Wuttke D S, Foster M P, Case D A, Gottesfeld J M, Wright P E
Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.
J Mol Biol. 1997 Oct 17;273(1):183-206. doi: 10.1006/jmbi.1997.1291.
The high resolution solution structure of a protein containing the three amino-terminal zinc fingers of Xenopus laevis transcription factor IIIA (TFIIIA) bound to its cognate DNA duplex was determined by nuclear magnetic resonance spectroscopy. The protein, which is designated zf1-3, binds with all three fingers in the DNA major groove, with a number of amino acids making base-specific contacts. The DNA structure is close to B-form. Although the mode of interaction of zf1-3 with DNA is similar to that of zif268 and other structurally characterized zinc finger complexes, the TFIIIA complex exhibits several novel features. Each zinc finger contacts four to five base-pairs and the repertoire of known base contact residues is extended to include a tryptophan at position +2 of the helix (finger 1) and arginine at position +10 (finger 3). Sequence-specific base contacts are made over virtually the entire length of the finger 3 helix. Lysine and histidine side-chains involved in base recognition are dynamically disordered in the solution structure; in the case of lysine, in particular, this could significantly decrease the entropic cost of DNA binding. The TGEKP(N) linker sequences, which are highly flexible in the unbound protein, adopt ordered conformations on DNA binding. The linkers appear to play an active structural role in stabilization of the protein-DNA complex. Substantial protein-protein contact surfaces are formed between adjacent fingers. As a consequence of these protein-protein interactions, the orientation of finger 1 in the major groove differs from that of the other fingers. Contributions to high affinity binding by zf1-3 come from both direct protein-DNA contacts and from indirect protein-protein interactions associated with structural organization of the linkers and formation of well-packed interfaces between adjacent zinc fingers in the DNA complex. The structures provide a molecular level explanation for the large body of footprinting and mutagenesis data available for the TFIIIA-DNA complex.
通过核磁共振光谱法确定了非洲爪蟾转录因子IIIA（TFIIIA）的含三个氨基末端锌指结构域的蛋白质与其同源DNA双链体结合的高分辨率溶液结构。该蛋白质被命名为zf1-3，其三个锌指均结合在DNA大沟中，有多个氨基酸与碱基形成特异性接触。DNA结构接近B型。尽管zf1-3与DNA的相互作用模式与zif268及其他已解析结构的锌指复合物相似，但TFIIIA复合物展现出一些新特征。每个锌指与4至5个碱基对接触，已知的碱基接触残基范围有所扩展，包括螺旋（指1）第+2位的色氨酸和指3第+10位的精氨酸。在指3螺旋的几乎整个长度上都存在序列特异性碱基接触。参与碱基识别的赖氨酸和组氨酸侧链在溶液结构中呈动态无序状态；特别是赖氨酸，这可能会显著降低DNA结合的熵成本。TGEKP(N)连接子序列在未结合蛋白质时高度灵活，在结合DNA时采取有序构象。这些连接子似乎在蛋白质-DNA复合物的稳定中发挥着积极的结构作用。相邻锌指之间形成了大量蛋白质-蛋白质接触表面。由于这些蛋白质-蛋白质相互作用，指1在大沟中的取向与其他锌指不同。zf1-3对高亲和力结合的贡献既来自直接的蛋白质-DNA接触，也来自与连接子的结构组织以及DNA复合物中相邻锌指之间紧密堆积界面形成相关的间接蛋白质-蛋白质相互作用。这些结构为TFIIIA-DNA复合物大量的足迹法和诱变数据提供了分子水平的解释。
