6RBM

TETR(D) E147A MUTANT IN COMPLEX WITH MINOCYCLINE AND MAGNESIUM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.216 

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This is version 1.1 of the entry. See complete history


Literature

Thermodynamics, cooperativity and stability of the tetracycline repressor (TetR) upon tetracycline binding.

Palm, G.J.Buchholz, I.Werten, S.Girbardt, B.Berndt, L.Delcea, M.Hinrichs, W.

(2020) Biochim Biophys Acta Proteins Proteom 1868: 140404-140404

  • DOI: 10.1016/j.bbapap.2020.140404
  • Primary Citation of Related Structures:  
    6FPM, 6FPL, 6FTS, 2XRL, 4B3A, 6QJX, 6QJW, 6RBM, 6RBL, 6RCR, 6RGX

  • PubMed Abstract: 
  • Allosteric regulation of the Tet repressor (TetR) homodimer relies on tetracycline binding that abolishes the affinity for the DNA operator. Previously, interpretation of circular dichroism data called for unfolding of the α-helical DNA-binding domains in absence of binding to DNA or tetracycline ...

    Allosteric regulation of the Tet repressor (TetR) homodimer relies on tetracycline binding that abolishes the affinity for the DNA operator. Previously, interpretation of circular dichroism data called for unfolding of the α-helical DNA-binding domains in absence of binding to DNA or tetracycline. Our small angle X-ray scattering of TetR(D) in solution contradicts this unfolding as a physiological process. Instead, in the core domain crystal structures analyses show increased immobilisation of helix α9 and two C-terminal turns of helix α8 upon tetracycline binding. Tetracycline complexes of TetR(D) and four single-site alanine variants were characterised by isothermal titration calorimetry, fluorescence titration, X-ray crystal structures, and melting curves. Five crystal structures confirm that Thr103 is a key residue for the allosteric events of induction, with the T103A variant lacking induction by any tetracycline. The T103A variant shows anti-cooperative inducer binding, and a melting curve of the tetracycline complex different to TetR(D) and other variants. For the N82A variant inducer binding is clearly anti-cooperative but triggers the induced conformation.


    Related Citations: 
    • Modular organisation of inducer recognition and allostery in the tetracycline repressor.
      Werten, S., Schneider, J., Palm, G.J., Hinrichs, W.
      (2016) FEBS J 283: 2102

    Organizational Affiliation

    Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 4, 17489 Greifswald, Germany. Electronic address: winfried.hinrichs@uni-greifswald.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tetracycline repressor protein class DA207Escherichia coliMutation(s): 2 
Gene Names: tetR
UniProt
Find proteins for P0ACT4 (Escherichia coli)
Explore P0ACT4 
Go to UniProtKB:  P0ACT4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MIY (Subject of Investigation/LOI)
Query on MIY

Download Ideal Coordinates CCD File 
B [auth A](4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE
C23 H27 N3 O7
DYKFCLLONBREIL-KVUCHLLUSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.216 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.67α = 90
b = 67.67β = 90
c = 178.74γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-21
    Type: Initial release
  • Version 1.1: 2020-03-18
    Changes: Database references