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Structural insights into human KAP1 PHD finger–bromodomain and its role in gene silencing

Nature Structural & Molecular Biology volume 15, pages 626–633 (2008)Cite this article

Abstract

The tandem PHD finger–bromodomain, found in many chromatin-associated proteins, has an important role in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). Here we report the three-dimensional solution structure of the tandem PHD finger–bromodomain of KAP1. The structure reveals a distinct scaffold unifying the two protein modules, in which the first helix, αZ, of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other. A comprehensive mutation-based structure-function analysis correlating transcriptional repression, ubiquitin-conjugating enzyme 9 (UBC9) binding and SUMOylation shows that the PHD finger and the bromodomain of KAP1 cooperate as one functional unit to facilitate lysine SUMOylation, which is required for KAP1 co-repressor activity in gene silencing. These results demonstrate a previously unknown unified function for the tandem PHD finger–bromodomain as an intramolecular small ubiquitin-like modifier (SUMO) E3 ligase for transcriptional silencing.

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Figure 1: Three-dimensional structure of the tandem PHD finger–bromodomain of human KAP1.
Figure 2: Interdomain interactions in tandem-domain motifs.
Figure 3: Structural features of the bromodomain and the PHD finger of KAP1.
Figure 4: Human KAP1 PHD finger–bromodomain acts as one functional unit in SUMOylation and transcriptional repression.

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Acknowledgements

We wish to acknowledge the use of the NMR facilities at the New York Structural Biology Center for this study. K.L.Y. was supported by a Terry Fox Foundation postdoctoral fellowship from the National Cancer Institute of Canada. F.J.R. was supported by grants from the US National Institutes of Health (CA095561 and CA092088), The Samuel Waxman Cancer Research Foundation, The Pardee Foundation and The Commonwealth Universal Research Enhancement Program, Pennsylvania Department of Health. M.-M.Z. was in part supported by funds from the Dr. Golden and Harold Lamport Chair, and grants from the US National Institutes of Health (CA087658) and the US National Science Foundation (#0517352).

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Authors and Affiliations

  1. Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York University, 1425 Madison Avenue, New York, 10029, New York, USA

    Lei Zeng, Kyoko L Yap, Xueqi Wang, Shiraz Mujtaba, Olga Plotnikova & Ming-Ming Zhou

  2. The Wistar Institute, 3601 Spruce Street, Philadelphia, 19104, Pennsylvania, USA

    Alexey V Ivanov & Frank J Rauscher III

  3. Department of Biochemistry, MBR Cancer Center, West Virginia University School of Medicine, Morgantown, West Virginia, 26506, USA

    Alexey V Ivanov

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Contributions

L.Z. determined the protein structure by NMR, K.L.Y. characterized the protein structure-function by NMR; A.V.I. performed in vitro SUMOylation and transcription repression studies; X.W., S.M., and O.P. contributed to molecular cloning, protein purification and characterization of the study. The project was directed by M.-M.Z. and F.J.R. All authors contributed to the preparation of the manuscript.

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Correspondence to Ming-Ming Zhou.

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Zeng, L., Yap, K., Ivanov, A. et al. Structural insights into human KAP1 PHD finger–bromodomain and its role in gene silencing. Nat Struct Mol Biol 15, 626–633 (2008). https://doi.org/10.1038/nsmb.1416

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