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



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
  • Structures With Same Primary Citation

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase IVA, F342Escherichia 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
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Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*TP*AP*GP*GP*(RDG)P*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')B, G18synthetic construct
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*TP*A*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')C, H18synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1FZ
Query on 1FZ

Download CCD File 
A, F
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 CCD File 
A, F
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 

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