5C5J | pdb_00005c5j

Poymerase Nucleotide complex

• PDB DOI: https://doi.org/10.2210/pdb5C5J/pdb
• NAKB: 5C5J

• Classification: Transferase/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-06-20 Released: 2016-06-22 
• Deposition Author(s): Nair, D.T., Kottur, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.274 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Reactive Oxygen Species Play an Important Role in the Bactericidal Activity of Quinolone Antibiotics

Kottur, J., Nair, D.T.

(2016) Angew Chem Int Ed Engl 55: 2397-2400

• PubMed: 26757158 
• DOI: https://doi.org/10.1002/anie.201509340
• Primary Citation Related Structures: 
  5C5J


• PubMed Abstract: 
  

  Recent studies posit that reactive oxygen species (ROS) contribute to the cell lethality of bactericidal antibiotics. However, this conjecture has been challenged and remains controversial. To resolve this controversy, we adopted a strategy that involves DNA polymerase IV (PolIV). The nucleotide pool of the cell gets oxidized by ROS and PolIV incorporates the damaged nucleotides (especially 8oxodGTP) into the genome, which results in death of the bacteria. By using a combination of structural and biochemical tools coupled with growth assays, it was shown that selective perturbation of the 8oxodGTP incorporation activity of PolIV results in considerable enhancement of the survival of bacteria in the presence of the norfloxacin antibiotic. Our studies therefore indicate that ROS induced in bacteria by the presence of antibiotics in the environment contribute significantly to cell lethality.

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Organizational Affiliation: 
• Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, India.
Manipal University, Madhav Nagar, Manipal, 576104, India.
Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, India. [e-mail].
National Centre for Biological Sciences, NCBS-TIFR, GKVK Campus, Bangalore, 560065, India. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 101.71 kDa 
• Atom Count: 7,204 
• Modeled Residue Count: 751 
• Deposited Residue Count: 776 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase IV	A [auth F], B [auth A]	352	Escherichia coli	Mutation(s): 0  Gene Names: dinB EC: 2.7.7.7
UniProt
Find proteins for Q47155 (Escherichia coli (strain K12)) Explore Q47155  Go to UniProtKB:  Q47155

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')	C [auth G], D [auth H], E [auth B], F [auth C]	18	Escherichia coli

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8GT	G [auth A]	8-OXO-GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O15 P3 JCHLKIQZUXYLPW-UMMCILCDSA-N
MG	H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.274 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.45	α = 90
b = 57.38	β = 94.51
c = 110.64	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-22 
Deposition Author(s): Nair, D.T., Kottur, J.

Revision History  

• Version 1.0: 2016-06-22
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description