6vw7 - Revision history

OCA at 14:40, 6 March 2024

OCA — Wed, 06 Mar 2024 14:40:07 GMT

←Older revision		Revision as of 14:40, 6 March 2024
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	<StructureSection load='6vw7' size='340' side='right'caption='[[6vw7]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6vw7' size='340' side='right'caption='[[6vw7]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vw7]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_17697_[[alcaligenes_eutrophus]] Atcc 17697 [[alcaligenes eutrophus]]~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VW7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6VW7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vw7]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Cupriavidus_necator Cupriavidus necator]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VW7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VW7 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 2Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fdsG, H16_A0640 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=106590 ATCC 17697 [[Alcaligenes eutrophus]]]), fdsB, H16_A0641 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=106590 ATCC 17697 [[Alcaligenes eutrophus]]])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Formate_dehydrogenase Formate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.2 1.2.1.2] </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=6vw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vw7 OCA], [https://pdbe.org/6vw7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vw7 RCSB], [https://www.ebi.ac.uk/pdbsum/6vw7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vw7 ProSAT]</span></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=6vw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vw7 OCA], [~~http~~://pdbe.org/6vw7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6vw7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6vw7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6vw7 ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q0KDY3_CUPNH Q0KDY3_CUPNH]
-	Formate oxidation to carbon dioxide is a key reaction in one-carbon compound metabolism, and its reverse reaction represents the first step in carbon assimilation in the acetogenic and methanogenic branches of many anaerobic organisms. The molybdenum-containing dehydrogenase FdsABG is a soluble NAD(+)-dependent formate dehydrogenase and a member of the NADH dehydrogenase superfamily. Here, we present the first structure of the FdsBG subcomplex of the cytosolic FdsABG formate dehydrogenase from the hydrogen-oxidizing bacterium Cupriavidus necator H16 both with and without bound NADH. The structures revealed that the two iron-sulfur clusters, Fe4S4 in FdsB and Fe2S2 in FdsG, are closer to the FMN than they are in other NADH dehydrogenases. Rapid kinetic studies and EPR measurements of rapid freeze-quenched samples of the NADH reduction of FdsBG identified a neutral flavin semiquinone, FMNH*, not previously been observed to participate in NADH-mediated reduction of the FdsABG holoenzyme. We found that this semiquinone forms through the transfer of one electron from the fully reduced FMNH , initially formed via NADH-mediated reduction, to the Fe2S2 cluster. This Fe2S2 cluster is not part of the on-path chain of iron-sulfur clusters connecting the FMN of FdsB with the active-site molybdenum-center of FdsA. According to the NADH-bound structure, the nicotinamide ring stacks onto the re-face of the FMN. However, NADH binding significantly reduced the electron density for the isoalloxazine ring of FMN and induced a conformational change in residues of the FMN-binding pocket that display peptide-bond flipping upon NAD(+) binding in proper NADH dehydrogenases.	+

-	Crystallographic and kinetic analyses of the FdsBG subcomplex of the cytosolic formate dehydrogenase FdsABG from Cupriavidus necator.,Young T, Niks D, Hakopian S, Tam TK, Yu X, Hille R, Blaha GM J Biol Chem. 2020 Apr 5. pii: RA120.013264. doi: 10.1074/jbc.RA120.013264. PMID:32249211<ref>PMID:32249211</ref>	+	==See Also==
-		+	*[[Formate dehydrogenase 3D structures\|Formate dehydrogenase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 6vw7" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Formate dehydrogenase~~]]	+	[[Category: Cupriavidus necator]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Young, T]]	+	[[Category: Young T]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rossmann fold]]~~	+
-	~~[[Category: Thioredoxin-like~~]]	+

