4D7N

TetR(D) in complex with anhydrotetracycline and potassium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Tetracycline Repressor Allostery Does not Depend on Divalent Metal Recognition.

Werten, S.Dalm, D.Palm, G.J.Grimm, C.C.Hinrichs, W.

(2014) Biochemistry 53: 7990

  • DOI: 10.1021/bi5012805
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Genes that render bacteria resistant to tetracycline-derived antibiotics are tightly regulated by repressors of the TetR family. In their physiologically relevant, magnesium-complexed form, tetracyclines induce allosteric rearrangements in the TetR h ...

    Genes that render bacteria resistant to tetracycline-derived antibiotics are tightly regulated by repressors of the TetR family. In their physiologically relevant, magnesium-complexed form, tetracyclines induce allosteric rearrangements in the TetR homodimer, leading to its release from the promoter and derepression of transcription. According to earlier crystallographic work, recognition of the tetracycline-associated magnesium ion by TetR is crucial and triggers the allosteric cascade. Nevertheless, the derivative 5a,6-anhydrotetracycline, which shows an increased affinity for TetR, causes promoter release even in the absence of magnesium. To resolve this paradox, it has been proposed that metal-free 5a,6-anhydrotetracycline acts via an exceptional, conformationally different induction mode that circumvents the normal magnesium requirement. We have tested this hypothesis by determining crystal structures of TetR-5a,6-anhydrotetracycline complexes in the presence of magnesium, ethylenediaminetetraacetic acid, or high concentrations of potassium. Analysis of these three structures reveals that, irrespective of the metal, the effects of 5a,6-anhydrotetracycline binding are indistinguishable from those of canonical induction by other tetracyclines. Together with a close scrutiny of the earlier evidence of a metal-triggered mechanism, these results demonstrate that magnesium recognition per se is not a prerequisite for tetracycline repressor allostery.


    Organizational Affiliation

    Department of Molecular Structural Biology, Institute for Biochemistry, University of Greifswald , Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TETRACYCLINE REPRESSOR, CLASS D
A
217N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
TDC
Query on TDC

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Download CCD File 
A
5A,6-ANHYDROTETRACYCLINE
C22 H22 N2 O7
CXCVEERYMJZMMM-DOCRCCHOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TDCKa: 23000000 M-1 BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.189 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 68.065α = 90.00
b = 68.065β = 90.00
c = 178.909γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2015-01-14
    Type: Database references
  • Version 1.2: 2015-04-22
    Type: Other