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Structural basis for the diversity of DNA recognition by bZIP transcription factors

Nature Structural Biology volume 7, pages 889–893 (2000)Cite this article

Abstract

The basic region leucine zipper (bZIP) proteins form one of the largest families of transcription factors in eukaryotic cells. Despite relatively high homology between the amino acid sequences of the bZIP motifs, these proteins recognize diverse DNA sequences. Here we report the 2.0 Å resolution crystal structure of the bZIP motif of one such transcription factor, PAP1, a fission yeast AP-1-like transcription factor that binds DNA containing the novel consensus sequence TTACGTAA. The structure reveals how the Pap1-specific residues of the bZIP basic region recognize the target sequence and shows that the side chain of the invariant Asn in the bZIP motif adopts an alternative conformation in Pap1. This conformation, which is stabilized by a Pap1-specific residue and its associated water molecule, recognizes a different base in the target sequence from that in other bZIP subfamilies.

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Figure 1: Amino acid sequence comparison of the basic regions of members from several bZIP subfamilies.
Figure 2: Sequences of the Pap1 bZIP motif and its cognate DNA oligomer.
Figure 3: DNA recognition of the Pap1 bZIP motif.
Figure 4: Details of PAP1–DNA interactions.

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Acknowledgements

This work was supported by Grants in Aid for Scientific Research from the Ministry of Education, Science, Sports and Culture of Japan (to T.H.). We thank Y. Kyogoku for support at the early stage of the project.

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Authors and Affiliations

  1. Department of Molecular Biology, Nara Institute of Science Technology, 8916-5 Takayama, Ikoma, 630-0101, Nara, Japan

    Yoshifumi Fujii, Toshiyuki Shimizu & Toshio Hakoshima

  2. Laboratory of Cell Regulation, Imperial Cancer Research Fund, P.O. Box 123, 44 Lincoln' Inn Fields, London, WC2A 3PX, UK

    Takashi Toda

  3. Department of Biophysics, Faculty of Science, Kyoto University, Kitashirakawa-oiwake, Sakyo-ku, 606-8502, Kyoto, Japan

    Mitsuhiro Yanagida

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  1. Yoshifumi Fujii
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  2. Toshiyuki Shimizu
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Correspondence to Toshio Hakoshima.

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Fujii, Y., Shimizu, T., Toda, T. et al. Structural basis for the diversity of DNA recognition by bZIP transcription factors. Nat Struct Mol Biol 7, 889–893 (2000). https://doi.org/10.1038/82822

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