Binding of Effector Molecules

The binding of low-molecular-weight effectors to regulatory DNA-binding protein can lead to an increase or decrease in the affinity of the protein for its recognition sequence. 

The strategies and mechanisms of action of effector molecules on regulatory DNA-binding proteins can be elucidated using the example of the Trp repressor of E. coli. In this system binding of the effector increases the affinity of the binding protein to its DNA element. 

The Trp repressor controls the transcription of a total of five enzymes required for the biosynthesis of tryptophan (Fig. 1.15a). The genes for the five enzymes are encoded in a single operon, whereby the binding site for the Trp repressor overlaps with the promotor. The bound repressor blocks the RNA polymerase s access to the promotor, thereby inhibiting transcription. 

The enzymes of Trp-biosynthesis are only required if too little tryptophan is available to the bacteria from the growth medium. In such a case the Trp requirement is fulfilled by the cell s own Trp biosynthesis. If, however, there is enough Trp supplied by the medium, then it is prudent to shut down the Trp operon. The sensor is the Trp concentration. The Trp repressor registers the current Trp concentration with the help of its own Trp-binding site. If a great deal of Trp is present, then the Trp-binding site of the repressor is occupied by Trp. The Trp repressor binds Trp with high affinity (Kd=10 9-1(T10 M), upon which transcription of the operon is then blocked. 

At low Trp concentration, the Trp repressor is mainly in the unbound, inactive form. The free form of the Trp repressor binds with a ca. 104-fold lower affinity to the recognition sequence than that of the Trp-bound form. The promotor remains free under these conditions, and transcription of the genes for Trp biosynthesis can occur. The shutting on and off of the Trp operon is based on the disparate DNA affinities of the free and Trp-bound repressor. 

Increase in the binding affinity upon binding of the effector  

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The comparison of the structure of a binding protein in the inactive form and in the active form boimd to DNA gives an impression of the conformational changes correlated with binding of effector molecules. The Trp repressor is, next to the Lac repressor from E. coli, one of the few examples in which the structural basis for the difference in DNA-binding affinity of the inactive vs. active form is understood (Fig. 1.22b). 

The regulation of the activity of enzymes by the binding of effector molecules is a ubiquitous and general principle for the fine timing and control of metabolic activity. Effector molecules are often low molecular weight organic compounds. Proteins and metal ions can also exercise the function of effectors. The effector molecules bind specifically to the enzymes and the binding results in inhibition or stimulation of enzymatic activity. 

Enzymes that are regulated by effector molecules in an allosteric maimer possess, apart from the binding site for the substrate, a specific binding site for the effector molecule. The binding of effector molecules to the effector site leads to a shift in equilibrium between the various conformations and thus to a change in activity (see 2.3). 

A select group of enzymes are regulated by one of two strategies modification of the covalent structure of the enzyme or modification of their structure by the reversible binding of effector molecules. 

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