Crystal structure of a Ferredoxin-Flavin Thioredoxin Reductase from Clostridium acetobutylicum at 1.9 A resolution

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report

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Ferredoxin-linked flavoenzyme defines a family of pyridine nucleotide-independent thioredoxin reductases.

Buey, R.M.Fernandez-Justel, D.de Pereda, J.M.Revuelta, J.L.Schurmann, P.Buchanan, B.B.Balsera, M.

(2018) Proc Natl Acad Sci U S A 115: 12967-12972

  • DOI: https://doi.org/10.1073/pnas.1812781115
  • Primary Citation of Related Structures:  
    6GN9, 6GNA, 6GNB, 6GNC, 6GND

  • PubMed Abstract: 

    Ferredoxin-dependent thioredoxin reductase was identified 35 y ago in the fermentative bacterium Clostridium pasteurianum [Hammel KE, Cornwell KL, Buchanan BB (1983) Proc Natl Acad Sci USA 80:3681-3685]. The enzyme, a flavoprotein, was strictly dependent on ferredoxin as reductant and was inactive with either NADPH or NADH. This early work has not been further pursued. We have recently reinvestigated the problem and confirmed that the enzyme, here designated ferredoxin-dependent flavin thioredoxin reductase (FFTR), is a flavoprotein. The enzyme differs from ferredoxin-thioredoxin reductase (FTR), which has a signature [4Fe-4S] cluster, but shows structural similarities to NADP-dependent thioredoxin reductase (NTR). Comparative amino acid sequence analysis showed that FFTR is present in a number of clostridial species, some of which lack both FTR and an archetypal NTR. We have isolated, crystallized, and determined the structural properties of FFTR from a member of this group, Clostridium acetobutylicum , both alone and in complex with Trx. The structures showed an elongated FFTR homodimer, each monomer comprising two Rossmann domains and a noncovalently bound FAD cofactor that exposes the isoalloxazine ring to the solvent. The FFTR structures revealed an alternative domain organization compared with NTR that enables the enzyme to accommodate Fdx rather than NADPH. The results suggest that FFTR exists in a range of conformations with varying degrees of domain separation in solution and that the stacking between the two redox-active groups for the transfer of reducing equivalents results in a profound structural reorganization. A mechanism in accord with the findings is proposed.

  • Organizational Affiliation

    Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas and Universidad de Salamanca, 37007 Salamanca, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin reductase288Clostridium acetobutylicum ATCC 824Mutation(s): 0 
Gene Names: CA_C3082
Find proteins for Q97EM8 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787))
Explore Q97EM8 
Go to UniProtKB:  Q97EM8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ97EM8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
C27 H33 N9 O15 P2
Query on PGE

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C [auth A],
D [auth A]
C6 H14 O4
Query on PEG

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E [auth A],
F [auth A],
G [auth A]
C4 H10 O3
Query on ACT

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
C2 H3 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.221α = 90
b = 40.942β = 103.76
c = 81.093γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Economy and CompetitivenessSpainBFU2016-80343-P

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2019-01-02
    Changes: Data collection, Database references