8bqg - Revision history

OCA at 13:39, 1 February 2024

OCA — Thu, 01 Feb 2024 13:39:57 GMT

←Older revision		Revision as of 13:39, 1 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8bqg]] 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=8BQG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BQG FirstGlance]. <br>		<table><tr><td colspan='2'>[[8bqg]] 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=8BQG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BQG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=MGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>MGD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=W:TUNGSTEN+ION'>W</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]] 1.946Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=MGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>MGD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=W:TUNGSTEN+ION'>W</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=8bqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8bqg OCA], [https://pdbe.org/8bqg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8bqg RCSB], [https://www.ebi.ac.uk/pdbsum/8bqg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8bqg 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=8bqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8bqg OCA], [https://pdbe.org/8bqg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8bqg RCSB], [https://www.ebi.ac.uk/pdbsum/8bqg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8bqg ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 8bqg" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 8bqg" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Formate dehydrogenase 3D structures\|Formate dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:28, 18 January 2023

OCA — Wed, 18 Jan 2023 07:28:39 GMT

←Older revision		Revision as of 07:28, 18 January 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 8bqg is ~~ON HOLD until Paper~~ Publication	+	==W-formate dehydrogenase from Desulfovibrio vulgaris - Soaking with Formate 1 min==
		+	<StructureSection load='8bqg' size='340' side='right'caption='[[8bqg]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8bqg]] 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=8BQG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BQG FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=MGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>MGD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=W:TUNGSTEN+ION'>W</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=8bqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8bqg OCA], [https://pdbe.org/8bqg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8bqg RCSB], [https://www.ebi.ac.uk/pdbsum/8bqg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8bqg ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q72EJ1_DESVH Q72EJ1_DESVH]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Metal-dependent formate dehydrogenases (Fdh) catalyze the reversible conversion of CO(2) to formate, with unrivalled efficiency and selectivity. However, the key catalytic aspects of these enzymes remain unknown, preventing us from fully benefiting from their capabilities in terms of biotechnological applications. Here, we report a time-resolved characterization by X-ray crystallography of the Desulfovibrio vulgaris Hildenborough SeCys/W-Fdh during formate oxidation. The results allowed us to model five different intermediate structures and to chronologically map the changes occurring during enzyme reduction. Formate molecules were assigned for the first time to populate the catalytic pocket of a Fdh. Finally, the redox reversibility of DvFdhAB in crystals was confirmed by reduction and reoxidation structural studies.

-	~~Authors~~:	+	Tracking W-Formate Dehydrogenase Structural Changes During Catalysis and Enzyme Reoxidation.,Vilela-Alves G, Manuel RR, Oliveira AR, Pereira IC, Romao MJ, Mota C Int J Mol Sci. 2022 Dec 28;24(1):476. doi: 10.3390/ijms24010476. PMID:36613918<ref>PMID:36613918</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8bqg" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Desulfovibrio vulgaris str. Hildenborough]]
		+	[[Category: Large Structures]]
		+	[[Category: Manuel RR]]
		+	[[Category: Mota C]]
		+	[[Category: Oliveira AR]]
		+	[[Category: Pereira IC]]
		+	[[Category: Romao MJ]]
		+	[[Category: Vilela-Alves G]]

OCA at 06:02, 21 December 2022

OCA — Wed, 21 Dec 2022 06:02:02 GMT

←Older revision		Revision as of 06:02, 21 December 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8bqg is ON HOLD	+	The entry 8bqg is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "8bqg" [edit=sysop:move=sysop]

OCA — Wed, 30 Nov 2022 08:24:37 GMT

Protected "8bqg" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:24, 30 November 2022

OCA: New page: '''Unreleased structure''' The entry 8bqg is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 30 Nov 2022 08:24:36 GMT

New page: '''Unreleased structure''' The entry 8bqg is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8bqg is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]