The three-dimensional structure of the C-terminal DNA-binding domain of human Ku70

The proteins Ku70 (69.8 kDa) and Ku80 (82.7 kDa) form a heterodimeric compl ex that is an essential component of the nonhomologous end joining DNA doub le-strand break repair pathway in mammalian cells. Interaction of Ku with D NA is central for the functions of Ku. Ku70, which is mainly responsible fo r the DNA binding activity of the Ku heterodimer, contains two DNA-binding domains. We have solved the solution structure of the Ku80-independent DNA- binding domain of Ku70 encompassing residues 536-609 using nuclear magnetic resonance spectroscopy. Residues 536-560 are highly flexible and have a ra ndom structure but form specific interactions with DNA. Residues 561-609 of Ku70 form a well defined structure with 3 alpha -helices and also interact with DNA. The three-dimensional structure indicates that all conserved hyd rophobic residues are in the hydrophobic core and therefore may be importan t for structural integrity. Most of the conserved positively charged residu es are likely to be critical for DNA recognition. The C-terminal DNA-bindin g domain of Ku70 contains a helix-extended strand-helix motif, which occurs in other nucleic acid-binding proteins and may represent a common nucleic acid binding motif.