LIG_RPA_C_Vert

RPA32C ligand-binding site

The RPA interacting motif is conserved in eukaryotes DNA repair and replication proteins UNG2, XPA, RAD14, TIPIN and SMARCAL1. It is involved in DNA replication and other DNA processing pathways by binding to RPA. This protein-mediated RPA conformation is also known as ‘hand-off’ model. The interaction between RPA interacting motif and RPA32C are weak but specific.

The RPA interacting motif is embedded in DNA replication and repair proteins UNG2 (P13051), XPA (P23025), TIPIN (Q9BVW5), SMARCAL1 (Q9NZC9) and RAD14 (P28519) and essential for RPA (PF08784) binding. This motif generally cooperates with the RPA32 C-terminal residues, adopting a compact globular α/β domain structure consisting of a right-handed three-helix bundle and a short three-stranded antiparallel β sheet. The binding involves hydrophobic and electrostatic interactions, which are mainly mediated by conserved hydrophobic and positively charged residues. The first amino acid of the motif is LYS or ARG, in rare cases SER. These amino acid residues interact with the negatively charged side chain of RAP32. The highly conserved hydrophobic amino acid isoleucine in the second position forms hydrophobic contacts with the side chains of S257 or T258. The charged amino acids in position five and six play an important role in the binding interaction of the motif by binding Y256 of RPA32. The aromatic ring of Y256 occupies a central position at the surface of RPA32 and participates in van der Waals contacts with the protons of positively charged amino acids. Alanine in the ninth position contributes in hydrophobic interactions with amino acid residues Y256 and T267 of the RPA32 molecule. The mostly positive charged amino acids in the twelfth and thirteenth position form hydrogen bonds with the backbone carbonyl of S250 and contribute in water-mediated hydrogen bonds with the RPA32C backbone hydroxyl group of T267. The last amino acid in the motif is LYS or ARG. These positively charged amino acids electrostatically interact with E252 of the RPA32 molecule (Mer,2000, 1DPU). The structure of SMARCAL1 binding to RPA32C shows a longer motif than described, but these amino acids are not highly conserved in other binding proteins and therefore are not required for binding to RPA32C, they just provide a better binding affinity (Xie,2014, 4MQV).

RPA_C (PF08784) Replication protein A C terminal (Stochiometry: 1 : 1)