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Structure of a HAP1–DNA complex reveals dramatically asymmetric DNA binding by a homodimeric protein

Nature Structural Biology volume 6, pages 64–71 (1999)Cite this article

Abstract

HAP1 is a member of a family of fungal transcription factors that contain a Zn2Cys6 binuclear cluster domain and bind as homodimers to sequences containing two DNA half sites. We have determined the 2.5 Å crystal structure of HAP1 bound to a cognate upstream activation sequence from the CYC7 gene. The structure reveals that HAP1 is bound in a dramatically asymmetric manner to the DNA target. This asymmetry aligns the Zn2Cys6 domains in a tandem head-to-tail fashion to contact two DNA half sites, positions an N-terminal arm of one of the protein subunits to interact with the inter-half site base pairs in the DNA minor groove, and suggests a mechanism by which DNA-binding facilitates asymmetric dimerization by HAP1. Comparisons with the DNA complexes of the related GAL4, PPR1 and PUT3 proteins illustrate how a conserved protein domain can be reoriented to recognize DNA half sites of different polarities and how homodimeric proteins adopt dramatically asymmetric structures to recognize cognate DNA targets.

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Figure 1: The HAP1 DNA Binding Domain, UASCYC7, and binding sites of various family members.
Figure 2: Overall structure of the HAP1–DNA, GAL4–DNA, PPR1–DNA and PUT3–DNA complexes.
Figure 3: Hydrophobic contacts mediated at the interface of the HAP1 dimer.
Figure 4: Protein–DNA contacts in the HAP1–DNA complex.
Figure 5: Mapping PC mutations onto the DNA-binding domain of HAP1.

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Acknowledgements

We thank A. Lukens, T. Stams, C. Lesburg, X. Li, Y. Mo, S. Benson, R. Venkataramani, and K. Swaminathan for useful discussions. This work was supported by a grant form the NIH and a junior faculty research award from the ACS to R.M.

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Authors and Affiliations

  1. The Wistar Institute and The Department of Chemistry, University of Pennsylvania, Philadelphia, 19104, Pennsylvania, USA

    Daniel A. King & Ronen Marmorstein

  2. Department of Biochemistry, New York University Medical Center, New York University, New York, 10016, New York, USA

    Li Zhang

  3. Department of Biology, Massachusetts Institute of Technology, Cambridge, 02129, Massachusetts, USA

    Leonard Guarente

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Correspondence to Ronen Marmorstein.

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King, D., Zhang, L., Guarente, L. et al. Structure of a HAP1–DNA complex reveals dramatically asymmetric DNA binding by a homodimeric protein. Nat Struct Mol Biol 6, 64–71 (1999). https://doi.org/10.1038/4940

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