4L1F

Electron transferring flavoprotein of Acidaminococcus fermentans: Towards a mechanism of flavin-based electron bifurcation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Studies on the Mechanism of Electron Bifurcation Catalyzed by Electron Transferring Flavoprotein (Etf) and Butyryl-CoA Dehydrogenase (Bcd) of Acidaminococcus fermentans.

Chowdhury, N.P.Mowafy, A.M.Demmer, J.K.Upadhyay, V.Koelzer, S.Jayamani, E.Kahnt, J.Hornung, M.Demmer, U.Ermler, U.Buckel, W.

(2014) J Biol Chem 289: 5145-5157

  • DOI: https://doi.org/10.1074/jbc.M113.521013
  • Primary Citation of Related Structures:  
    4KPU, 4L1F, 4L2I

  • PubMed Abstract: 

    Electron bifurcation is a fundamental strategy of energy coupling originally discovered in the Q-cycle of many organisms. Recently a flavin-based electron bifurcation has been detected in anaerobes, first in clostridia and later in acetogens and methanogens. It enables anaerobic bacteria and archaea to reduce the low-potential [4Fe-4S] clusters of ferredoxin, which increases the efficiency of the substrate level and electron transport phosphorylations. Here we characterize the bifurcating electron transferring flavoprotein (EtfAf) and butyryl-CoA dehydrogenase (BcdAf) of Acidaminococcus fermentans, which couple the exergonic reduction of crotonyl-CoA to butyryl-CoA to the endergonic reduction of ferredoxin both with NADH. EtfAf contains one FAD (α-FAD) in subunit α and a second FAD (β-FAD) in subunit β. The distance between the two isoalloxazine rings is 18 Å. The EtfAf-NAD(+) complex structure revealed β-FAD as acceptor of the hydride of NADH. The formed β-FADH(-) is considered as the bifurcating electron donor. As a result of a domain movement, α-FAD is able to approach β-FADH(-) by about 4 Å and to take up one electron yielding a stable anionic semiquinone, α-FAD, which donates this electron further to Dh-FAD of BcdAf after a second domain movement. The remaining non-stabilized neutral semiquinone, β-FADH(•), immediately reduces ferredoxin. Repetition of this process affords a second reduced ferredoxin and Dh-FADH(-) that converts crotonyl-CoA to butyryl-CoA.


  • Organizational Affiliation

    From the Laboratorium für Mikrobiologie, Fachbereich Biologie and SYNMIKRO, Philipps-Universität, 35032 Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl-CoA dehydrogenase domain protein
A, B
383Acidaminococcus fermentans DSM 20731Mutation(s): 0 
UniProt
Find proteins for D2RL84 (Acidaminococcus fermentans (strain ATCC 25085 / DSM 20731 / CCUG 9996 / CIP 106432 / VR4))
Explore D2RL84 
Go to UniProtKB:  D2RL84
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2RL84
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COS
Query on COS

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
COENZYME A PERSULFIDE
C21 H36 N7 O16 P3 S2
REVPHPVBPSIEKM-IBOSZNHHSA-N
FAD
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
J [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
PDO
Query on PDO

Download Ideal Coordinates CCD File 
F [auth A]1,3-PROPANDIOL
C3 H8 O2
YPFDHNVEDLHUCE-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A],
G [auth A],
K [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.1α = 90
b = 141.4β = 90
c = 64.1γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SHARPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-15
    Type: Initial release
  • Version 1.1: 2014-03-12
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations