Hashimoto Hideharu, Wang Dongxue, Horton John R, Zhang Xing, Corces Victor G, Cheng Xiaodong
Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta, GA 30322, USA.
Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta, GA 30322, USA; Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Mol Cell. 2017 Jun 1;66(5):711-720.e3. doi: 10.1016/j.molcel.2017.05.004. Epub 2017 May 18.
The multidomain CCCTC-binding factor (CTCF), containing a tandem array of 11 zinc fingers (ZFs), modulates the three-dimensional organization of chromatin. We crystallized the human CTCF DNA-binding domain in complex with a known CTCF-binding site. While ZF2 does not make sequence-specific contacts, each finger of ZF3-7 contacts three bases of the 15-bp consensus sequence. Each conserved nucleotide makes base-specific hydrogen bonds with a particular residue. Most of the variable base pairs within the core sequence also engage in interactions with the protein. These interactions compensate for deviations from the consensus sequence, allowing CTCF to adapt to sequence variations. CTCF is sensitive to cytosine methylation at position 2, but insensitive at position 12 of the 15-bp core sequence. These differences can be rationalized structurally. Although included in crystallizations, ZF10 and ZF11 are not visible, while ZF8 and ZF9 span the backbone of the DNA duplex, conferring no sequence specificity but adding to overall binding stability.
多结构域的CCCTC结合因子（CTCF）包含一个由11个锌指（ZF）组成的串联阵列，可调节染色质的三维结构。我们使人类CTCF DNA结合结构域与一个已知的CTCF结合位点形成复合物并进行了结晶。虽然锌指2不形成序列特异性接触，但锌指3 - 7的每个指与15个碱基的共有序列中的三个碱基接触。每个保守核苷酸与特定残基形成碱基特异性氢键。核心序列内的大多数可变碱基对也与蛋白质发生相互作用。这些相互作用补偿了与共有序列的偏差，使CTCF能够适应序列变异。CTCF对15个碱基核心序列中第2位的胞嘧啶甲基化敏感，但对第12位不敏感。这些差异可以从结构上得到合理的解释。虽然锌指10和锌指11包含在结晶中，但不可见，而锌指8和锌指9跨越DNA双链的主链，不赋予序列特异性，但增加了整体结合稳定性。
