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HBP1 and Mad1 repressors bind the Sin3 corepressor PAH2 domain with opposite helical orientations

Nature Structural & Molecular Biology volume 11, pages 738–746 (2004)Cite this article

Abstract

Recruitment of the histone deacetylase (HDAC)-associated Sin3 corepressor is an obligatory step in many eukaryotic gene silencing pathways. Here we show that HBP1, a cell cycle inhibitor and regulator of differentiation, represses transcription in a HDAC/Sin3-dependent manner by targeting the mammalian Sin3A (mSin3A) PAH2 domain. HBP1 is unrelated to the Mad1 repressor for which high-resolution structures in complex with PAH2 have been described. We show that like Mad1, the HBP1 transrepression domain binds through a helical structure to the hydrophobic cleft of mSin3A PAH2. Notably, the HBP1 helix binds PAH2 in a reversed orientation relative to Mad1 and, equally unexpectedly, this is correlated with a chain reversal of the minimal Sin3 interaction motifs. These results not only provide insights into how multiple, unrelated transcription factors recruit the same coregulator, but also have implications for how sequence similarity searches are conducted.

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Figure 1: HBP1 binds mSin3.
Figure 2: Defining the minimal interaction domains of HBP1 and mSin3A.
Figure 3: NMR spectra establishing a specific interaction between mSin3A PAH2 and HBP1 SID.
Figure 4: Solution structures of the mSin3A PAH2–HBP1 SID complex and the newly refined mSin3A PAH2–Mad1 SID complex.
Figure 5: HBP1 SID binds to a deep hydrophobic cleft in the mSin3A PAH2 domain.
Figure 6: A comparison of intermolecular interactions in the PAH2–HBP1 SID and PAH2–Mad1 SID complexes.

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Acknowledgements

We thank M. Adams for assistance with pull-down assays. This work was supported by funds from the March of Dimes Birth Defects Foundation (no. 5-FY00-605) and the US National Institutes of Health (NIH) (GM 64715) to I.R. and by funds from the NIH (CA 57138) and an American Cancer Society research professorship to R.N.E. K.A.S. was supported by an NIH molecular biophysics training grant and P.S.K. is a special fellow of the Leukemia and Lymphoma Society. We are grateful to the Lurie Comprehensive Cancer Center for supporting structural biology research at Northwestern and the Keck Biophysics Facility for access to instrumentation.

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Author notes

  1. Kurt A Swanson and Paul S Knoepfler: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, 60208-3500, Illinois, USA

    Kurt A Swanson, Kai Huang, Richard S Kang & Ishwar Radhakrishnan

  2. Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, 98109, Washington, USA

    Paul S Knoepfler, Shaun M Cowley, Carol D Laherty & Robert N Eisenman

  3. Structural Biology NMR Facility, Northwestern University, Evanston, 60208-3500, Illinois, USA

    Kai Huang

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Correspondence to Robert N Eisenman or Ishwar Radhakrishnan.

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Supplementary information

Supplementary Fig. 1

ITC binding isotherms resulting from titrations of mSin3A PAH2 with HBP1 SID peptide (residues 358–380). (PDF 29 kb)

Supplementary Fig. 2

Primary and secondary NMR data establishing a helical conformation for HBP1 SID and the mode of interaction with the mSin3A PAH2 domain. (PDF 263 kb)

Supplementary Fig. 3

Primary and secondary NMR data establishing a helical conformation for Mad1 SID and the mode of interaction with the mSin3A PAH2 domain. (PDF 144 kb)

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Swanson, K., Knoepfler, P., Huang, K. et al. HBP1 and Mad1 repressors bind the Sin3 corepressor PAH2 domain with opposite helical orientations. Nat Struct Mol Biol 11, 738–746 (2004). https://doi.org/10.1038/nsmb798

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