Crystal structure of the human FOXK1a-DNA complex and its implications on the diverse binding specificity of winged helix/forkhead proteins.
Interleukin enhancer binding factor (ILF) is a human transcription factor and a new member of the winged helix/forkhead family. ILF can bind to purine-rich regulatory motifs such as the human T-cell leukemia virus-long terminal region and the interleukin-2 promoter. Here we report the 2.4 A crystal structure of two DNA binding domains of ILF (FOXK1a) binding to a 16-bp DNA duplex containing a promoter sequence. Electrophoretic mobility shift assay studies demonstrate that two ILF-DNA binding domain molecules cooperatively bind to DNA. In addition to the recognition helix recognizing the core sequences through the major groove, the structure shows that wing 1 interacts with the minor groove of DNA, and the H2-H3 loop region makes ionic bonds to the phosphate group, which permits the recognition of DNA. The structure also reveals that the presence of the C-terminal alpha-helix in place of a typical wing 2 in a member of this family alters the orientation of the C-terminal basic residues (RKRRPR) when binding to DNA outside the core sequence. These results provide a new insight into how the DNA binding specificities of winged helix/forkhead proteins may be regulated by their less conserved regions.
Tsai
Kuang-Lei
KL
Institute of Molecular Biology, Academia Sinica, Taipei 115; Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300.
Huang
Cheng-Yang
CY
Institute of Molecular Biology, Academia Sinica, Taipei 115.
Chang
Chia-Hao
CH
Department of Biochemistry, National Cheng Kung University, College of Medicine, Tainan 701, Taiwan.
Sun
Yuh-Ju
YJ
Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300.
Chuang
Woei-Jer
WJ
Department of Biochemistry, National Cheng Kung University, College of Medicine, Tainan 701, Taiwan. Electronic address: wjcnmr@mail.ncku.edu.tw.
Hsiao
Chwan-Deng
CD
Institute of Molecular Biology, Academia Sinica, Taipei 115. Electronic address: hsiao@gate.sinica.edu.tw.
D000595:Amino Acid Sequence; D020029:Base Pairing; D018360:Crystallography, X-Ray; D051858:Forkhead Transcription Factors / Q000737:chemistry*; D006801:Humans; D008958:Models, Molecular; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid
C491001:FOXL1 protein, human; D051858:Forkhead Transcription Factors