Crystal structure of NimA from D. radiodurans

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

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Structural Basis of 5-Nitroimidazole Antibiotic Resistance: The Crystal Structure of Nima from Deinococcus Radiodurans

Leiros, H.-K.S.Kozielski-Stuhrmann, S.Kapp, U.Terradot, L.Leonard, G.A.Mcsweeney, S.M.

(2004) J Biol Chem 279: 55840

  • DOI: https://doi.org/10.1074/jbc.M408044200
  • Primary Citation of Related Structures:  
    1W3O, 1W3P, 1W3Q, 1W3R

  • PubMed Abstract: 

    5-Nitroimidazole-based antibiotics are compounds extensively used for treating infections in humans and animals caused by several important pathogens. They are administered as prodrugs, and their activation depends upon an anaerobic 1-electron reduction of the nitro group by a reduction pathway in the cells. Bacterial resistance toward these drugs is thought to be caused by decreased drug uptake and/or an altered reduction efficiency. One class of resistant strains, identified in Bacteroides, has been shown to carry Nim genes (NimA, -B, -C, -D, and -E), which encode for reductases that convert the nitro group on the antibiotic into a non-bactericidal amine. In this paper, we have described the crystal structure of NimA from Deinococcus radiodurans (drNimA) at 1.6 A resolution. We have shown that drNimA is a homodimer in which each monomer adopts a beta-barrel fold. We have identified the catalytically important His-71 along with the cofactor pyruvate and antibiotic binding sites, all of which are found at the monomer-monomer interface. We have reported three additional crystal structures of drNimA, one in which the antibiotic metronidazole is bound to the protein, one with pyruvate covalently bound to His-71, and one with lactate covalently bound to His-71. Based on these structures, a reaction mechanism has been proposed in which the 2-electron reduction of the antibiotic prevents accumulation of the toxic nitro radical. This mechanism suggests that Nim proteins form a new class of reductases, conferring resistance against 5-nitroimidazole-based antibiotics.

  • Organizational Affiliation

    Macromolecular Crystallography Group, European Synchrotron Radiation Facility, BP 220, 6 Rue Jules Horowitz, F-38043 Grenoble Cedex 09, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NIMA-RELATED PROTEIN216Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RW27 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
Explore Q9RW27 
Go to UniProtKB:  Q9RW27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RW27
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.863α = 90
b = 38.947β = 114.25
c = 59.811γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-18
    Type: Initial release
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Other