Crystal structure of Ku Heterodimer unbound to DNA [1]
PubMed Abstract
The ( and subunits) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. The crystal structure of the human Ku heterodimer was determined both alone and bound to a 55-nucleotide element at 2.7 and 2.5 A resolution, respectively. Ku70 and Ku80 share a common topology and form a dyad-symmetrical molecule with a preformed ring that encircles duplex DNA. The binding site can cradle two full turns of DNA while encircling only the central 3-4 base pairs (bp). Ku makes no contacts with DNA bases and few with the sugar-phosphate backbone, but it fits sterically to major and minor groove contours so as to position the DNA helix in a defined path through the protein ring. These features seem well designed to structurally support broken DNA ends and to bring the DNA helix into phase across the junction during end processing and ligation. [2]
Ku Ring
The is composed of a broad base of beta barrels that cradle the DNA, and a narrow bridge that serves to protect the double strand break from base pairing with other DNA base pairs and degradation [3]. There is little interaction between the ring and the backbone or base pairs of DNA; instead, the ring associates with DNA by the cradle fitting into the major grooves of the helix [4]. The positive electrostatic charge caused by polarization of the ring also allows the negatively charged backbone of DNA to be guided into the correct position [5] (NEED SCENE OF POS CHARGE OR POLARIZATION). The Ku protein also has a high affinity to DNA due to its form being preset for the helix. As a result of the asymmetric ring, there is a strong preference (Kd value of 1.5 to 4 X 10^-10 M[6]) for the to slide onto the ends of DNA [7]. In addition, other asymmetric features, such as a abundance of Asp residues on the N terminus of the (NEED SCENE OF ASP ON N-TERMINUS OR MAYBE JUST ASP IN GENERAL), prevent the Ku protein from sliding further on the DNA helix. While wrapping over the entire helix, the is thin over the bridge, allowing ligases and polymerases to efficiently interact in non-homologous end joining (NHEJ). [8]
Domains
Consisting of three domains (, , ), the dimerizes with the to form the protein [9]. Unlike other DNA binding proteins, the Ku protein is asymmetrical from the differences between the Ku70 and Ku80 subunits. This asymmetry leads to different favorable locations for DNA based on major and minor grooves [10]. The is angled closer to at the double strand break, providing protectiion and interaction with its domains (SOURCE #2). In contrast, the associates with away from the free end [11]. Once a homodimer, the protein has diverged into two domains that are now 15% similar in residues (SOURCE #3).
Contained inside the is a Rossman fold at the N terminus that is used to bind nucleotides in [12]. In terms of protein structure, the contributes little to the dimer interface between the subunits. The C terminus of the domain can be bound to other repair molecules, using as a scaffold [13].
The is the main source of interactions of the itself and , with each being composed of seven β strands with the majority in antiparallel arrangement [14]. The quantity of the strands lends the structures to be symmetrical. Both in the dimer form the base of the cradle by fitting in the grooves of .
The is an α-helical domain that associates with the β-barrel of the opposite subunit, with the arm stretching across the [15]. As a result, the strengthens the cradle composed of the two β-barrels.
The DNA binding ring on the open end of DNA is associated with the . By binding , Ku realigns the the strands and protects the molecule from degradation and unwanted bonds while NHEJ occurs [16]. The regulation of the DNA binding ring of Ku is still under research, with data supporting oxidative stress and redox reactions decreasing the association of the with through alterations in cysteine residues on the (NEED SOURCE 3 and 4, NEED SCENE OF CYSTEINES).
Function
The serves to assist in non-homologous end joining (NHEJ), and also in telomere synthesis and protection. These functions are separate interactions based on key residues that are being identified through current research. Recent research also links the Ku protein with heterochromatin formation through interaction with Rif and Sir proteins (NEED SOURCE 3 and 4).
