5H58

Structural and dynamics studies of the TetR family protein, CprB from Streptomyces coelicolor in complex with its biological operator sequence


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.991 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and dynamics studies of the TetR family protein, CprB from Streptomyces coelicolor in complex with its biological operator sequence

Bhukya, H.Jana, A.K.Sengupta, N.Anand, R.

(2017) J. Struct. Biol. 198: 134-146

  • DOI: 10.1016/j.jsb.2017.03.006

  • PubMed Abstract: 
  • In Streptomycetes, tetracycline repressor family of transcription regulators (TetR-FTRs) controls various biological processes including antibiotic biosynthesis, cellular morphology and innate resistance. Here, we focus on understanding the structura ...

    In Streptomycetes, tetracycline repressor family of transcription regulators (TetR-FTRs) controls various biological processes including antibiotic biosynthesis, cellular morphology and innate resistance. Here, we focus on understanding the structural basis of transcription regulation by CprB, a member of TetR-FTRs from S. coelicolor. CprB is implicated as a receptor of γ-butyrolactones, a class of quorum sensing molecules, responsible for initiating secondary metabolic pathways. In order to understand the molecular mechanism of DNA recognition, the X-ray structure of CprB in complex with its biological relevant operator sequence was solved to a resolution of 3.95Å. Furthermore, to refine and compliment the results, atomistic molecular dynamics simulations were carried out using the X-ray structure as the template. The studies reveal that CprB binds to DNA as dimer of dimers with this mode of interaction results in minimal distortion in the DNA, enabling these proteins to recognize multiple sequences with varying affinity. Another crucial finding from our simulation results was that the positively charged N-terminal arm of CprB brings extra stability to the protein-DNA complex by interacting with the minor-groove of the DNA and anchoring itself to the phosphate backbone. Corroborating electrophoretic mobility shift assay and fluorescence anisotropy experiments showed that the mutant ΔN6-CprB exhibited about 7-8 fold reduced DNA binding. Comparison with other TetR-FTRs reveals that this strategy is also employed by over 25% of TetR-FTRs, where N-terminal anchoring mechanism is used to enhance selectivity for a particular DNA sequence.


    Organizational Affiliation

    Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; IITB-Monash Research Academy, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CprB
A, B, C, D
215N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*GP*C*AP*GP*GP*CP*GP*GP*CP*AP*CP*GP*GP*TP*CP*TP*GP*TP*TP*GP*AP*GP*TP*TP*C)-3')E27Streptomyces coelicolor A3(2)
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*A*CP*TP*CP*AP*AP*CP*AP*GP*AP*CP*CP*GP*TP*GP*CP*CP*GP*CP*CP*TP*GP*CP*CP*T)-3')F27Streptomyces coelicolor A3(2)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.991 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.217 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 149.810α = 90.00
b = 149.810β = 90.00
c = 70.460γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
BRNSIndia20150237B02RP00614-BRNS
IIT BombayIndia--

Revision History 

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-05-31
    Type: Database references