Bacterial Nod genes are activated to initiate nodulation in plants by plant signals flavonoids

TLS Online TPP Program

#Id: 6485

#Unit 3. Fundamental Processes

Model for the Interaction Between TBP and Promoters

TLS Online TPP Program

#Id: 6486

#Unit 3. Fundamental Processes

TBP Binds to and Distorts DNA Using a b Sheet Inserted into the Minor Groove

TBP uses an extensive region of  sheet to recognize the minor groove of the TATA element . This is unusual. More typically, proteins recognize DNA using  helices inserted into the major groove of DNA, as we have seen and also for the factor .

TLS Online TPP Program

#Id: 6487

#Unit 3. Fundamental Processes

TBP–DNA complex. TBP (purple) is complexed with the DNA TATA sequence (gray) found at the start of many Pol II genes. 

TLS Online TPP Program

#Id: 6488

#Unit 3. Fundamental Processes

TBP causes the minor groove to be widened to an almost flat conformation; it also bends the DNA by an angle of 80. The interaction between TBP and DNA involves only a limited number of hydrogen bonds between the protein and the edges of the base pairs in the minor groove.  Instead, much of the specificity is imposed by two pairs of phenylalanine side chains that intercalate between the base pairs at either end of the recognition sequence and drive the strong bend in the DNA.

TLS Online TPP Program

#Id: 6489

#Unit 3. Fundamental Processes

A:T base pairs are thus favored because they are more readily distorted to allow the initial opening of the minor groove. There are also extensive interactions between the phosphate backbone and basic residues in the b sheet, adding to the overall binding energy of the interaction.

TLS Online TPP Program

#Id: 6490

#Unit 3. Fundamental Processes

Strikingly, a number of TAFs resemble histones: nine of 14 TAPs contain a histone fold domain, though in most cases the TAFs lack the residues of this domain that are responsible for DNA binding.