OCA at 06:13, 22 April 2020

OCA — Wed, 22 Apr 2020 06:13:05 GMT

←Older revision		Revision as of 06:13, 22 April 2020
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	<StructureSection load='6vw7' size='340' side='right'caption='[[6vw7]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6vw7' size='340' side='right'caption='[[6vw7]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vw7]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VW7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VW7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vw7]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_17697_[[alcaligenes_eutrophus]] Atcc 17697 [[alcaligenes eutrophus]]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VW7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VW7 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fdsG, H16_A0640 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=106590 ATCC 17697 [[Alcaligenes eutrophus]]]), fdsB, H16_A0641 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=106590 ATCC 17697 [[Alcaligenes eutrophus]]])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Formate_dehydrogenase Formate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.2 1.2.1.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Formate_dehydrogenase Formate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.2 1.2.1.2] </span></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=6vw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vw7 OCA], [http://pdbe.org/6vw7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vw7 RCSB], [http://www.ebi.ac.uk/pdbsum/6vw7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vw7 ProSAT]</span></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=6vw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vw7 OCA], [http://pdbe.org/6vw7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vw7 RCSB], [http://www.ebi.ac.uk/pdbsum/6vw7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vw7 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Formate oxidation to carbon dioxide is a key reaction in one-carbon compound metabolism, and its reverse reaction represents the first step in carbon assimilation in the acetogenic and methanogenic branches of many anaerobic organisms. The molybdenum-containing dehydrogenase FdsABG is a soluble NAD(+)-dependent formate dehydrogenase and a member of the NADH dehydrogenase superfamily. Here, we present the first structure of the FdsBG subcomplex of the cytosolic FdsABG formate dehydrogenase from the hydrogen-oxidizing bacterium Cupriavidus necator H16 both with and without bound NADH. The structures revealed that the two iron-sulfur clusters, Fe4S4 in FdsB and Fe2S2 in FdsG, are closer to the FMN than they are in other NADH dehydrogenases. Rapid kinetic studies and EPR measurements of rapid freeze-quenched samples of the NADH reduction of FdsBG identified a neutral flavin semiquinone, FMNH*, not previously been observed to participate in NADH-mediated reduction of the FdsABG holoenzyme. We found that this semiquinone forms through the transfer of one electron from the fully reduced FMNH , initially formed via NADH-mediated reduction, to the Fe2S2 cluster. This Fe2S2 cluster is not part of the on-path chain of iron-sulfur clusters connecting the FMN of FdsB with the active-site molybdenum-center of FdsA. According to the NADH-bound structure, the nicotinamide ring stacks onto the re-face of the FMN. However, NADH binding significantly reduced the electron density for the isoalloxazine ring of FMN and induced a conformational change in residues of the FMN-binding pocket that display peptide-bond flipping upon NAD(+) binding in proper NADH dehydrogenases.
		+
		+	Crystallographic and kinetic analyses of the FdsBG subcomplex of the cytosolic formate dehydrogenase FdsABG from Cupriavidus necator.,Young T, Niks D, Hakopian S, Tam TK, Yu X, Hille R, Blaha GM J Biol Chem. 2020 Apr 5. pii: RA120.013264. doi: 10.1074/jbc.RA120.013264. PMID:32249211<ref>PMID:32249211</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6vw7" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:00, 8 April 2020

OCA — Wed, 08 Apr 2020 07:00:40 GMT

←Older revision		Revision as of 07:00, 8 April 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6vw7 is ON HOLD~~	+	==Formate Dehydrogenase FdsABG subcomplex FdsBG from C. necator - NADH bound==
-		+	<StructureSection load='6vw7' size='340' side='right'caption='[[6vw7]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~Authors: Young, T.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6vw7]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VW7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VW7 FirstGlance]. <br>
-	~~Description:~~ Formate Dehydrogenase FdsABG subcomplex FdsBG from C. necator -NADH bound	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Formate_dehydrogenase Formate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.2 1.2.1.2] </span></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=6vw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vw7 OCA], [http://pdbe.org/6vw7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vw7 RCSB], [http://www.ebi.ac.uk/pdbsum/6vw7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vw7 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Formate dehydrogenase]]
		+	[[Category: Large Structures]]
	[[Category: Young, T]]		[[Category: Young, T]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Rossmann fold]]
		+	[[Category: Thioredoxin-like]]

OCA at 06:04, 11 March 2020

OCA — Wed, 11 Mar 2020 06:04:18 GMT

←Older revision		Revision as of 06:04, 11 March 2020
Line 5:		Line 5:
	Authors: Young, T.		Authors: Young, T.

-	Description: Formate Dehydrogenase FdsABG subcomplex FdsBG from C. necator -~~reduced state with~~ NADH bound	+	Description: Formate Dehydrogenase FdsABG subcomplex FdsBG from C. necator -NADH bound
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Young, T]]		[[Category: Young, T]]

OCA at 05:37, 4 March 2020

OCA — Wed, 04 Mar 2020 05:37:01 GMT

←Older revision		Revision as of 05:37, 4 March 2020
Line 5:		Line 5:
	Authors: Young, T.		Authors: Young, T.

-	Description: Formate Dehydrogenase FdsABG subcomplex FdsBG from C. necator -reduced state with ~~NAD+~~ bound	+	Description: Formate Dehydrogenase FdsABG subcomplex FdsBG from C. necator -reduced state with NADH bound
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Young, T]]		[[Category: Young, T]]

OCA: Protected "6vw7" [edit=sysop:move=sysop]

OCA — Wed, 26 Feb 2020 08:13:28 GMT

Protected "6vw7" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:13, 26 February 2020

OCA: New page: '''Unreleased structure''' The entry 6vw7 is ON HOLD Authors: Young, T. Description: Formate Dehydrogenase FdsABG subcomplex FdsBG from C. necator -reduced state with NAD+ bound [[Cate...

OCA — Wed, 26 Feb 2020 08:13:27 GMT

New page: '''Unreleased structure''' The entry 6vw7 is ON HOLD Authors: Young, T. Description: Formate Dehydrogenase FdsABG subcomplex FdsBG from C. necator -reduced state with NAD+ bound [[Cate...

New page

'''Unreleased structure'''

The entry 6vw7 is ON HOLD

Authors: Young, T.

Description: Formate Dehydrogenase FdsABG subcomplex FdsBG from C. necator -reduced state with NAD+ bound
[[Category: Unreleased Structures]]
[[Category: Young, T]]