Involved in countering a host defense mechanism which, following viral infection, activates the host anticodon nuclease and shuts off viral translation. Repairs 5'-PO4 and 3'-OH groups in the cleaved host tRNA (PubMed:16671895, PubMed:17068206, PubMed:2444436). The nick ligation reaction entails three nucleotidyl transfer steps (PubMed:12766156). In the first step, the RNA ligase reacts with ATP in the absence of nucleic acid to form a covalent ligase-AMP intermediate and release pyrophosphate (PubMed:12766156). In step 2, the ligase-AMP binds to the nicked duplex nucleic acid and transfers the adenylate to the 5'-PO4 terminus to form an adenylylated nicked intermediate (PubMed:12766156). In step 3, the RNA ligase directs the attack of the nick 3'-OH on the 5'-phosphoanhydride linkage, resulting in a repaired 3'-5' phosphodiester and release of AMP (By similarity) (PubMed:12766156). ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-(ribonucleotide)m = (ribonucleotide)n+m + AMP + diphosphate. Binds 2 magnesium ions that perform the catalytic activity via a two-metal mechanism (PubMed:28223499, PubMed:16263720). One of the catalytic Mg(2+), which is coordinated by 5 water molecules, engages the lysine nucleophile and the ATP alpha phosphate while the Mg(2+) orients the PPi leaving group (PubMed:28223499). Optimum pH is 8.0. The N-terminus contains the nucleotidyltransferase domain (PubMed:17585047). The C-terminus probably confers tRNA specificity (PubMed:17585047). Belongs to the Tequatrovirus RNA ligase 1 family. An interaction between the carbonyl oxygen of Gly-269 and the magnesium ion may occur.