Resonance assignments, solution structure, and backbone dynamics of the DNA- and RPA-binding domain of human repair factor XPA

XPA is involved in the damage recognition step of nucleotide excision repai r (NER), XPA binds to other repair factors, and acts as a key element in NE R complex formation. The central domain of human repair factor XPA (residue s Met98 to Phe219) is responsible for the preferential binding to damaged D NA and to replication protein A (RPA), The domain consists of a zinc-contai ning subdomain with a compact globular structure and a C-terminal subdomain with a positively charged cleft in a novel alpha/beta structure. The reson ance assignments and backbone dynamics of the central domain of human XPA w ere studied by multidimensional heteronuclear NMR methods, N-15 relaxation data were obtained at two static magnetic fields, and analyzed by means of the model-free formalism under the assumption of isotropic or anisotropic r otational diffusion, In addition, exchange contributions were estimated by analysis of the spectral density function at zero frequency. The results sh ow that the domain exhibits a rotational diffusion anisotropy (D-parallel t o/D-perpendicular to) of 1.38, and that most of the flexible regions exist on the DNA binding surface in the cleft in the C-terminal subdomain, This f lexibility may be involved in the interactions of XPA with various kinds of damaged DNA.