1o3q
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PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES
OverviewOverview
The catabolite activator protein (CAP) makes no direct contact with the, consensus base-pair T:A at position 6 of the DNA half-site, 5'-A(1)A(2)A(3)T(4)G(5)T(6)G(7)A(8)T(9)C(10)T(11)-3' but, nevertheless, exhibits strong specificity for T:A at position 6. Binding of CAP results, in formation of a sharp DNA kink, with a roll angle of approximately 40, degrees and a twist angle of approximately 20 degrees, between positions 6, and 7 of the DNA half-site. The consensus base-pair T:A at position 6 and, the consensus base-pair G:C at position 7 form a T:A/G:C step, which is, known to be associated with DNA flexibility. It has been proposed that, specificity for T:A at position 6 is a consequence of formation of the DNA, kink between positions 6 and 7, and of effects of the T:A(6)/G:C(7) step, on the geometry of DNA kinking, or the energetics of DNA kinking. In this, work, we determine crystallographic structures of CAP-DNA complexes having, the consensus base-pair T:A at position 6 or the non-consensus base-pair, C:G at position 6. We show that complexes containing T:A or C:G at, position 6 exhibit similar overall DNA bend angles and local geometries of, DNA kinking. We infer that indirect readout in this system does not, involve differences in the geometry of DNA kinking but, rather, solely, differences in the energetics of DNA kinking. We further infer that the, main determinant of DNA conformation in this system is protein-DNA, interaction, and not DNA sequence.
About this StructureAbout this Structure
1O3Q is a Single protein structure of sequence from Escherichia coli with CMP as ligand. This structure superseeds the now removed PDB entry 1DB7. Full crystallographic information is available from OCA.
ReferenceReference
Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking., Chen S, Vojtechovsky J, Parkinson GN, Ebright RH, Berman HM, J Mol Biol. 2001 Nov 16;314(1):63-74. PMID:11724532
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