Structural insights into the C-terminal domain of human KIN protein

KIN is a DNA/RNA-binding protein conserved evolutionarily from yeast to humans and expressed ubiquitously in mammals. It is an essential nuclear protein involved in cellular processes, such as DNA replication, class-switch recombination, cell cycle regulation, and response to UV or ionizing radiation-induced DNA damage. It was reported that KIN protein accumulates in the nucleus and forms intranuclear foci. The overexpression of this protein results in large intranuclear structures which prevent cell-cycle progression possibly through a disruption of the nuclear morphology which seems to modify the intranuclear network required during the DNA replication. It was also shown that the deletion of the C-terminal domain of KIN suppresses the formation of these large intranuclear structures, suggesting the fundamental role of this domain in binding to the nuclear matrix and in the anti- proliferation effect of the full-length protein. In this sense, the present study aimed to determine the three-dimensional structure of the C-terminal domain of the human KIN protein in solution, as well as to characterize the structural stability of this domain against variations in temperature, pH, and chaotropic agent and to investigate its interaction with nucleic acids of specific and non-specific sequence. The results reveal that the C-terminal domain of KIN shows a structure of tandem SH3-like subdomains, presenting a tendency to irreversible formation of amyloid-like β-structures due to increased temperature and buffer acidification and a preference for the binding to poly(G) and poly(C) RNA fragments with the interaction interface occurring between the subdomains. The findings of the present study suggest that the C-terminal domain of KIN may be responsible for the formation of the large intranuclear structures, as aggregate-like structures, and its nucleic acid binding site is broader
than that initially proposed for the KOW motif comprising 27 residues in one of the subdomains.

This work was supported by CNPq (141886/2019-6, 317157/2023-0), FAPERJ (255.940/2020,202.279/2018), Fundação Araucaria (40/2016), FAPESP (2022/13050-5, 2023/01632-2), and FINEP.