Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 67967.65 
• Atom Count: 4783 
• Residue Count: 609 
• Unique protein chains: 2

4KPU

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

• DOI: 10.2210/pdb4KPU/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Acidaminococcus fermentans (strain ATCC 25085 / DSM 20731 / VR4)
• Expression System: Escherichia coli


• Deposited: 2013-05-14 Released: 2014-01-15 
• Deposition Author(s): Mowafy, A.M., Chowdhury, N.P., Demmer, J., Upadhyay, V., Kolzer, S., Jayamani, E., Kahnt, J., Demmer, U., Ermler, U., Buckel, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.191 
• R-Value Work: 0.161 

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

• PubMed: 24379410 
• DOI: 10.1074/jbc.M113.521013
• Primary Citation of Related Structures:  
  4L2I, 4L1F


• 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Electron transfer flavoprotein alpha subunit	A	346	Acidaminococcus fermentans (strain ATCC 25085 / DSM 20731 / VR4)	Mutation(s): 0
Find proteins for D2RIQ3 (Acidaminococcus fermentans (strain ATCC 25085 / DSM 20731 / VR4)) Go to UniProtKB:  D2RIQ3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Electron transfer flavoprotein alpha/beta-subunit	B	263	Acidaminococcus fermentans (strain ATCC 25085 / DSM 20731 / VR4)	Mutation(s): 0
Find proteins for D2RIQ2 (Acidaminococcus fermentans (strain ATCC 25085 / DSM 20731 / VR4)) Go to UniProtKB:  D2RIQ2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
FAD	A, B	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.191 
• R-Value Work: 0.161 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 80.180	α = 90.00
b = 84.890	β = 90.00
c = 106.730	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
HKL-2000	data collection
REFMAC	refinement
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-05-14 
• Released Date: 2014-01-15 
• Deposition Author(s): Mowafy, A.M., Chowdhury, N.P., Demmer, J., Upadhyay, V., Kolzer, S., Jayamani, E., Kahnt, J., Demmer, U., Ermler, U., Buckel, W.

Revision History 

• Version 1.0: 2014-01-15
  Type: Initial release
• Version 1.1: 2014-03-12
  Type: Database references