5OL2

The electron transferring flavoprotein/butyryl-CoA dehydrogenase complex from Clostridium difficile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The semiquinone swing in the bifurcating electron transferring flavoprotein/butyryl-CoA dehydrogenase complex from Clostridium difficile.

Demmer, J.K.Pal Chowdhury, N.Selmer, T.Ermler, U.Buckel, W.

(2017) Nat Commun 8: 1577-1577

  • DOI: 10.1038/s41467-017-01746-3

  • PubMed Abstract: 
  • The electron transferring flavoprotein/butyryl-CoA dehydrogenase (EtfAB/Bcd) catalyzes the reduction of one crotonyl-CoA and two ferredoxins by two NADH within a flavin-based electron-bifurcating process. Here we report on the X-ray structure of the ...

    The electron transferring flavoprotein/butyryl-CoA dehydrogenase (EtfAB/Bcd) catalyzes the reduction of one crotonyl-CoA and two ferredoxins by two NADH within a flavin-based electron-bifurcating process. Here we report on the X-ray structure of the Clostridium difficile (EtfAB/Bcd)4 complex in the dehydrogenase-conducting D-state, α-FAD (bound to domain II of EtfA) and δ-FAD (bound to Bcd) being 8 Å apart. Superimposing Acidaminococcus fermentans EtfAB onto C. difficile EtfAB/Bcd reveals a rotation of domain II of nearly 80°. Further rotation by 10° brings EtfAB into the bifurcating B-state, α-FAD and β-FAD (bound to EtfB) being 14 Å apart. This dual binding mode of domain II, substantiated by mutational studies, resembles findings in non-bifurcating EtfAB/acyl-CoA dehydrogenase complexes. In our proposed mechanism, NADH reduces β-FAD, which bifurcates. One electron goes to ferredoxin and one to α-FAD, which swings over to reduce δ-FAD to the semiquinone. Repetition affords a second reduced ferredoxin and δ-FADH-, which reduces crotonyl-CoA.


    Organizational Affiliation

    Max-Planck-Institut für Biophysik, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Electron transfer flavoprotein large subunit
A, D
331Clostridioides difficile ATCC 9689 = DSM 1296Mutation(s): 0 
Gene Names: etfA2
Find proteins for A0A125V455 (Clostridioides difficile ATCC 9689 = DSM 1296)
Go to UniProtKB:  A0A125V455
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Electron transfer flavoprotein small subunit
B, E
260Clostridioides difficile ATCC 9689 = DSM 1296Mutation(s): 0 
Gene Names: etfB2
Find proteins for A0A125V3V6 (Clostridioides difficile ATCC 9689 = DSM 1296)
Go to UniProtKB:  A0A125V3V6
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Acyl-CoA dehydrogenase
C, F
378Clostridioides difficile ATCC 9689 = DSM 1296Mutation(s): 0 
Gene Names: bcd2
EC: 1.3.8.1
Find proteins for A0A125V4E7 (Clostridioides difficile ATCC 9689 = DSM 1296)
Go to UniProtKB:  A0A125V4E7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B, C, D, E, F
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, C, D, E, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
COS
Query on COS

Download SDF File 
Download CCD File 
C, F
COENZYME A PERSULFIDE
C21 H36 N7 O16 P3 S2
REVPHPVBPSIEKM-IBOSZNHHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.209 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 177.060α = 90.00
b = 177.060β = 90.00
c = 493.150γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
German Research FoundationGermany--
SYNMIKROGermany--

Revision History 

  • Version 1.0: 2017-11-29
    Type: Initial release