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6vw8

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Current revision (14:40, 6 March 2024) (edit) (undo)
 
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<StructureSection load='6vw8' size='340' side='right'caption='[[6vw8]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
<StructureSection load='6vw8' size='340' side='right'caption='[[6vw8]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6vw8]] 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=6VW8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VW8 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6vw8]] 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=6VW8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VW8 FirstGlance]. <br>
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</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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
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<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>
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<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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6vw8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vw8 OCA], [https://pdbe.org/6vw8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vw8 RCSB], [https://www.ebi.ac.uk/pdbsum/6vw8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vw8 ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6vw8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vw8 OCA], [http://pdbe.org/6vw8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vw8 RCSB], [http://www.ebi.ac.uk/pdbsum/6vw8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vw8 ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q0KDY3_CUPNH Q0KDY3_CUPNH]
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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.
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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>
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==See Also==
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*[[Formate dehydrogenase 3D structures|Formate dehydrogenase 3D structures]]
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6vw8" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Formate dehydrogenase]]
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[[Category: Cupriavidus necator]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Young, T]]
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[[Category: Young T]]
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[[Category: Oxidoreductase]]
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[[Category: Rossmann fold]]
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[[Category: Thioredoxin-like]]
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Current revision

Formate Dehydrogenase FdsABG subcomplex FdsBG from C. necator

PDB ID 6vw8

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