Vi. Ivanov et al., CRP-DNA COMPLEXES - INDUCING THE A-LIKE FORM IN THE BINDING-SITES WITH AN EXTENDED CENTRAL SPACER, Journal of Molecular Biology, 245(3), 1995, pp. 228-240
The consensus DNA sequence for binding of the Escherichia coli cyclic
AMP receptor protein (CRP) has two symmetrically related inverted reco
gnition elements TGTGA:TCACA, separated by a variable spacer, normally
6 bp long. We have shown that the CRP-cAMP complex, when bound to syn
thetic binding sites with an extended 8 bp spacer segment, induces an
increase in the DNA circular dichroism (CD). The CD change at lambda >
275 nm agrees with the shift of approximately one helical turn of DNA
into A-like form. The B-conformation is preserved for CRP binding sit
es similar to that in the Inc and uxaCA promoters with 6 bp spacers. A
nother effect accompanying DNA binding is a dramatic increase of the n
egative CD magnitude in the spectral region of the ligand cAMP, at lam
bda < 272 nm. This effect is observed when CRP binds to specific sites
with 6 or 8 bp spacers as well as to non-specific DNA. We reason that
the A-like form arises by compressing and unwinding the DNA in CRP-DN
A complexes having 8 bp central spacers. This serves to maintain a fix
ed length and twisting angle anal is controlled by the protein's relat
ively rigid frame. This model is consistent with the observation that
some binding sites with 6 bp spacers may also show the CD increase inh
erent to the sites with the extended 8 bp spacers. These 6 bp spacers
are characterized by an increased twisting angle that requires their u
nwinding to bind to CRP. We propose that a mutual adaptation between C
RP and binding sites by local untwisting and a B-->A-like transition i
n the DNA is of general importance and may occur in other protein-DNA
complexes, such as the complex of RNA polymerase with promoter DNA.