9FDJ

Crystal structure of the NuoEF variant R66G (NuoF) from Aquifex aeolicus bound to NADH under anoxic conditions (short soak)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.158 

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Ligand Structure Quality Assessment 


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Literature

Structural robustness of the NADH binding site in NADH:ubiquinone oxidoreductase (complex I).

Goppert-Asadollahpour, S.Wohlwend, D.Friedrich, T.

(2024) Biochim Biophys Acta Bioenerg 1865: 149491-149491

  • DOI: https://doi.org/10.1016/j.bbabio.2024.149491
  • Primary Citation of Related Structures:  
    9FDJ, 9FDK, 9FDV, 9FE0, 9FE5, 9FE7, 9FE8, 9FEA, 9FIF, 9FIH, 9FII, 9FIJ, 9FIL

  • PubMed Abstract: 

    Energy converting NADH:ubiquinone oxidoreductase, complex I, is the first enzyme of respiratory chains in most eukaryotes and many bacteria. Mutations in genes encoding subunits of human complex I may lead to its dysfunction resulting in a diverse clinical pattern. The effect of mutations on the protein structure is not known. Here, we focus on mutations R88G, E246K, P252R and E377K that are found in subunit NDUFV1 comprising the NADH binding site of complex I. Homologous mutations were introduced into subunit NuoF of Aquifex aeolicus complex I and it was attempted to crystallize variants of the electron input module, NuoEF, with bound substrates in the oxidized and reduced state. The E377K variant did not form crystals most likely due to an improper protein assembly. The architecture of the NADH binding site is hardly affected by the other mutations indicating its unexpected structural robustness. The R88G, E246K and P252R mutations led to small local structural rearrangements that might be related to their pathogenicity. These minor structural changes involve substrate binding, product release and the putative formation of reactive oxygen species. The structural consequences of the mutations as obtained with the bacterial enzyme might thus help to contribute to the understanding of disease causing mutations.


  • Organizational Affiliation

    Albert-Ludwigs-Universität Freiburg, Institut für Biochemie, Albertstr. 21, D-79104 Freiburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit E
A, C
160Aquifex aeolicus VF5Mutation(s): 0 
Gene Names: nuoEaq_574
EC: 7.1.1
UniProt
Find proteins for O66842 (Aquifex aeolicus (strain VF5))
Explore O66842 
Go to UniProtKB:  O66842
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66842
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit F
B, D
434Aquifex aeolicus VF5Mutation(s): 1 
Gene Names: nuoF
UniProt
Find proteins for O66841 (Aquifex aeolicus (strain VF5))
Explore O66841 
Go to UniProtKB:  O66841
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66841
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAI (Subject of Investigation/LOI)
Query on NAI

Download Ideal Coordinates CCD File 
L [auth B],
Z [auth D]
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
K [auth B],
Y [auth D]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
J [auth B],
X [auth D]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
E [auth A],
S [auth C]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
F [auth A]
G [auth A]
H [auth A]
BA [auth D],
CA [auth D],
F [auth A],
G [auth A],
H [auth A],
N [auth B],
T [auth C],
U [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth D],
M [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A],
O [auth B],
V [auth C],
W [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
DA [auth D]
EA [auth D]
FA [auth D]
GA [auth D]
HA [auth D]
DA [auth D],
EA [auth D],
FA [auth D],
GA [auth D],
HA [auth D],
P [auth B],
Q [auth B],
R [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.241α = 90
b = 116.156β = 90
c = 189.026γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyGRK2202; 235777276/RTG

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-17
    Type: Initial release