FMN-dependent Nitroreductase (CDR20291_0767) from Clostridium difficile R20291

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.190 

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This is version 1.3 of the entry. See complete history


Crystal structures of two nitroreductases from hypervirulent Clostridium difficile and functionally related interactions with the antibiotic metronidazole.

Wang, B.Powell, S.M.Hessami, N.Najar, F.Z.Thomas, L.M.Karr, E.A.West, A.H.Richter-Addo, G.B.

(2016) Nitric Oxide 60: 32-39

  • DOI: https://doi.org/10.1016/j.niox.2016.09.003
  • Primary Citation of Related Structures:  
    5J62, 5J6C

  • PubMed Abstract: 

    Nitroreductases (NRs) are flavin mononucleotide (FMN)-dependent enzymes that catalyze the biotransformation of organic nitro compounds (RNO 2 ; R = alkyl, aryl) to the nitroso RN=O, hydroxylamino RNHOH, or amine RNH 2 derivatives. Metronidazole (Mtz) is a nitro-containing antibiotic that is commonly prescribed for lower-gut infections caused by the anaerobic bacterium Clostridium difficile. C. difficile infections rank number one among hospital acquired infections, and can result in diarrhea, severe colitis, or even death. Although NRs have been implicated in Mtz resistance of C. difficile, no NRs have been characterized from the hypervirulent R20291 strain of C. difficile. We report the first expression, purification, and three-dimensional X-ray crystal structures of two NRs from the C. difficile R20291 strain. The X-ray crystal structures of the two NRs were solved to 2.1 Å resolution. Their homodimeric structures exhibit the classic NR α+β fold, with each protomer binding one FMN cofactor near the dimer interface. Functional assays demonstrate that these two NRs metabolize Mtz with associated re-oxidation of the proteins. Importantly, these results represent the first isolation and characterization of NRs from the hypervirulent R20291 strain of relevance to organic RNO 2 (e.g., Mtz) metabolism.

  • Organizational Affiliation

    Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman 73019, United States; Department of Chemistry and Biochemistry, University of Oklahoma, Norman 73019, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative reductase
A, B
201Clostridioides difficile R20291Mutation(s): 0 
Gene Names: CDR20291_0767
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.908α = 90
b = 70.732β = 90
c = 87.882γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Price Family FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-10-05
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description