1ZRD

4 crystal structures of CAP-DNA with all base-pair substitutions at position 6, CAP-[6A;17T]ICAP38 DNA

Summary for 1ZRD

• Entry DOI: 10.2210/pdb1zrd/pdb
• Related: 1ZRC 1ZRE 1ZRF
• Descriptor: 5'-D(*AP*TP*TP*TP*CP*GP*AP*AP*AP*AP*AP*TP*GP*AP*GP*AP*T)-3', 5'-D(*CP*TP*AP*GP*AP*TP*CP*TP*CP*AP*TP*TP*TP*TP*TP*CP*GP*AP*AP*AP*T)-3', Catabolite gene activator, ... (5 entities in total)
• Functional Keywords: protein-dna complex, cap, cap-dna, catabolite gene activator protein, camp receptor protein, crp, gene regulation-dna complex, gene regulation/dna
• Biological source: Escherichia coli
• Total number of polymer chains: 6
• Total formula weight: 71032.13

Authors

Berman, H.M.,Napoli, A.A. (deposition date: 2005-05-19, release date: 2006-03-21, Last modification date: 2023-08-23)

Primary citation

Napoli, A.A.,Lawson, C.L.,Ebright, R.H.,Berman, H.M.
Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps.
J.Mol.Biol., 357:173-183, 2006

PubMed Abstract: 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.

PubMed: 16427082
DOI: 10.1016/j.jmb.2005.12.051

Experimental method

X-RAY DIFFRACTION (2.8 Å)