6FAH | pdb_00006fah

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 (Depositor), 0.293 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.237 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 231.36 kDa 
  • Atom Count: 15,985 
  • Modeled Residue Count: 2,064 
  • Deposited Residue Count: 2,074 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:
|  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:
|  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:
|  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 (Depositor), 0.293 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.237 (Depositor) 
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

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Ligand Structure Quality Assessment 


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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
  • Version 1.3: 2025-10-01
    Changes: Advisory, Derived calculations, Structure summary