Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking
Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking
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DOI：
10.1006/jmbi.2001.5089
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发表时间：
2001-11-16
影响因子：
5.6
通讯作者：
Berman, HM
中科院分区：
文献类型：
--
作者：
Chen, SF;Vojtechovsky, J;Berman, HM
分解代谢激活蛋白 (CAP) 与 DNA 半位点 5'-A(1)A(2)A(3)T(4)G(5)T(6)G(7)A(8)T(9)C(10)T(11)-3' 位置 6 处的共有碱基对 T:A 不直接接触，但对位置 6 处的 T:A 表现出很强的特异性。CAP 的结合导致形成尖锐的DNA 扭结，在 DNA 半位点的位置 6 和 7 之间，具有类似于 40 度的滚动角和类似于 20 度的扭曲角。第 6 位的共有碱基对 T:A 和第 7 位的共有碱基对 G:C 形成 T:A/G:C 步骤，已知该步骤与 DNA 灵活性相关。有人提出，第 6 位 T:A 的特异性是第 6 位和第 7 位之间 DNA 扭结形成的结果，也是 T:A(6)/G:C-7 步骤对 DNA 扭结几何形状或 DNA 扭结能量学影响的结果。在这项工作中，我们确定了在位置 6 具有共有碱基对 T:A 或在位置 6 具有非共有碱基对 C:G 的 CAP-DNA 复合物的晶体结构。我们表明，在位置 6 包含 T:A 或 C:G 的复合物表现出相似的整体 DNA 弯曲角度和 DNA 扭结的局部几何形状。我们推断，该系统中的间接读出不涉及 DNA 扭结几何形状的差异，而仅涉及 DNA 扭结能量学的差异。我们进一步推断，该系统中 DNA 构象的主要决定因素是蛋白质-DNA 相互作用，而不是 DNA 序列。 (C) 2001 年学术出版社。
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 similar to 40 degrees and a twist angle of similar to 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. (C) 2001 Academic Press.