Tandem binding in crystals of a trp represser/operator half-site complex

@article{Lawson1993TandemBI,
  title={Tandem binding in crystals of a trp represser/operator half-site complex},
  author={Catherine L. Lawson and Jannette Carey},
  journal={Nature},
  year={1993},
  volume={366},
  pages={178-182}
}
THE crystal structure of trp represser tandemly bound in a 2:1 complex to a 16-base-pair palindromic DNA containing a central trp operator half-site has been determined and refined to 2.4 & Aring; resolution. Despite dramatically different DNA sequence contexts and crystallization conditions, the protein/DNA interface is essentially identical to that seen in the original trp represser/operator complex structure1. Water-mediated sequence recognition by trp represser is likely to be related… 
In vivo and in vitro studies of TrpR-DNA interactions.
TLDR
The results indicate that the optimal half-site sequence for recognition by one helix-turn-helix motif of one TrpR dimer is 3'CNTGA5'5'GNACT3', consistent with contacts observed by X-ray diffraction analysis of cocrystalline 1:1 and 2:1 complexes.
Probing the Interface of the trp Repressor–Operator Complex Using Operator Sequences Containing Isosteric Base-Pair Analogues☆
TLDR
A series of base pair analogues, dI-dM and dD-dU, have been used in place of the native dA-dT and dG-dC residues to probe the interface between the trp repressor and its operator sequence, resulting in differences in binding by these analogue sequences.
Specific purine N7-nitrogens are critical for high affinity binding by the trp repressor
TLDR
It is concluded that the crystal structure obtained by Otwinowski et al. reflects high–affinity sequence–specific binding of the trp represser to thetrp operator, and that in some cases proteins can use water molecules to extend amino acid side chains in order to derive favorable binding energy in complex formation.
Probing the role of water in the tryptophan repressor‐operator complex
TLDR
A study of binding as a function of betaine concentration revealed that this osmolyte at low concentration results in a stabilization of the 1:1 TR/operator complex, but at higher concentrations leads to a switching between binding modes to favor tandem binding.
Probing the physical basis for trp repressor-operator recognition.
TLDR
This work has studied the binding of trp repressor to a series of mutated operator targets using fluorescence anisotropy, which provides very high quality data allowing fairly precise estimations of the affinities involved, and concludes that even on very small targets, the repressor binds slightly cooperatively, populating a 2:1 dimer/DNA complex, and then at higher concentrations a third dimer is bound with significantly lower affinity.
Repressor assembly at trp binding sites is dependent on the identity of the intervening dinucleotide between the binding half sites.
TLDR
The observations presented here support the model that in vivo regulation of trp operators is due to their differential ability to bind multiple repressor molecules and ascribes this ability to two sequence-dependent factors which act together: the identity and number of half-site sequences, recognized by water-mediated hydrogen bonds, and the ability of the intervening dinucleotides to form direct bidentate hydrogen bonds to the repressor.
Flexibility of dna binding domain of trp repressor required for recognition of different operator sequences
TLDR
It is found that the alanine to valine change stabilizes the flexible DNA‐binding domain of the repressor, and the flexibility exhibited by the wild‐type repressor allows a broader range of repressor/DNA interactions, whereas the increased rigidity resulting from the AV77 change limits the repression's effectiveness at some operators.
Structure and function of Escherichia coli met repressor: similarities and contrasts with trp repressor.
  • S. Phillips, P. Stockley
  • Biology
    Philosophical transactions of the Royal Society of London. Series B, Biological sciences
  • 1996
TLDR
X-ray crystallographic studies show how the ligand-activated met and trp repressors in Escherichia coli have totally different three-dimensional structures and specifically recognize their respective DNA operator sequences in different ways.
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References

SHOWING 1-10 OF 28 REFERENCES
Crystal structure of trp represser/operator complex at atomic resolution
The crystal structure of the trp repressor/operator complex shows an extensive contact surface, including 24 direct and 6 solvent-mediated hydrogen bonds to the phosphate groups of the DNA. There are
Flexibility of the DNA‐binding domains of trp repressor
TLDR
It is concluded that while L‐tryptophan binding is essential for forming a specific complex with trp operator DNA, the corepressor ligand does not lock the repressor into a single conformation that is complementary to the operator.
How does trp repressor bind to its operator?
How Trp repressor binds to its operator.
TLDR
It is shown here that the Trp repressor binds to a sequence whose center is located four base pairs either to the right or to the left of the central axis of symmetry that was previously identified.
The DNA target of the trp repressor.
TLDR
The sequence consensus in trpR‐repressible promoters is reexamined and found fully consistent with the interactions of the traditional operator sequence seen in the crystal structure, and stereochemically inconsistent with the above referenced alternative model.
Cocrystals of Escherichia coli trp repressor bound to an alternative operator DNA sequence.
TLDR
Cocrystals of a 2:1 complex of trp repressor dimers with a DNA duplex containing a single, central operator half-site sequence are described, suitable for structural analysis by X-ray diffraction.
Escherichia coli tryptophan repressor binds multiple sites within the aroH and trp operators.
TLDR
DNase I footprinting and methylation protection studies have been used to analyze the binding of Escherichia coli Trp repressor to the trpR, aroH, and trp operators and support the simplest model that explains the difference in Trp Repressor interaction at the three operators.
Structure and Mechanism of the trp Repressor/Operator System
The trp aporepressor of Escherichia coli exists as a homodimer of two 107-amino acid chains and is activated to the trp repressor by the non-cooperative binding of two molecules of the co-repressor,
The crystal structure of trp aporepressor at 1.8 Å shows how binding tryptophan enhances DNA affinity
Comparison of the crystal structure of inactive unliganded trp aporepressor with that of trp repressor shows that binding tryptophan activates the dimer a thousandfold by moving two
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