Furui J, Uegaki K, Yamazaki T, Shirakawa M, Swindells M B, Harada H, Taniguchi T, Kyogoku Y
Institute for Protein Research, Osaka University, Suita, Osaka, 565, Japan.
Structure. 1998 Apr 15;6(4):491-500. doi: 10.1016/s0969-2126(98)00050-1.
The transcription of interferon (IFN) and IFN-inducible genes is mainly regulated by the interferon regulatory factor (IRF) family of proteins, which recognize a unique AAGTGA hexamer repeat motif in the regulatory region of IFN genes. A DNA-binding domain of approximately 100 amino acids has been commonly found in the IRF family of proteins, but it has no sequence homology to known DNA-binding motifs. Elucidation of the structures of members of the IRF family is therefore useful to the understanding of the regulation and evolution of the immune system at the structural level.
The solution structure of the DNA-binding domain of interferon regulatory factor-2 (IRF-2) has been determined by NMR spectroscopy. It is composed of a four-stranded antiparallel beta sheet and three alpha helices, and its global fold is similar to those of the winged helix-turn-helix (wHTH) family of proteins. A long loop (Pro37-Asp51) is found immediately before the HTH motif, which is not found in other wHTH proteins. The NMR signals of residues in this long loop, as well as the second helix of the HTH motif, are strongly affected upon the addition of the hexamer repeat DNA, suggesting that these structural elements participate in DNA recognition and binding.
The structural similarity of the DNA-binding domain of IRF-2 with those of proteins in the wHTH family shows that the IRF proteins belong to the wHTH family, even though there is no apparent sequence homology among proteins of the two families. The sequential structure alignment program (SSAP) shows that IRF-2 has a slightly different structure from typical wHTH proteins, mainly in the orientation of helix 2. The IRF family of proteins should therefore be categorized into a subfamily of the wHTH family. The evidence here implies that the evolutional pathway of the IRF family is distinct from that of the other wHTH proteins, in other words, the immune system diverged from an evolutional stem at an early stage.
干扰素（IFN）及干扰素诱导基因的转录主要受干扰素调节因子（IRF）家族蛋白调控，这些蛋白可识别IFN基因调控区域中独特的AAGTGA六聚体重复基序。在IRF家族蛋白中普遍发现了一个约100个氨基酸的DNA结合结构域，但它与已知的DNA结合基序没有序列同源性。因此，阐明IRF家族成员的结构有助于从结构层面理解免疫系统的调控和进化。
通过核磁共振光谱法确定了干扰素调节因子-2（IRF-2）DNA结合结构域的溶液结构。它由一个四链反平行β折叠片和三个α螺旋组成，其整体折叠与翼状螺旋-转角-螺旋（wHTH）家族蛋白相似。在HTH基序之前紧邻发现一个长环（Pro37-Asp51），这在其他wHTH蛋白中未发现。添加六聚体重复DNA后，该长环以及HTH基序第二个螺旋中残基的核磁共振信号受到强烈影响，表明这些结构元件参与DNA识别和结合。
IRF-2的DNA结合结构域与wHTH家族蛋白的结构相似性表明，IRF蛋白属于wHTH家族，尽管这两个家族的蛋白之间没有明显的序列同源性。序列结构比对程序（SSAP）显示，IRF-2与典型的wHTH蛋白结构略有不同，主要在于螺旋2的方向。因此，IRF家族蛋白应归类为wHTH家族的一个亚家族。此处证据表明，IRF家族的进化途径与其他wHTH蛋白不同，换句话说，免疫系统在早期从一个进化主干分化而来。
