2VPR

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

Summary for 2VPR

• Entry DOI: 10.2210/pdb2vpr/pdb
• Descriptor: TETRACYCLINE RESISTANCE REPRESSOR PROTEIN, 5A,6-ANHYDROTETRACYCLINE, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: transcription, metal-binding, antibiotic resistance, transcription regulator, transcription regulation dna-binding
• Biological source: PASTEURELLA MULTOCIDA
• Total number of polymer chains: 1
• Total formula weight: 23758.16

Authors

Schuldt, L.,Palm, G.,Hinrichs, W. (deposition date: 2008-03-03, release date: 2008-03-11, Last modification date: 2023-12-13)

Primary citation

Aleksandrov, A.,Schuldt, L.,Hinrichs, W.,Simonson, T.
Tet Repressor Induction by Tetracycline: A Molecular Dynamics, Continuum Electrostatics, and Crystallographic Study
J.Mol.Biol., 378:896-, 2008

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 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.

PubMed: 18395746
DOI: 10.1016/J.JMB.2008.03.022

Experimental method

X-RAY DIFFRACTION (2.49 Å)