Structure of a Deazaflavin-dependent nitroreductase from Nocardia farcinica, with co-factor F420

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

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Structure of Ddn, the deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824.

Cellitti, S.E.Shaffer, J.Jones, D.H.Mukherjee, T.Gurumurthy, M.Bursulaya, B.Boshoff, H.I.Choi, I.Nayyar, A.Lee, Y.S.Cherian, J.Niyomrattanakit, P.Dick, T.Manjunatha, U.H.Barry, C.E.Spraggon, G.Geierstanger, B.H.

(2012) Structure 20: 101-112

  • DOI: https://doi.org/10.1016/j.str.2011.11.001
  • Primary Citation of Related Structures:  
    3R5L, 3R5P, 3R5R, 3R5W, 3R5Y, 3R5Z

  • PubMed Abstract: 

    Tuberculosis continues to be a global health threat, making bicyclic nitroimidazoles an important new class of therapeutics. A deazaflavin-dependent nitroreductase (Ddn) from Mycobacterium tuberculosis catalyzes the reduction of nitroimidazoles such as PA-824, resulting in intracellular release of lethal reactive nitrogen species. The N-terminal 30 residues of Ddn are functionally important but are flexible or access multiple conformations, preventing structural characterization of the full-length, enzymatically active enzyme. Several structures were determined of a truncated, inactive Ddn protein core with and without bound F(420) deazaflavin coenzyme as well as of a catalytically competent homolog from Nocardia farcinica. Mutagenesis studies based on these structures identified residues important for binding of F(420) and PA-824. The proposed orientation of the tail of PA-824 toward the N terminus of Ddn is consistent with current structure-activity relationship data.

  • Organizational Affiliation

    Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121-1125, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized protein
A, B, C, D
147Nocardia farcinicaMutation(s): 0 
Gene Names: NFA_33440
Find proteins for Q5YUF0 (Nocardia farcinica (strain IFM 10152))
Explore Q5YUF0 
Go to UniProtKB:  Q5YUF0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5YUF0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.956α = 90
b = 71.956β = 90
c = 115.469γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
BOSdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-18
    Type: Initial release
  • Version 1.1: 2012-03-21
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description