H71S mutant of the antibiotic resistance protein NimA from Deinococcus radiodurans

Experimental Data Snapshot

  • Resolution: 1.55 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

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Biophysical Characterization and Mutational Analysis of the Antibiotic Resistance Protein Nima from Deinococcus Radiodurans.

Leiros, H.S.Brandsdal, B.O.Mcsweeney, S.M.

(2010) Biochim Biophys Acta 1804: 967

  • DOI: https://doi.org/10.1016/j.bbapap.2010.01.010
  • Primary Citation of Related Structures:  
    2X1J, 2X1K

  • PubMed Abstract: 

    Metronidazole (MTZ) is an antibiotic commonly used to treat anaerobic bacterial infections in humans and animals. Antibiotic resistance toward this class of 5-nitroimidazole (5-Ni) drug derivatives has been related to the Nim genes thought to encode a reductase. Here we report the biophysical characteristics of the NimA protein from Deinococcus radiodurans (DrNimA) binding to MTZ and three other 5-Ni drugs. The interaction energies of the protein and antibiotic are studied by isothermal titration calorimetry (ITC) and with free energy and linear interaction energy (LIE) calculations, where the latter method revealed that the antibiotic binding is mainly of hydrophobic character. ITC measurements further found that one DrNimA dimer has two antibiotic binding sites which were not affected by mutation of the reactive His71. The observed association constants (K(a)) were in the range of 5.1-4910(4)M(-1) and the enthalpy release upon binding to DrNimA for the four drugs studied was relatively low (approximately -1 kJ/mol) but still measurable. The drug binding is mainly entropy driven and along with the hydrophobic drug binding site found by crystallography, this possibly explains the low observed enthalpy values. The effect of the His71 mutation and the presence of MTZ were studied by differential scanning calorimetry (DSC). Native DrNimA is a yellow colored protein where the interaction from His71 to the cofactor is thought to be responsible for the coloring. Mutations of His71 to Ala, Ser, Leu or Asp all gave transparent, colorless protein solutions, and the two mutant crystal structures of DrNimA-H71A and DrNimA-H71S presented revealed no cofactor binding.

  • Organizational Affiliation

    The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway. hanna-kirsti.leiros@chem.uit.no

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NIMA-RELATED PROTEIN216Deinococcus radioduransMutation(s): 1 
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
Experimental Data & Validation

Experimental Data

  • Resolution: 1.55 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.899α = 90
b = 38.969β = 113.89
c = 59.792γ = 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: 2010-11-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description