Structural Characterization of the DNA Repair Protein Complex SbcC-SbcD of Thermotoga maritima

DNA damage poses a considerable threat to genomic integrity and
cell survival. One of the most harmful forms of DNA damage are
double-strand breaks that arise spontaneously during regular DNA
processing like replication or meiosis. In addition, they can also
be induced by a variety of DNA damaging agents like UV light, cell
toxins or anti-cancer drugs. Failure of the rapid repair of these
breaks can lead to chromosomal rearrangements and ultimately
tumorigenesis in humans. In response to these genomic threats, a
highly developed DNA repair network of protein factors has evolved,
where the Mre11/Rad50/Nbs1 (MRN) complex is sought to play a key
role in sensing, processing and repair of DNA double-strand breaks.
Orthologs of Mre11 and Rad50, but not Nbs1, are found in all
taxonomic kingdoms of life, suggesting that Mre11 and Rad50 form
the core of this complex. In this work structural studies were
performed to decipher the overall architecture and the interaction
of SbcC and SbcD, the bacterial orthologs of Rad50 and Mre11. Using
X-ray crystallographic and small angle X-ray scattering techniques
the crystal as well as the in solution structures of the Thermotoga
maritima SbcC ATPase domain in complex with full-length SbcD were
solved. The crystal and in solution structure match well fortifying
the calculated models that reveal an open, elongated complex with
dimensions of approximately 210 Å * 75 Å * 65 Å. The
heterotetrameric protein assembly consists of two SbcD molecules
that homodimerize at domains I to form the central portion of the
complex. Located at the outer areas of this homodimer domains II
are arranged close to lobe II of SbcC building a small
protein-protein interface. The C-terminal domains III of SbcD are
connected to domains II via a flexible linker and associate through
hydrophobic interactions with the coiled-coils of SbcC. These
arrangements in combination with earlier findings lead to a model
where upon ATP-binding the complex performs a conformational switch
resulting in a ring-shaped structure. This conformation would bear
a central cavity to harbor DNA strands that can be processed by the
inwards oriented nuclease active sites of SbcD.