4Q45

DNA Polymerase- damaged DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Unique structural features in DNA polymerase IV enable efficient bypass of the N2 adduct induced by the nitrofurazone antibiotic

Kottur, J.Sharma, A.Gore, K.R.Narayanan, N.Samanta, B.Pradeepkumar, P.I.Nair, D.T.

(2015) Structure 23: 56-67

  • DOI: 10.1016/j.str.2014.10.019
  • Primary Citation of Related Structures:  
    4Q43, 4Q44, 4Q45

  • PubMed Abstract: 
  • The reduction in the efficacy of therapeutic antibiotics represents a global problem of increasing intensity and concern. Nitrofuran antibiotics act primarily through the formation of covalent adducts at the N(2) atom of the deoxyguanosine nucleotide in genomic DNA ...

    The reduction in the efficacy of therapeutic antibiotics represents a global problem of increasing intensity and concern. Nitrofuran antibiotics act primarily through the formation of covalent adducts at the N(2) atom of the deoxyguanosine nucleotide in genomic DNA. These adducts inhibit replicative DNA polymerases (dPols), leading to the death of the prokaryote. N(2)-furfuryl-deoxyguanosine (fdG) represents a stable structural analog of the nitrofuran-induced adducts. Unlike other known dPols, DNA polymerase IV (PolIV) from E. coli can bypass the fdG adduct accurately with high catalytic efficiency. This property of PolIV is central to its role in reducing the sensitivity of E. coli toward nitrofuran antibiotics such as nitrofurazone (NFZ). We present the mechanism used by PolIV to bypass NFZ-induced adducts and thus improve viability of E. coli in the presence of NFZ. Our results can be used to develop specific inhibitors of PolIV that may potentiate the activity of nitrofuran antibiotics.


    Organizational Affiliation

    Regional Centre for Biotechnology, 180, Udyog Vihar, Phase 1, Gurgaon 122016, India; National Centre for Biological Sciences (NCBS-TIFR), GKVK Campus, Bellary Road, Bangalore 560065, India. Electronic address: deepak@rcb.res.in.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase IVB [auth A], A [auth F]342Escherichia coli K-12Mutation(s): 0 
Gene Names: dinBdinPb0231JW0221
EC: 2.7.7.7
Find proteins for Q47155 (Escherichia coli (strain K12))
Explore Q47155 
Go to UniProtKB:  Q47155
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*CP*TP*AP*GP*GP*(RDG)P*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')C [auth G], E [auth B]18synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*CP*TP*A*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')D [auth H], F [auth C]18synthetic construct
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      1FZ
      Query on 1FZ

      Download Ideal Coordinates CCD File 
      G [auth F], J [auth A]5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine
      C10 H18 N3 O13 P3
      YRKUYVYMPXAOAT-XLPZGREQSA-N
       Ligand Interaction
      MG
      Query on MG

      Download Ideal Coordinates CCD File 
      H [auth F], I [auth F], K [auth A], L [auth A]MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.18 Å
      • R-Value Free: 0.257 
      • R-Value Work: 0.212 
      • R-Value Observed: 0.214 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 85.5α = 90
      b = 57.9β = 90.44
      c = 111.04γ = 90
      Software Package:
      Software NamePurpose
      PHASERphasing
      PHENIXrefinement
      MOSFLMdata reduction
      SCALAdata scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2015-05-06
        Type: Initial release