7b0n
From Proteopedia
(Difference between revisions)
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| - | ==== | + | ==A 3.7-angstrom structure of Yarrowia lipolytica complex I with an R121M mutation in NUCM.== |
| - | <StructureSection load='7b0n' size='340' side='right'caption='[[7b0n]]' scene=''> | + | <StructureSection load='7b0n' size='340' side='right'caption='[[7b0n]], [[Resolution|resolution]] 3.70Å' 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= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7b0n]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Yarrowia_lipolytica Yarrowia lipolytica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7B0N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7B0N FirstGlance]. <br> |
| - | </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=7b0n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7b0n OCA], [https://pdbe.org/7b0n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7b0n RCSB], [https://www.ebi.ac.uk/pdbsum/7b0n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7b0n ProSAT]</span></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PE:1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE'>3PE</scene>, <scene name='pdbligand=CDL:CARDIOLIPIN'>CDL</scene>, <scene name='pdbligand=EHZ:~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl]+(3~{S})-3-oxidanyltetradecanethioate'>EHZ</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=PLC:DIUNDECYL+PHOSPHATIDYL+CHOLINE'>PLC</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7b0n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7b0n OCA], [https://pdbe.org/7b0n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7b0n RCSB], [https://www.ebi.ac.uk/pdbsum/7b0n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7b0n ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/S5TMS4_YARLL S5TMS4_YARLL] Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.[RuleBase:RU003640][SAAS:SAAS01013641] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Respiratory complex I (NADH:ubiquinone oxidoreductase), the first enzyme of the electron-transport chain, captures the free energy released by NADH oxidation and ubiquinone reduction to translocate protons across an energy-transducing membrane and drive ATP synthesis during oxidative phosphorylation. The cofactor that transfers the electrons directly to ubiquinone is an iron-sulfur cluster (N2) located in the NDUFS2/NUCM subunit. A nearby arginine residue (R121), which forms part of the second coordination sphere of the N2 cluster, is known to be posttranslationally dimethylated but its functional and structural significance are not known. Here, we show that mutations of this arginine residue (R121M/K) abolish the quinone-reductase activity, concomitant with disappearance of the N2 signature from the electron paramagnetic resonance (EPR) spectrum. Analysis of the cryo-EM structure of NDUFS2-R121M complex I at 3.7 A resolution identified the absence of the cubane N2 cluster as the cause of the dysfunction, within an otherwise intact enzyme. The mutation further induced localized disorder in nearby elements of the quinone-binding site, consistent with the close connections between the cluster and substrate-binding regions. Our results demonstrate that R121 is required for the formation and/or stability of the N2 cluster and highlight the importance of structural analyses for mechanistic interpretation of biochemical and spectroscopic data on complex I variants. | ||
| + | |||
| + | A conserved arginine residue is critical for stabilizing the N2 FeS cluster in mitochondrial complex I.,Hameedi MA, Grba DN, Richardson KH, Jones AJY, Song W, Roessler MM, Wright JJ, Hirst J J Biol Chem. 2021 Jan-Jun;296:100474. doi: 10.1016/j.jbc.2021.100474. Epub 2021 , Feb 26. PMID:33640456<ref>PMID:33640456</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7b0n" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: | + | [[Category: Yarrowia lipolytica]] |
| + | [[Category: Grba D]] | ||
| + | [[Category: Hirst J]] | ||
Revision as of 08:28, 7 December 2022
A 3.7-angstrom structure of Yarrowia lipolytica complex I with an R121M mutation in NUCM.
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