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Dürr, Harald (2005): X-Ray Structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase Core and its Complex with DNA. Dissertation, LMU München: Faculty of Chemistry and Pharmacy
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Abstract

Dynamic remodeling of chromatin or other persistent protein:DNA complexes is essential for genome expression and maintenance. Proteins of the SWI2/SNF2 family catalyze rearrangements of diverse protein:DNA complexes. Although SWI2/SNF2 enzymes exhibit a diverse domain organisation, they share a conserved catalytic ATPase domain that is related to superfamily II helicases through the presence of seven conserved sequence motifs. In contrast to helicases, SWI2/SNF2 enzymes lack helicase activity, but use ATP hydrolysis to translocate on DNA and to generate superhelical torsion into DNA. How these features implicate remodeling function or how ATP hydrolysis is coupled to these rearrangements is poorly understood and suffers from the lack of structural information regarding the catalytic domain of SWI2/SNF2 ATPase In this PhD thesis I characterized the catalytic domain of Sulfolobus solfataricus Rad54 homolog (SsoRad54cd). Like the eukaryotic SWI2/SNF2 ATPases, SsoRad54cd exhibits dsDNA stimulated ATPase activity, lacks helicase activity and has dsDNA translocation and distortion activity. These activities are thereby features of the conserved catalytic ATPase domain itself. Furthermore, the crystal structures of SsoRad54cd in absence and in complex with its dsDNA substrate were determined. The Sulfolobus solfataricus Rad54 homolog catalytic domain consists of two RecA-like domains with two helical SWI2/SNF2 specific subdomains, one inserted in each domain. A deep cleft separates the two domains. Fully base paired duplex DNA binds along the domain 1: domain 2 interface in a position, where rearrangements of the two RecA-like domains can directly be translated in DNA manipulation. The binding mode of DNA to SsoRad54cd is consistent with an enzyme that translocate along the minor groove of DNA. The structure revealed a remarkable similarity to superfamily II helicases. The related composite ATPase active site as well as the mode of DNA recognition suggests that ATP-driven transport of dsDNA in the active site of SWI2/SNF2 enzymes is mechanistically related to ATP-driven ssDNA in the active site of helicases. Based on structure-function analysis a specific model for SWI2/SNF2 function is suggested that links ATP hydrolysis to dsDNA translocation and DNA distortion. The represented results have structural implications for the core mechanism of remodeling factors. If SWI2/SNF2 ATPases are anchored to the substrate protein:DNA complex by additional substrate interacting domains or subunits, ATP-driven cycles of translocation could transport DNA towards or away from the substrate or generate torsional stress at the substrate:DNA interface. Finally, I provide a molecular framework for understanding mutations in Cockayne and X-linked mental retardation syndromes. Mapping of the mutations on the structure of SsoRad54cd reveal that the mutations colocalize in two surface clusters: Cluster I is located adjacent to a hydrophobic surface patch that may provide a macromolecular interaction site. Cluster II is situated in the domain 1 : domain 2 interface near the proposed pivot region and may interfere with ATP driven conformational changes between domain 1 and domain 2.