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Crystallographic structure of the T domain–DNA complex of the Brachyury transcription factor

Nature volume 389, pages 884–888 (1997)Cite this article

Abstract

The mouse Brachyury (T) gene is the prototype of a growing family of so-called T-box genes which encode transcriptional regulators and have been identified in a variety of invertebrates and vertebrates, including humans1,2,3,4,5,6. Mutations in Brachyury and other T-box genes result in drastic embryonic phenotypes, indicating that T-box gene products are essential in tissue specification, morphogenesis and organogenesis7,8,9,10,11. The T-box encodes a DNA-binding domain of about 180 amino-acid residues, the T domain12. Here we report the X-ray structure of the T domain from Xenopus laevis2 in complex with a 24-nucleotide palindromic DNA duplex. We show that the protein is bound as a dimer, interacting with the major and the minor grooves of the DNA. A new type of specific DNA contact is seen, in which a carboxy-terminal helix is deeply embedded into an enlarged minor groove without bending the DNA. Hydrophobic interactions and an unusual main-chain carbonyl contact to a guanine account for sequence-specific recognition in the minor groove by this helix. Thus the structure of this T domain complex with DNA reveals a new way in which a protein can recognize DNA.

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Figure 1: Sequence of the 226 amino-terminal residues of T Xlaevis (Xbra)2 used for co-crystallization aligned with T mouse (T)1, TbxT chick (TbxT)5, TBX5 human (TBX5/HOS)11, Tbx6 mouse (Tbx6)4, eomesodermin (eomes)6 and optomotor-blind Drosophila (omb)10.
Figure 2: Ribbon diagram of the T-domain dimer bound to DNA.
Figure 3: Ribbon diagram of the T-domain dimer bound to DNA.
Figure 4: DNA recognition by the T domain.
Figure 5: DNA recognition by the T domain.
Figure 6: DNA recognition by the T domain.

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Acknowledgements

We thank A. Thompson (EMBL, Grenoble Outstation) for access and support at beamline BM14, P. Pattison for access and support at BM1 at the European Synchrotron Radiation Facility (ESRF, Grenoble), R. Eritja (EMBL, Heidelberg) for oligonucleotide synthesis, B. Kazimierczak and B. Koschorz for technical assistance, J. Brickman for initiating our interest in the structure determination project, and colleagues at the EMBL Grenoble for comments on the manuscript.

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  1. European Molecular Biology Laboratory, Grenoble Outstation, c/o ILL BP 156, Grenoble, Cedex 9, 38042, France

    Christoph W. Müller

  2. Max-Planck-Institut für Immunbiologie, Stübeweg 51, D-79108, Freiburg, Germany

    Bernhard G. Herrmann

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Correspondence to Christoph W. Müller.

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Müller, C., Herrmann, B. Crystallographic structure of the T domain–DNA complex of the Brachyury transcription factor. Nature 389, 884–888 (1997). https://doi.org/10.1038/39929

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