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 1.1 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: 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 ...

    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

    Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe-Universität Frankfurt am Main, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Caffeyl-CoA reductase-Etf complex subunit CarEA, E396Acetobacterium woodii DSM 1030Mutation(s): 0 
Gene Names: carEAwo_c15740
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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Caffeyl-CoA reductase-Etf complex subunit CarDB, F262Acetobacterium woodii DSM 1030Mutation(s): 0 
Gene Names: carDAwo_c15730
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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Caffeyl-CoA reductase-Etf complex subunit CarCC, D379Acetobacterium woodii DSM 1030Mutation(s): 0 
Gene Names: carCAwo_c15720
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
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-VKOJMFJBAC
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
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

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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