6FAH

Molecular basis of the flavin-based electron-bifurcating caffeyl-CoA reductase reaction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.13 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Molecular basis of the flavin-based electron-bifurcating caffeyl-CoA reductase reaction.

Demmer, J.K.Bertsch, J.Oppinger, C.Wohlers, H.Kayastha, K.Demmer, U.Ermler, U.Muller, V.

(2018) FEBS Lett 592: 332-342

  • DOI: https://doi.org/10.1002/1873-3468.12971
  • Primary Citation of Related Structures:  
    6FAH

  • PubMed Abstract: 

    Flavin-based electron bifurcation (FBEB) is a recently discovered mode of energy coupling in anaerobic microorganisms. The electron-bifurcating caffeyl-CoA reductase (CarCDE) catalyzes the reduction of caffeyl-CoA and ferredoxin by oxidizing NADH. The 3.5 Å structure of the heterododecameric Car(CDE) 4 complex of Acetobacterium woodii, presented here, reveals compared to other electron-transferring flavoprotein/acyl dehydrogenase family members an additional ferredoxin-like domain with two [4Fe-4S] clusters N-terminally fused to CarE. It might serve, in vivo, as specific adaptor for the physiological electron acceptor. Kinetic analysis of a CarCDE(∆Fd) complex indicates the bypassing of the ferredoxin-like domain by artificial electron acceptors. Site-directed mutagenesis studies substantiated the crucial role of the C-terminal arm of CarD and of ArgE203, hydrogen-bonded to the bifurcating FAD, for FBEB.


  • Organizational Affiliation

    Max-Planck-Institut für Biophysik, Frankfurt am Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Caffeyl-CoA reductase-Etf complex subunit CarE
A, E
396Acetobacterium woodii DSM 1030Mutation(s): 0 
EC: 1.3.1.108
UniProt
Find proteins for H6LGM8 (Acetobacterium woodii (strain ATCC 29683 / DSM 1030 / JCM 2381 / KCTC 1655 / WB1))
Explore H6LGM8 
Go to UniProtKB:  H6LGM8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH6LGM8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Caffeyl-CoA reductase-Etf complex subunit CarD
B, F
262Acetobacterium woodii DSM 1030Mutation(s): 0 
EC: 1.3.1.108
UniProt
Find proteins for H6LGM7 (Acetobacterium woodii (strain ATCC 29683 / DSM 1030 / JCM 2381 / KCTC 1655 / WB1))
Explore H6LGM7 
Go to UniProtKB:  H6LGM7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH6LGM7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Caffeyl-CoA reductase-Etf complex subunit CarC
C, D
379Acetobacterium woodii DSM 1030Mutation(s): 0 
EC: 1.3.1.108
UniProt
Find proteins for H6LGM6 (Acetobacterium woodii (strain ATCC 29683 / DSM 1030 / JCM 2381 / KCTC 1655 / WB1))
Explore H6LGM6 
Go to UniProtKB:  H6LGM6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH6LGM6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
G [auth A]
J [auth B]
K [auth C]
Q [auth D]
T [auth E]
G [auth A],
J [auth B],
K [auth C],
Q [auth D],
T [auth E],
W [auth F]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
U [auth E],
V [auth E]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
L [auth C]
M [auth C]
N [auth C]
O [auth C]
P [auth C]
L [auth C],
M [auth C],
N [auth C],
O [auth C],
P [auth C],
R [auth D],
S [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.13 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 213.74α = 90
b = 144.26β = 98.93
c = 102.84γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-24
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description