1O3S

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

Replaces:  1DB9

Summary for 1O3S

• Entry DOI: 10.2210/pdb1o3s/pdb
• Related: 1O3Q 1O3R 1O3T
• Descriptor: 5'-D(*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*T)-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: 3
• Total formula weight: 31142.69

Authors

Chen, S.,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.,Gunasekera, A.,Zhang, X.,Kunkel, T.A.,Ebright, R.H.,Berman, H.M.
Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP-DNA Complex: Alteration of DNA Binding Specificity Through Alteration of DNA Kinking
J.Mol.Biol., 314:75-82, 2001

PubMed Abstract: The catabolite activator protein (CAP) sharply bends DNA in the CAP-DNA complex, introducing a 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'-A(1)A(2)A(3)T(4)G(5)T(6)G(7)A(8)T(9)C(10)T(11)-3' ("primary kink"). CAP recognizes the base-pair immediately 5' to the primary-kink site, T:A(6), through an "indirect-readout" mechanism involving sequence effects on the energetics of primary-kink formation. CAP recognizes the base-pair immediately 3' to the primary-kink site, G:C(7), through a "direct-readout" mechanism involving formation of a hydrogen bond between Glu181 of CAP and G:C(7). Here, we report that substitution of the carboxylate side-chain of Glu181 of CAP by the one-methylene-group-shorter carboxylate side-chain of Asp changes DNA binding specificity at position 6 of the DNA half site, changing specificity for T:A(6) to specificity for C:G(6), and we report a crystallographic analysis defining the structural basis of the change in specificity. The Glu181-->Asp substitution eliminates the primary kink and thus eliminates indirect-readout-based specificity for T:A(6). The Glu181-->Asp substitution does not eliminate hydrogen-bond formation with G:C(7), and thus does not eliminate direct-readout-based specificity for G:C(7).

PubMed: 11724533
DOI: 10.1006/jmbi.2001.5090

Experimental method

X-RAY DIFFRACTION (3 Å)