6HLI

wild-type NuoEF from Aquifex aeolicus - reduced form bound to NAD+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A mechanism to prevent production of reactive oxygen species by Escherichia coli respiratory complex I.

Schulte, M.Frick, K.Gnandt, E.Jurkovic, S.Burschel, S.Labatzke, R.Aierstock, K.Fiegen, D.Wohlwend, D.Gerhardt, S.Einsle, O.Friedrich, T.

(2019) Nat Commun 10: 2551-2551

  • DOI: 10.1038/s41467-019-10429-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Respiratory complex I plays a central role in cellular energy metabolism coupling NADH oxidation to proton translocation. In humans its dysfunction is associated with degenerative diseases. Here we report the structure of the electron input part of A ...

    Respiratory complex I plays a central role in cellular energy metabolism coupling NADH oxidation to proton translocation. In humans its dysfunction is associated with degenerative diseases. Here we report the structure of the electron input part of Aquifex aeolicus complex I at up to 1.8 Å resolution with bound substrates in the reduced and oxidized states. The redox states differ by the flip of a peptide bond close to the NADH binding site. The orientation of this peptide bond is determined by the reduction state of the nearby [Fe-S] cluster N1a. Fixation of the peptide bond by site-directed mutagenesis led to an inactivation of electron transfer and a decreased reactive oxygen species (ROS) production. We suggest the redox-gated peptide flip to represent a previously unrecognized molecular switch synchronizing NADH oxidation in response to the redox state of the complex as part of an intramolecular feed-back mechanism to prevent ROS production.


    Organizational Affiliation

    Boehringer Ingelheim Pharma GmbH & Co. KG, Lead Identification and Optimization Sup, 88397, Biberach, Germany.,BIOSS Centre for Biological Signalling Studies, Schänzlestrasse 1, 79104, Freiburg, Germany.,Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany. Friedrich@bio.chemie.uni-freiburg.de.,Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit E
A, C
160Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: nuoE
EC: 7.1.1.-
Find proteins for O66842 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O66842
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit F
B, D
434Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: nuoF
EC: 7.1.1.-
Find proteins for O66841 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O66841
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
B, D
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FMN
Query on FMN

Download SDF File 
Download CCD File 
B, D
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
B, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
FES
Query on FES

Download SDF File 
Download CCD File 
A, C
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.590α = 90.00
b = 116.040β = 90.00
c = 189.875γ = 90.00
Software Package:
Software NamePurpose
AutoPROCdata scaling
BUSTERrefinement
MOLREPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyRTG 2202

Revision History 

  • Version 1.0: 2019-06-26
    Type: Initial release