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The SAND domain structure defines a novel DNA-binding fold in transcriptional regulation

Nature Structural Biology volume 8, pages 626–633 (2001)Cite this article

Abstract

The SAND domain is a conserved sequence motif found in a number of nuclear proteins, including the Sp100 family and NUDR. These are thought to play important roles in chromatin-dependent transcriptional regulation and are linked to many diseases. We have determined the three-dimensional (3D) structure of the SAND domain from Sp100b. The structure represents a novel α/β fold, in which a conserved KDWK sequence motif is found within an α-helical, positively charged surface patch. For NUDR, the SAND domain is shown to be sufficient to mediate DNA binding. Using mutational analyses and chemical shift perturbation experiments, the DNA binding surface is mapped to the α-helical region encompassing the KDWK motif. The DNA binding activity of wild type and mutant proteins in vitro correlates with transcriptional regulation activity of full length NUDR in vivo. The evolutionarily conserved SAND domain defines a new DNA binding fold that is involved in chromatin-associated transcriptional regulation.

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Figure 1: Three-dimensional structure of the Sp100b SAND domain.
Figure 2: Charge distribution and sequence conservation of the Sp100b SAND domain.
Figure 3: DNA binding of wild type and mutant NUDR Peptide-J and the SAND domain.
Figure 4: DNA binding surface of the SAND domain.
Figure 5: Functional activity of full length wild type and mutant NUDR in in vivo transcription assays.

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Protein Data Bank

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Acknowledgements

M.J.B. and Z.L. are grateful for EMBO/EMBL fellowships. This work was supported by the DFG (M.S.), the American Cancer Society (J.I.H.) and the NIH (M.W.C.). We are grateful to G. Stier for providing plasmids for TEV purifications, A. Urbani for advice with fluorescence titrations, H. Oschkinat and P. Schmieder (FMP, Berlin) for recording a NOESY spectrum at 750 MHz, R. Sprangers for help with the structure refinement and M. Saraste for critical reading of the manuscript.

This contribution is dedicated to the memory of Matti Saraste.

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Authors and Affiliations

  1. European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, 69117, Germany

    Matthew J. Bottomley, Zhihong Liu, Toby J. Gibson & Michael Sattler

  2. Department of Physiology, Southern Illinois University School of Medicine, Carbondale, 62901-6523, Illinois, USA

    Michael W. Collard & Jodi I. Huggenvik

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  1. Matthew J. Bottomley
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Correspondence to Michael Sattler.

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Bottomley, M., Collard, M., Huggenvik, J. et al. The SAND domain structure defines a novel DNA-binding fold in transcriptional regulation. Nat Struct Mol Biol 8, 626–633 (2001). https://doi.org/10.1038/89675

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