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<StructureSection load='1JEY' size='350' side='right' caption='Structure of the Ku heterodimer bound to DNA (PDB entry [[1jey]])' scene='56/567269/Ku_heterodimer/4'> == Overview == The '''Ku protein''' or '''X-ray repair cross-complementing protein''' binds to the ends of double-strand breaks and it is required in DNA-repair for non-homologous end joining. The eukaryotic Ku protein is a <scene name='56/567269/Ku_heterodimer/3'>heterodimer</scene> composed of a <scene name='56/567269/Ku70_subunit/3'>Ku70 subunit</scene> or '''X-ray repair cross-complementing protein 6''' and a <scene name='56/567269/Ku80_subunit/3'>Ku80 subunit</scene> or '''X-ray repair cross-complementing protein 5''' . This 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 <scene name='56/567269/Bound_dna/3'>bound to a 55-nucleotide DNA</scene> 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. <ref name="Walker"> PMID: 11493912</ref> [[Image:1jeq.jpg|350px|center|thumb| Crystal structure of Ku Heterodimer unbound to DNA<ref name="Walker"/>]] {{clear}} == Structure == === Ku Ring === The <scene name='56/567269/Ku_ring/1'>Ku Ring</scene> 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 <ref name="Walker"/>. 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 <ref name="Walker"/>. 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 <ref name="Walker"/>. 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<ref name="Walker"/>) for the Ku ring to slide onto the ends of DNA <ref name="Walker"/>. In addition, other asymmetric features, such as a abundance of Asp residues on the N terminus of the Ku Ring, prevent the Ku protein from sliding further on the DNA helix. While wrapping over the entire helix, the Ku ring is thin over the bridge, allowing ligases and polymerases to efficiently interact in [http://en.wikipedia.org/wiki/Non-homologous_end_joining non-homologous end joining (NHEJ)]. <ref name="Walker"/> == Domains == Consisting of <scene name='56/567269/Ku70_dimer/9'>four domains</scene> (α/β-Domain, β-barrel, C-terminal arm, DNA-binding ring), the Ku70 subunit dimerizes with the Ku80 subunit to form the protein.<ref name="Walker"/> 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.<ref name="Walker"/> The Ku70 subunit is <scene name='56/567269/Ku70_subunit/5'>angled closer</scene> to DNA at the double strand break, providing protection and interaction with its domains.<ref name="source2"> PMID: 19715578</ref> In contrast, the Ku80 subunit <scene name='56/567269/Ku80_subunit/5'>associates with</scene> DNA away from the free end.<ref name="Walker"/> Once a homodimer, the protein has diverged into two domains that are now 15% similar in residues. <ref name="source3"> PMID: 9663392</ref> === α/β-Domain === Contained inside the <scene name='56/567269/Ku70_dimer/2'>α/β-Domain</scene> is a [http://en.wikipedia.org/wiki/Rossman_fold Rossman fold] at the N terminus that is used to bind nucleotides in DNA.<ref name="Walker"/> In terms of protein structure, the α/β-Domain contributes little to the dimer interface between the subunits. The C terminus of the domain can be bound to other repair molecules, using the α/β-Domain as a scaffold.<ref name="Walker"/> === β-barrel === The <scene name='56/567269/Ku70_dimer/4'>β-barrel</scene> is the main source of interactions of the Ku heterodimer itself and DNA helix, with each β-barrel being composed of seven β strands with the majority in antiparallel arrangement.<ref name="Walker"/> The quantity of the strands lends the structures to be symmetrical. Both β-barrel in the dimer form the base of the cradle by fitting in the grooves of DNA. === C-terminal arm === The <scene name='56/567269/Ku70_dimer/7'>C-terminal arm</scene> is an α-helical domain that associates with the β-barrel of the opposite subunit, with the arm stretching across the DNA helix.<ref name="Walker"/> As a result, the C-terminal arm strengthens the cradle composed of the two β-barrels. === DNA binding ring === The <scene name='56/567269/Ku70_dimer/6'>DNA binding ring</scene> on the open end of DNA is associated with the Ku70 subunit. By binding DNA, Ku realigns the the strands and protects the molecule from degradation and unwanted bonds while NHEJ occurs.<ref name="Walker"/> 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 Ku heterodimer with bound DNA through alterations in cysteine residues on the Ku70 subunit. <ref name="source3"/> <ref name="source4"> PMID: 14585978</ref> == Function == The <scene name='56/567269/Ku_heterodimer/3'>Ku heterodimer</scene> serves to assist in [http://en.wikipedia.org/wiki/Non-homologous_end_joining 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 [http://en.wikipedia.org/wiki/Rif_(GTPase) Rif proteins] and [http://en.wikipedia.org/wiki/Sir2 Sir proteins]. <ref name="source3"/><ref name="source4"/> <ref>Berg, Jeremy M., John L. Tymoczko, and Lubert Stryer. Biochemistry. 7th ed. New York: W.H. Freeman and, 2012. [http://www.whfreeman.com/Catalog/product/biochemistry-seventhedition-berg ISBN-10: 1-4292-2936-5]</ref> </StructureSection> == 3D Structures of Ku protein == Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}} [[1jey]], [[5y58]] – hKu70 + Ku80 + DNA – human<br /> [[1jeq]] – hKu70 + Ku80 <br /> [[7axz]] – hKu70 + Ku80 – Cryo EM<br /> [[6zh6]] – hKu80 + DNA-dependent protein kinase – Cryo EM<br /> [[7k0y]], [[7k1j]], [[7k1k]], [[7k1n]] – hKu70 + Ku80 + DNA-dependent protein kinase – Cryo EM<br /> [[6erf]], [[6erg]], [[6erh]] – hKu70 + Ku80 + non-homologous end-joining factor + DNA <br /> [[1jjr]] – hKu70 C terminal - NMR <br /> [[1rw2]], [[1q2z]] – hKu80 C terminal - NMR <br /> [[6tyt]], [[6tyu]], [[6tyv]], [[6tyw]], [[6tyx]], [[6tyz]] – hKu80 von Willebrand domain 1-242 (mutant) + peptide <br /> [[7lt3]] – hKu70 + Ku80 in NHEJ synaptic complex – Cryo EM<br /> == References== <references /> [[Category:Topic Page]]

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