2VKE

Tet repressor class D complexed with cobalt and tetracycline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Specific Binding of Divalent Metal Ions to Tetracycline and to the Tet Repressor/Tetracycline Complex.

Palm, G.J.Lederer, T.Orth, P.Saenger, W.Takahashi, M.Hillen, W.Hinrichs, W.

(2008) J.Biol.Inorg.Chem. 13: 1097

  • DOI: 10.1007/s00775-008-0395-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tetracyclines coordinate metal(II) ions under physiological conditions forming chelate complexes with their ketoenolate moiety at rings B and C. These metal(II) complexes are the biologically relevant molecules conferring the antibiotic character of ...

    Tetracyclines coordinate metal(II) ions under physiological conditions forming chelate complexes with their ketoenolate moiety at rings B and C. These metal(II) complexes are the biologically relevant molecules conferring the antibiotic character of the drug by inhibiting ribosomal protein biosynthesis in prokaryotes. The Tet repressor, TetR, is the molecular switch for tetracycline resistance determinants in gram-negative bacteria. TetR controls transcription of a gene encoding the integral membrane protein TetA, which mediates active efflux of a tetracycline-metal(II) cation, [MeTc](+), by equimolar antiport with a proton. We evaluated distinct characteristics of the metal binding by crystal structure determination of TetR/[MeTc](+) complexes and of association equilibrium constants of [MeTc](+) and TetR/[MeTc](+) complexes. Various divalent metal ions bind to the same octahedral coordination site, defined by a histidine side chain of TetR, the tetracycline, and three water molecules. Whereas association constants for [MeTc](+) vary within 3 orders of magnitude, association of the [MeTc](+) cation to TetR is very similar for all measured divalent metals. Taking intracellular cation concentrations into account, it is evident that no other metal ion can compete with Mg(2+) for TetR/[MeTc](+) complex formation.


    Organizational Affiliation

    Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17489, Greifswald, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TETRACYCLINE REPRESSOR PROTEIN CLASS D
A
207Escherichia coliMutation(s): 0 
Gene Names: tetR
Find proteins for P0ACT4 (Escherichia coli)
Go to UniProtKB:  P0ACT4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TAC
Query on TAC

Download SDF File 
Download CCD File 
A
TETRACYCLINE
C22 H24 N2 O8
OFVLGDICTFRJMM-WESIUVDSSA-N
 Ligand Interaction
CL
Query on CL

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

Download SDF File 
Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.245 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 67.014α = 90.00
b = 67.014β = 90.00
c = 180.806γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
d*TREKdata scaling
d*TREKdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2012-11-28
    Type: Database references, Derived calculations, Other
  • Version 1.3: 2019-05-08
    Type: Data collection, Experimental preparation, Other