Chap. 9 DNA-Protein Interactions in Bacteria

The Family of Repressors Repressors have recognition helices that lie in the major groove of appropriate operator Specificity of this binding depends on amino acids in the recognition helices

Helix-turn-helix motif

Probing Binding Specificity by Site- Directed Mutagenesis Key amino acids in recognition helices of 2 repressors are proposed These amino acids are largely different between the two repressors

Wheel diagram; view at the end

-The binding of lambda repressor can be seen by DNaseI footprinting. -Multiple operators exist for the repressor binding. -OR1, OR2, OR3

9-7 The Role of Tryptophan The trp repressor requires tryptophan to force the recognition helices of the repressor dimer into proper position for interacting with the trp operator

A DNA-binding protein can approach either of these grooves to interact with the base pair. As it does so, it “ sees" four possible contours in each groove, depending on whether the base pair is a T -A, A-T, C- G, or G-C pair.

Major groove minor groove

Major groove minor groove D A H donor H acceptor