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1zrd
From Proteopedia
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4 crystal structures of CAP-DNA with all base-pair substitutions at position 6, CAP-[6A;17T]ICAP38 DNA
Overview
The catabolite activator protein (CAP) bends DNA in the CAP-DNA complex, typically introducing 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, 5'-A1A2A3T4G5T6G7A8T9C10T11 -3', ("primary kink"). In previous work, we showed that CAP recognizes the, nucleotide immediately 5' to the primary-kink site, T6, through an, "indirect-readout" mechanism involving sequence effects on energetics of, primary-kink formation. Here, to understand further this example of, indirect readout, we have determined crystal structures of CAP-DNA, complexes containing each possible nucleotide at position 6. The, structures show that CAP can introduce a DNA kink at the primary-kink site, with any nucleotide at position 6. The DNA kink is sharp with the, consensus pyrimidine-purine step T6G7 and the non-consensus, pyrimidine-purine step C6G7 (roll angles of approximately 42 degrees, twist angles of approximately 16 degrees ), but is much less sharp with, the non-consensus purine-purine steps A6G7 and G6G7 (roll angles of, approximately 20 degrees, twist angles of approximately 17 degrees). We, infer that CAP discriminates between consensus and non-consensus, pyrimidine-purine steps at positions 6-7 solely based on differences in, the energetics of DNA deformation, but that CAP discriminates between the, consensus pyrimidine-purine step and non-consensus purine-purine steps at, positions 6-7 both based on differences in the energetics of DNA, deformation and based on qualitative differences in DNA deformation. The, structures further show that CAP can achieve a similar, approximately 46, degrees per DNA half-site, overall DNA bend through a sharp DNA kink, a, less sharp DNA kink, or a smooth DNA bend. Analysis of these and other, crystal structures of CAP-DNA complexes indicates that there is a large, approximately 28 degrees per DNA half-site, out-of-plane component of, CAP-induced DNA bending in structures not constrained by end-to-end DNA, lattice interactions and that lattice contacts involving CAP tend to, involve residues in or near biologically functional surfaces.
About this Structure
1ZRD is a Single protein structure of sequence from Escherichia coli with CMP as ligand. Full crystallographic information is available from OCA.
Reference
Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps., Napoli AA, Lawson CL, Ebright RH, Berman HM, J Mol Biol. 2006 Mar 17;357(1):173-83. Epub 2006 Jan 3. PMID:16427082
Page seeded by OCA on Wed Nov 21 07:37:10 2007
