1O3T

PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES

Replaces:  1DBC

Summary for 1O3T

• Entry DOI: 10.2210/pdb1o3t/pdb
• Related: 1O3Q 1O3R 1O3S
• Descriptor: 5'-D(*GP*CP*GP*AP*AP*AP*AP*AP*TP*GP*CP*GP*AP*T)-3', 5'-D(*CP*TP*AP*GP*AP*TP*CP*GP*CP*AP*TP*TP*TP*TP*TP*CP*G)-3', CATABOLITE GENE ACTIVATOR PROTEIN, ... (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: 64786.98

Authors

Chen, S.,Vojtechovsky, J.,Parkinson, G.N.,Ebright, R.H.,Berman, H.M. (deposition date: 2003-03-18, release date: 2003-04-08, Last modification date: 2023-12-27)

Primary citation

Chen, S.,Vojtechovsky, J.,Parkinson, G.N.,Ebright, R.H.,Berman, H.M.
Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP-DNA Complex: DNA Binding Specificity Based on Energetics of DNA Kinking
J.Mol.Biol., 314:63-74, 2001

PubMed Abstract: 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.

PubMed: 11724532
DOI: 10.1006/jmbi.2001.5089

Experimental method

X-RAY DIFFRACTION (2.8 Å)