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 Export

@article{citeulike:3268697, abstract = {The catabolite activator protein (CAP) sharply bends DNA in the CAP-DNA complex, introducing a DNA kink, with a roll angle of \~{}40° and a twist angle of \~{}20°, between positions 6 and 7 of the DNA half-site, 5'-A1A2A3T4G5T6G7A8T9C10T11-3' ("primary kink"). CAP recognizes the base-pair immediately 5' to the primary-kink site, T:A6, 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:C7, through a "direct-readout" mechanism involving formation of a hydrogen bond between Glu181 of CAP and G:C7. 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:A6 to specificity for C:G6, 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:A6. The Glu181-->Asp substitution does not eliminate hydrogen-bond formation with G:C7, and thus does not eliminate direct-readout-based specificity for G:C7.}, author = {Chen, Shengfeng and Gunasekera, Angelo and Zhang, Xiaoping and Kunkel, Thomas A. and Ebright, Richard H. and Berman, Helen M.}, citeulike-article-id = {3268697}, citeulike-linkout-0 = {http://dx.doi.org/10.1006/jmbi.2001.5090}, citeulike-linkout-1 = {http://www.sciencedirect.com/science/article/B6WK7-457CXW2-2H/2/3424988a6636016caeaf1d6e5e431aa9}, day = {16}, doi = {10.1006/jmbi.2001.5090}, journal = {Journal of Molecular Biology}, keywords = {allostery, cap, cap\_dna, protein}, month = {November}, number = {1}, pages = {75--82}, posted-at = {2008-09-15 10:54:44}, priority = {2}, title = {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}, url = {http://dx.doi.org/10.1006/jmbi.2001.5090}, volume = {314}, year = {2001} }

TY - JOUR ID - citeulike:3268697 L3 - citeulike-article-id:3268697 N2 - The catabolite activator protein (CAP) sharply bends DNA in the CAP-DNA complex, introducing a DNA kink, with a roll angle of ~40° and a twist angle of ~20°, between positions 6 and 7 of the DNA half-site, 5'-A1A2A3T4G5T6G7A8T9C10T11-3' ("primary kink"). CAP recognizes the base-pair immediately 5' to the primary-kink site, T:A6, 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:C7, through a "direct-readout" mechanism involving formation of a hydrogen bond between Glu181 of CAP and G:C7. 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:A6 to specificity for C:G6, 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:A6. The Glu181-->Asp substitution does not eliminate hydrogen-bond formation with G:C7, and thus does not eliminate direct-readout-based specificity for G:C7. IS - 1 JF - Journal of Molecular Biology EP - 82 TI - 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 VL - 314 SP - 75 KW - allostery KW - cap KW - cap_dna KW - protein AU - Chen, Shengfeng AU - Gunasekera, Angelo AU - Zhang, Xiaoping AU - Kunkel, Thomas AU - Ebright, Richard AU - Berman, Helen PY - 2001/11/16/ UR - http://dx.doi.org/10.1006/jmbi.2001.5090 ER -