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Architecture of nonspecific protein–DNA interactions in the Sso7d–DNA complex

Nature Structural Biology volume 5, pages 579–584 (1998)Cite this article

Abstract

Many biochemical processes, including DNA packing, maintenance and control, rely on non-sequence specific protein–DNA interactions. Nonspecific DNA-binding proteins have evolved to tolerate a wide range of DNA sequences, yet bind with a respectable affinity. The nonspecific binding requirement is in contrast to that imposed on, for example, transcription factors and implies a different structural basis for the biomolecular recognition process. To address this issue, and the mechanism for archaeal DNA packing, we determined the structure of the Sso7d protein from Sulfolobus solfataricus in complex with DNA. Sso7d binds DNA by placing a triple-stranded β-sheet across the DNA minor groove. The protein is anchored in this position by the insertion of hydrogen bond-donating side chains into the groove and additionally stabilized by electrostatic and non-polar interactions with the DNA backbone. This structure explains how strong binding can be achieved independent of DNA sequence. Sso7d binding also distorts the DNA conformation and introduces significant unwinding of the helix. This effect suggests a mechanism for DNA packing in Sulfolobus based on negative DNA supercoiling.

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Figure 1: Sequence and secondary structure elements of the Sso7d protein from Sulfolobus solfataricus.
Figure 2: Scatchard plot based on a titration of GC3 DNA on Sso7d.
Figure 3
Figure 4: Illustration of the GC3 DNA sequence and observed intermolecular Sso7d–DNA NOE connectivities.
Figure 5: A set of calculated (SA) structures of a monomeric part of the Sso7d–DNA complex superimposed by the backbone atoms of the protein.
Figure 6: Topology of the dimeric Sso7d–DNA complex.
Figure 7: View of protein interactions in the DNA minor groove.
Figure 8: Comparison of the DNA structure in the Sso7d–DNA complex with that of standard B-form DNA.

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Acknowledgements

This work was supported by the Swedish Natural Sciences Research Council (NFR), the Magn. Bervall Foundation and by the EC project Biotechnology of Extremophiles. We thank Mats Wikström and Toshi Nishida at Pharmacia & Upjohn for providing measurement time on an 800 MHz NMR spectrometer.

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Authors and Affiliations

  1. Department of Biotechnology, Center for Structural Biochemistry, The Royal Institute of Technology (KTH), S-141 57 Huddinge, Novum, Sweden

    Peter Agback & Torleif Härd

  2. Department of Biosciences, Karolinska Institute, S-141 57 Huddinge, Novum, Sweden

    Herbert Baumann, Stefan Knapp & Rudolf Ladenstein

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Correspondence to Torleif Härd.

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Agback, P., Baumann, H., Knapp, S. et al. Architecture of nonspecific protein–DNA interactions in the Sso7d–DNA complex. Nat Struct Mol Biol 5, 579–584 (1998). https://doi.org/10.1038/836

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