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Structure of the SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54

Nature Structural & Molecular Biology volume 12, pages 350–356 (2005)Cite this article

Abstract

SWI2/SNF2 chromatin-remodeling proteins mediate the mobilization of nucleosomes and other DNA-associated proteins. SWI2/SNF2 proteins contain sequence motifs characteristic of SF2 helicases but do not have helicase activity. Instead, they couple ATP hydrolysis with the generation of superhelical torsion in DNA. The structure of the nucleosome-remodeling domain of zebrafish Rad54, a protein involved in Rad51-mediated homologous recombination, reveals that the core of the SWI2/SNF2 enzymes consist of two α/β-lobes similar to SF2 helicases. The Rad54 helicase lobes contain insertions that form two helical domains, one within each lobe. These insertions contain SWI2/SNF2-specific sequence motifs likely to be central to SWI2/SNF2 function. A broad cleft formed by the two lobes and flanked by the helical insertions contains residues conserved in SWI2/SNF2 proteins and motifs implicated in DNA-binding by SF2 helicases. The Rad54 structure suggests that SWI2/SNF2 proteins use a mechanism analogous to helicases to translocate on dsDNA.

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Figure 1: Overview of the structure of zebrafish Rad54 (dnRad54ΔN).
Figure 2: Surface conservation of Rad54.
Figure 3: Overview of the SWI2/SNF2-specific domains HD1 and HD2.
Figure 4: The position of canonical helicase motifs and SWI2/SNF2-specific helicase motifs in Rad54.
Figure 5: Juxtapositions of nucleic acid–bound RecG and HCV NS3 with the structure of Rad54.

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Acknowledgements

The authors thank C. Ogata at APS 8BM, and A. Mulichak and L. Keefe at APS IMCA-CAT ID17, for help during data collection; and M. Lu of the Weill Cornell Medical Center (New York) for help with the analytical ultracentrifugation experiments. N.H.T would like to acknowledge the Human Frontiers Science Program for a long-term fellowship.

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Authors and Affiliations

  1. Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, 10021, New York, USA

    Nicolas H Thomä, Bryan K Czyzewski & Nikola P Pavletich

  2. Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, 10021, New York, USA

    Bryan K Czyzewski & Nikola P Pavletich

  3. Division of Biological Sciences, Sections of Microbiology and of Molecular and Cellular Biology, University of California, Davis, 95616-8665, California, USA

    Andrei A Alexeev & Stephen C Kowalczykowski

  4. Department of Biochemistry, Drexel University College of Medicine, Philadelphia, 19102-1192, Pennsylvania, USA

    Alexander V Mazin

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Correspondence to Nikola P Pavletich.

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Supplementary information

Supplementary Fig. 1

The zebrafish Rad54 crystallization construct is active in supercoiling assays. (PDF 501 kb)

Supplementary Fig. 2

Alignment of Rad54 orthologs. (PDF 137 kb)

Supplementary Fig. 3

Section of the electron density map of Rad54. (PDF 883 kb)

Supplementary Fig. 4

DNA binding activity of Rad54. (PDF 486 kb)

Supplementary Fig. 5

Analytical ultra-centrifugation indicated that Rad54 is monomeric in solution. (PDF 116 kb)

Supplementary Table 1

Zebrafish Rad54 has DNA dependent ATPase activity comparable to that of the human enzyme. (PDF 96 kb)

Supplementary Table 2

Conservation of helicase motifs. (PDF 115 kb)

Supplementary Methods (PDF 76 kb)

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Thomä, N., Czyzewski, B., Alexeev, A. et al. Structure of the SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54. Nat Struct Mol Biol 12, 350–356 (2005). https://doi.org/10.1038/nsmb919

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