Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 67.97 kDa 
• Atom Count: 5380 
• Modelled Residue Count: 601 
• Deposited Residue Count: 609 
• Unique protein chains: 2

4KPU

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

• PDB DOI: 10.2210/pdb4KPU/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Acidaminococcus fermentans DSM 20731
• Expression System: Escherichia coli
• Mutation(s): No 


• 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: 1.60 Å
• R-Value Free: 0.191 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 

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:  
  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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Electron transfer flavoprotein alpha subunit	A	346	Acidaminococcus fermentans DSM 20731	Mutation(s): 0  Gene Names: Acfer_0555, Acfer_0556
UniProt
Find proteins for D2RIQ3 (Acidaminococcus fermentans (strain ATCC 25085 / DSM 20731 / CCUG 9996 / CIP 106432 / VR4)) Explore D2RIQ3  Go to UniProtKB:  D2RIQ3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Electron transfer flavoprotein alpha/beta-subunit	B	263	Acidaminococcus fermentans DSM 20731	Mutation(s): 0  Gene Names: Acfer_0555, Acfer_0556
UniProt
Find proteins for D2RIQ2 (Acidaminococcus fermentans (strain ATCC 25085 / DSM 20731 / CCUG 9996 / CIP 106432 / VR4)) Explore D2RIQ2  Go to UniProtKB:  D2RIQ2

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.191 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.18	α = 90
b = 84.89	β = 90
c = 106.73	γ = 90

Software Package:

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

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
  Changes: Database references