Journal: J Biol Chem / Year: 2021 Title: A conserved arginine residue is critical for stabilizing the N2 FeS cluster in mitochondrial complex I. Authors: Mikhail A Hameedi / Daniel N Grba / Katherine H Richardson / Andrew J Y Jones / Wei Song / Maxie M Roessler / John J Wright / Judy Hirst / Abstract: 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 ...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 Å 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.
History
Deposition
Nov 20, 2020
-
Header (metadata) release
Mar 10, 2021
-
Map release
Mar 10, 2021
-
Update
Dec 7, 2022
-
Current status
Dec 7, 2022
Processing site: PDBe / Status: Released
-
Structure visualization
Movie
Surface view with section colored by density value
Name: NADH-ubiquinone oxidoreductase chain 1 / type: protein_or_peptide / ID: 8 Details: ligands (PLC)(3PE)(3PE) are not in the polypeptide sequence (FME) is at the start of the polypeptide sequence Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Macromolecule #9: Subunit NUIM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
Macromolecule
Name: Subunit NUIM of protein NADH:Ubiquinone Oxidoreductase (Complex I) type: protein_or_peptide / ID: 9 Details: Ligands (SF4)(SF4) are not in the polypeptide sequence Number of copies: 1 / Enantiomer: LEVO / EC number: NADH dehydrogenase
Name: NADH-ubiquinone oxidoreductase chain 5 / type: protein_or_peptide / ID: 12 Details: ligands (PLC)(3PE)(3PE)(3PE)(3PE) are not in the polypeptide sequence (FME) is in the polypeptide sequence Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Name: NADH-ubiquinone oxidoreductase chain 4 / type: protein_or_peptide / ID: 13 Details: ligands (CDL)(PLC)(PLC)(3PE)(LMT)(3PE) are not in the polypeptide sequence (FME) is in the polypeptide sequence Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Name: NADH dehydrogenase subunit 2 / type: protein_or_peptide / ID: 14 Details: ligands (PLC)(PLC)(3PE) are not in the polypeptide sequence (FME) is in the polypeptide sequence Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Macromolecule #15: Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)
Macromolecule
Name: Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I) type: protein_or_peptide / ID: 15 / Details: (CDL) is not in the polypeptide sequence / Number of copies: 1 / Enantiomer: LEVO
Source (natural)
Organism: Yarrowia lipolytica (yeast)
Molecular weight
Theoretical: 18.588209 KDa
Recombinant expression
Organism: Yarrowia lipolytica (yeast)
Sequence
String:
MSSSTPLVKT SVNYSYGDYP LIDADPHFKR VVGYMRPSDY GVIGLATAAL PAGICFAEWL DPVKGKFARP SVKFLRVATM LGFAVGFGA AYARSSLRFF GVTENAREYK KDEAQMAARK AAGLEPYGTS SLTPELQEIA AKNSAHSIAG LFIFPWFNFV N HPYHGREQ K
+
Macromolecule #16: Epimerase domain-containing protein
Macromolecule
Name: Epimerase domain-containing protein / type: protein_or_peptide / ID: 16 / Details: (NDP) is not in the polypeptide chain / Number of copies: 1 / Enantiomer: LEVO
Macromolecule #17: Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)
Macromolecule
Name: Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I) type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)
Organism: Yarrowia lipolytica (yeast)
Molecular weight
Theoretical: 18.65608 KDa
Recombinant expression
Organism: Yarrowia lipolytica (yeast)
Sequence
String:
MLSRSLRQLS QPSVRSFATS ARLLQKKDVP EVGVNLDNVP AHEIVSGAPA ELSRNRVVRI YQQAKPATQS GEYGTFAWRL DWDIVDVAN RWENDLIGWQ SSGDYMQATQ MKFTSKESAI KFANKQGWDF YIQEPHHRKF RVKQYANNFV HSYGKLKHIR T K
+
Macromolecule #18: zf-CHCC domain-containing protein
Macromolecule
Name: zf-CHCC domain-containing protein / type: protein_or_peptide / ID: 18 / Details: (ZN) is not in the polypeptide chain / Number of copies: 1 / Enantiomer: LEVO
Name: Acyl carrier protein / type: protein_or_peptide / ID: 20 / Details: (EHZ) is not in the polypeptide chain / Number of copies: 1 / Enantiomer: LEVO
Source (natural)
Organism: Yarrowia lipolytica (yeast)
Molecular weight
Theoretical: 8.821807 KDa
Recombinant expression
Organism: Yarrowia lipolytica (yeast)
Sequence
String:
RPDAEKRIAA VLESFDKISN PAAITPTASF AKDLNLDSLD TVEVVVAIEE EFGIEIPDKE ADEIKSVNQA VEYILAQPDA K
+
Macromolecule #21: Acyl carrier protein
Macromolecule
Name: Acyl carrier protein / type: protein_or_peptide / ID: 21 / Details: (EHZ) is not in the polypeptide chain / Number of copies: 1 / Enantiomer: LEVO
Macromolecule #28: subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
Macromolecule
Name: subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I) type: protein_or_peptide / ID: 28 Details: ligands (CDL)(3PE)(3PE) are not in the polypeptide chain Number of copies: 1 / Enantiomer: LEVO
Model: UltrAuFoil / Material: GOLD / Support film - Material: GOLD / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 90 sec. / Details: PEG-thiol treated
Vitrification
Cryogen name: ETHANE
-
Electron microscopy
Microscope
FEI TITAN KRIOS
Image recording
Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2241 / Average electron dose: 48.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi