2VPR

Tet repressor class H in complex with 5a,6- anhydrotetracycline-Mg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Tet Repressor Induction by Tetracycline: A Molecular Dynamics, Continuum Electrostatics, and Crystallographic Study

Aleksandrov, A.Schuldt, L.Hinrichs, W.Simonson, T.

(2008) J.Mol.Biol. 378: 896

  • DOI: 10.1016/j.jmb.2008.03.022

  • PubMed Abstract: 
  • The Tet repressor (TetR) mediates the most important mechanism of bacterial resistance against tetracycline (Tc) antibiotics. In the absence of Tc, TetR is tightly bound to its operator DNA; upon binding of Tc with an associated Mg(2+) ion, it dissoc ...

    The Tet repressor (TetR) mediates the most important mechanism of bacterial resistance against tetracycline (Tc) antibiotics. In the absence of Tc, TetR is tightly bound to its operator DNA; upon binding of Tc with an associated Mg(2+) ion, it dissociates from the DNA, allowing expression of the repressed genes. Its tight control by Tc makes TetR broadly useful in genetic engineering. The Tc binding site is over 20 A from the DNA, so the binding signal must propagate a long distance. We use molecular dynamics simulations and continuum electrostatic calculations to test two models of the allosteric mechanism. We simulate the TetR:DNA complex, the Tc-bound, "induced" TetR, and the transition pathway between them. The simulations support the model inferred previously from the crystal structures and reveal new details. When [Tc:Mg](+) binds, the Mg(2+) ion makes direct and water-mediated interactions with helix 8 of one TetR monomer and helix 6 of the other monomer, and helix 6 is pulled in towards the central core of the structure. Hydrophobic interactions with helix 6 then pull helix 4 in a pendulum motion, with a maximal displacement at its N-terminus: the DNA interface. The crystal structure of an additional TetR reported here corroborates this motion. The N-terminal residue of helix 4, Lys48, is highly conserved in DNA-binding regulatory proteins of the TetR class and makes the largest contribution of any amino acid to the TetR:DNA binding free energy. Thus, the conformational changes lead to a drastic reduction in the TetR:DNA binding affinity, allowing TetR to detach itself from the DNA. Tc plays the role of a specific Mg(2+) carrier, whereas the Mg(2+) ion itself makes key interactions that trigger the allosteric transition in the TetR:Tc complex.


    Related Citations: 
    • Structural Basis of Gene Regulation by the Tetracycline Inducible Tet Repressor-Operator System
      Orth, P.,Schnappinger, D.,Hillen, W.,Saenger, W.,Hinrichs, W.
      (2000) Nat.Struct.Mol.Biol. 7: 215
    • Structure of the Tet Repressor - Tetracycline Complex and Regulation of Antibiotic Resistance
      Hinrichs, W.,Kisker, C.,Duevel, M.,Mueller, A.,Tovar, K.,Hillen, W.,Saenger, W.
      (1994) Science 264: 418


    Organizational Affiliation

    Laboratoire de Biochimie (CNRS UMR7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TETRACYCLINE RESISTANCE REPRESSOR PROTEIN
A
207Pasteurella multocidaMutation(s): 0 
Gene Names: tetR
Find proteins for P51561 (Pasteurella multocida)
Go to UniProtKB:  P51561
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
TDC
Query on TDC

Download SDF File 
Download CCD File 
A
5A,6-ANHYDROTETRACYCLINE
C22 H22 N2 O7
CXCVEERYMJZMMM-DOCRCCHOSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.201 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 56.361α = 90.00
b = 108.744β = 90.00
c = 68.976γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2019-07-24
    Type: Data collection