Nucleic acid binding by SAMHD1 contributes to the antiretroviral activity and is enhanced by the GpsN modification

• Published in: Nature communications 2021-02, Vol.12 (1), p.731-14, Article 731
• Main Authors: Yu, Corey H., Bhattacharya, Akash, Persaud, Mirjana, Taylor, Alexander B., Wang, Zhonghua, Bulnes-Ramos, Angel, Xu, Joella, Selyutina, Anastasia, Martinez-Lopez, Alicia, Cano, Kristin, Demeler, Borries, Kim, Baek, Hardies, Stephen C., Diaz-Griffero, Felipe, Ivanov, Dmitri N.
• Format: Article
• Language: English
• Subjects: 140/131; 38/71; 631/45/535/1266; 631/535; 692/308; 82/16; 82/6; 82/83; Allosteric properties; Antiretroviral agents; Antiretroviral drugs; BASIC BIOLOGICAL SCIENCES; Binding sites; Crystal structure; Dephosphorylation; Depletion; Design modifications; Drug development; Enzymatic activity; Guanosine triphosphate; Humanities and Social Sciences; Humans; Immunity; Immunity, Innate - genetics; Immunity, Innate - physiology; Immunomodulation; Innate immunity; Lymphocytes; Lymphocytes T; medical research; multidisciplinary; Mutation; Mutation - genetics; Myeloid cells; Nucleic acids; Nucleotides; Nucleotides - metabolism; Occupancy; Oligonucleotides; Oxidoreductases Acting on CH-CH Group Donors - genetics; Oxidoreductases Acting on CH-CH Group Donors - metabolism; Phosphorothioate; Prokaryotes; SAM Domain and HD Domain-Containing Protein 1 - genetics; SAM Domain and HD Domain-Containing Protein 1 - metabolism; Science; Science (multidisciplinary); structural biology; x-ray crystallography
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-021-21023-8

SAMHD1 impedes infection of myeloid cells and resting T lymphocytes by retroviruses, and the enzymatic activity of the protein—dephosphorylation of deoxynucleotide triphosphates (dNTPs)—implicates enzymatic dNTP depletion in innate antiviral immunity. Here we show that the allosteric binding sites of the enzyme are plastic and can accommodate oligonucleotides in place of the allosteric activators, GTP and dNTP. SAMHD1 displays a preference for oligonucleotides containing phosphorothioate bonds in the Rp configuration located 3’ to G nucleotides (GpsN), the modification pattern that occurs in a mechanism of antiviral defense in prokaryotes. In the presence of GTP and dNTPs, binding of GpsN-containing oligonucleotides promotes formation of a distinct tetramer with mixed occupancy of the allosteric sites. Mutations that impair formation of the mixed-occupancy complex abolish the antiretroviral activity of SAMHD1, but not its ability to deplete dNTPs. The findings link nucleic acid binding to the antiretroviral activity of SAMHD1, shed light on the immunomodulatory effects of synthetic phosphorothioated oligonucleotides and raise questions about the role of nucleic acid phosphorothioation in human innate immunity. SAMHD1 catalyses the dephosphorylation of deoxynucleotide triphosphates (dNTPs) and has antiretroviral activity. Here, the authors present the crystal structures of SAMHD1-oligonucleotide complexes, which reveal that the allosteric binding sites of SAMHD1 are plastic and can fit oligonucleotides in place of the two allosteric activators GTP and dNTP, and they also show that SAMHD1 recognises GpsN phosphorothioation modifications in nucleic acids, which is of interest in drug design.