2X9D

Tet repressor (class D) in complex with iso-7-chlortetracycline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Recognition of Drug Degradation Products by Target Proteins: Isotetracycline Binding to Tet Repressor.

Volkers, G.Petruschka, L.Hinrichs, W.

(2011) J.Med.Chem. 54: 5108

  • DOI: 10.1021/jm200332e
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tetracycline antibiotics and their degradation products appear in medically treated tissues, food, soil, and manure sludge in the environment. In the context of protein interactions with various tetracyclines we performed crystal structure analyses o ...

    Tetracycline antibiotics and their degradation products appear in medically treated tissues, food, soil, and manure sludge in the environment. In the context of protein interactions with various tetracyclines we performed crystal structure analyses of the tetracycline repressor in complex with weak or noninducing tetracycline derivatives. Isotetracyclines are degradation products of tetracyclines, which occur under physiological conditions. The typical framework of the antibiotic is irreversibly broken at the BC-ring connection, leading to a modified orientation of the AB to the new C*D ring fragments. The shape of the zwitterionic AB-ring fragment is unchanged and still binds to the TetR recognition site in a manner comparable to the intact antibiotic but without typical Mg(2+) chelation. This work is an example that drug degradation products can still bind to specific targets and should be discussed in light of potential and critical side effects.


    Related Citations: 
    • Structure of the Tet Repressor-Tetracycline Complex and Regulation of Antibiotic Resistance.
      Hinrichs, W.,Kisker, C.,Duvel, M.,Muller, A.,Tovar, K.,Hillen, W.,Saenger, W.
      (1994) Science 264: 418


    Organizational Affiliation

    Department of Molecular Structural Biology, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TETRACYCLINE REPRESSOR PROTEIN CLASS D
A
207Escherichia coliMutation(s): 1 
Gene Names: tetR
Find proteins for P0ACT4 (Escherichia coli)
Go to UniProtKB:  P0ACT4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
ITC
Query on ITC

Download SDF File 
Download CCD File 
A
ISO-7-CHLORTETRACYCLINE
(4S,4AS,6S,8AS)-6-[(1S)-7-CHLORO-4-HYDROXY-1-METHYL-3-OXO-1,3-DIHYDRO-2-BENZOFURAN-1-YL]-4-(DIMETHYLAMINO)-3,8A-DIHYDROXY-1,8-DIOXO-1,4,4A,5,6,7,8,8A-OCTAHYDRONAPHTHALENE-2-CARBOXAMIDE
C22 H23 Cl N2 O8
GFSLIMZISCAANG-AXVXPIMKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.234 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 68.253α = 90.00
b = 68.253β = 90.00
c = 179.271γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-23
    Type: Initial release
  • Version 1.1: 2012-02-01
    Type: Database references, Version format compliance