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Structure and mechanism of the Swi2/Snf2 remodeller Mot1 in complex with its substrate TBP

Nature volume 475, pages 403–407 (2011)Cite this article

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Abstract

Swi2/Snf2-type ATPases regulate genome-associated processes such as transcription, replication and repair by catalysing the disruption, assembly or remodelling of nucleosomes or other protein–DNA complexes1,2. It has been suggested that ATP-driven motor activity along DNA disrupts target protein–DNA interactions in the remodelling reaction3,4,5. However, the complex and highly specific remodelling reactions are poorly understood, mostly because of a lack of high-resolution structural information about how remodellers bind to their substrate proteins. Mot1 (modifier of transcription 1 in Saccharomyces cerevisiae, denoted BTAF1 in humans) is a Swi2/Snf2 enzyme that specifically displaces the TATA box binding protein (TBP) from the promoter DNA and regulates transcription globally by generating a highly dynamic TBP pool in the cell6,7. As a Swi2/Snf2 enzyme that functions as a single polypeptide and interacts with a relatively simple substrate, Mot1 offers an ideal system from which to gain a better understanding of this important enzyme family. To reveal how Mot1 specifically disrupts TBP–DNA complexes, we combined crystal and electron microscopy structures of Mot1–TBP from Encephalitozoon cuniculi with biochemical studies. Here we show that Mot1 wraps around TBP and seems to act like a bottle opener: a spring-like array of 16 HEAT (huntingtin, elongation factor 3, protein phosphatase 2A and lipid kinase TOR) repeats grips the DNA-distal side of TBP via loop insertions, and the Swi2/Snf2 domain binds to upstream DNA, positioned to weaken the TBP–DNA interaction by DNA translocation. A ‘latch’ subsequently blocks the DNA-binding groove of TBP, acting as a chaperone to prevent DNA re-association and ensure efficient promoter clearance. This work shows how a remodelling enzyme can combine both motor and chaperone activities to achieve functional specificity using a conserved Swi2/Snf2 translocase.

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Figure 1: Overview of the EcMot1(NTD)–EcTBP structure.
Figure 2: Details of the interaction interfaces and latch function.
Figure 3: Three-dimensional reconstruction of the EcMot1–EcTBP complex and model of the EcMot1–EcTBP–DNA complex.
Figure 4: Proposed remodelling mechanism.

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Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors for the reported crystal structures have been deposited with the Protein Data Bank under accession codes 3OCI (EcTBP) and 3OC3 (EcTBP–EcMot1(NTD) complex).

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Acknowledgements

We thank the Max-Planck Crystallization Facility Martinsried. We thank M. Lucas, A. Schele, C. Ungewickell, J. Goetzl and Y. Hiruma for help with experimentation. We thank J.-P. Armache and M. Turk for help with electron microscopy data. We are grateful to G. Miller and S. Hahn for advice. We thank the staff at the SLS and ESRF for help with data collection. We thank P. Cramer and members of the Hopfner and Auble laboratories for discussions and comments on the manuscript. This work was supported by the German Research Council (SFB 646 and SFB/TR5) and Excellence Initiative (Center for Integrated Protein Science, Munich) to K.-P.H. and R.B., by DFG grant WE4628/1 to P.Wendler and by NIH grant GM55763 to D.T.A.

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  1. Sheng Cui

    Present address: Present address: Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 9, Dong Dan San Tiao, Beijing 100730, China.,

Authors and Affiliations

  1. Department of Biochemistry, Ludwig-Maximilians University, Feodor-Lynen-Strasse 25, 81377 Munich, Germany,

    Petra Wollmann, Sheng Cui, Otto Berninghausen, Manuela Moldt, Gregor Witte, Agata Butryn, Petra Wendler, Roland Beckmann & Karl-Peter Hopfner

  2. Munich Center for Advanced Photonics, Gene Center Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany ,

    Petra Wollmann, Gregor Witte & Karl-Peter Hopfner

  3. Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, 22908, Virginia, USA

    Ramya Viswanathan, Melissa N. Wells & David T. Auble

  4. Center for Integrated Protein Science, Gene Center Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany ,

    Gregor Witte, Roland Beckmann & Karl-Peter Hopfner

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Contributions

S.C. and M.M. cloned, purified and crystallized EcTBP; S.C. solved its structure. S.C., A.B., M.M. and P.Wollmann cloned, purified and crystallized EcTBP–EcMot1(NTD); P.Wollmann collected data and P.Wollmann, G.W. and K.-P.H. solved the complex structures. R.V. performed FeBABE experiments, M.N.W. conducted yeast molecular biological manipulations and D.T.A. performed gelshifts. P.Wendler, O.B. and R.B. performed and interpreted electron microscopy experiments. P.Wollmann, P.Wendler, R.B., D.T.A. and K.-P.H. planned and interpreted the experiments. D.T.A. and K.-P.H. wrote the manuscript and all authors provided editorial input.

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Correspondence to David T. Auble or Karl-Peter Hopfner.

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Wollmann, P., Cui, S., Viswanathan, R. et al. Structure and mechanism of the Swi2/Snf2 remodeller Mot1 in complex with its substrate TBP. Nature 475, 403–407 (2011). https://doi.org/10.1038/nature10215

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