Metal ions govern coronavirus endoribonuclease activity

Coronavirus nonstructural protein 15 (nsp15) is an endoribonuclease that restricts viral double-stranded RNA (dsRNA) accumulation in the cytosol to evade host immunity. Given the co-localization of nsp15 and replicating viral RNA, the mechanism controlling nsp15 activity is essential, yet poorly understood. Although metal ions are widely used as cofactors for enzymes, their role in nsp15 remains elusive. Here, we show that Co2+ or Ni2+ potently activates, whereas Zn2+ inhibits nsp15 of multiple coronaviruses. In the presence of Co2+, cryo-electron microscopy structures of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nsp15/dsRNA complexes indicate higher dsRNA-binding affinity. Active-site mutation H249A weakens the effects of Co2+, Ni2+, and Zn2+ on SARS-CoV-2 nsp15. Furthermore, the Co2+- or Ni2+-dependent activation of nsp15 is inhibited upon Zn2+ addition, suggesting competitive regulation. Overall, our work identifies the activator and inhibitor ions of nsp15 and suggests a metal-dependent regulatory mechanism of nsp15 activity.