CRP-DNA complexes: inducing the A-like form in the binding sites with an extended central spacer

J Mol Biol. 1995 Jan 20;245(3):228-40. doi: 10.1006/jmbi.1994.0019.

Abstract

The consensus DNA sequence for binding of the Escherichia coli cyclic AMP receptor protein (CRP) has two symmetrically related inverted recognition elements TGTGA:TCACA, separated by a variable spacer, normally 6 bp long. We have shown that the CRP-cAMP complex, when bound to synthetic 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 sites similar to that in the lac and uxaCA promoters with 6 bp spacers. Another effect accompanying DNA binding is a dramatic increase of the negative CD magnitude in the spectral region of the ligand cAMP, at lambda < 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-DNA complexes having 8 bp central spacers. This serves to maintain a fixed length and twisting angle and is controlled by the protein's relatively rigid frame. This model is consistent with the observation that some binding sites with 6 bp spacers may also show the CD increase inherent to the sites with the extended 8 bp spacers. These 6 bp spacers are characterized by an increased twisting angle that requires their unwinding to bind to CRP. We propose that a mutual adaptation between CRP and binding sites by local untwisting and a B-->A-like transition in the DNA is of general importance and may occur in other protein-DNA complexes, such as the complex of RNA polymerase with promoter DNA.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Sequence
  • Circular Dichroism
  • Cyclic AMP / chemistry
  • Cyclic AMP / metabolism
  • Cyclic AMP Receptor Protein / metabolism*
  • DNA / chemistry*
  • DNA / metabolism*
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • Protein Binding

Substances

  • Cyclic AMP Receptor Protein
  • DNA, Bacterial
  • DNA
  • Cyclic AMP