carbon monoxide dehydrogenase (2 day air exposure)==
-		+	<StructureSection load='6vx1' size='340' side='right'caption='[[6vx1]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VX1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VX1 FirstGlance]. <br>
-	~~Description~~:	+	</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=6vx1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vx1 OCA], [http://pdbe.org/6vx1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vx1 RCSB], [http://www.ebi.ac.uk/pdbsum/6vx1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vx1 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Drennan CL]]
		+	[[Category: Wittenborn EC]]

OCA at 05:37, 4 March 2020

2020-03-04T05:37:15Z

←Older revision		Revision as of 05:37, 4 March 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6vx1 is ON HOLD	+	The entry 6vx1 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6vx1" [edit=sysop:move=sysop]

2020-02-26T08:15:23Z

Protected "6vx1" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:15, 26 February 2020

OCA: New page: '''Unreleased structure''' The entry 6vx1 is ON HOLD Authors: Description: Category: Unreleased Structures

2020-02-26T08:15:22Z

New page: '''Unreleased structure''' The entry 6vx1 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6vx1 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

6vx1 - Revision history

OCA at 08:22, 11 October 2023

OCA at 11:10, 29 July 2020

OCA at 05:37, 4 March 2020

OCA: Protected "6vx1" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 6vx1 is ON HOLD Authors: Description: Category: Unreleased Structures