X-Ray Structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase Core and its Complex with DNA

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.