Fungal tRNA ligase (Trl1) is an essential enzyme that repairs RNA breaks with 2,3-cyclic-PO4 and 5-OH ends inflicted during tRNA splicing and noncanonical mRNA splicing in the fungal unfolded protein response. Trl1 is composed of C-terminal cyclic phosphodiesterase (CPD) and central GTPdependent polynucleotide kinase (KIN) domains that heal the broken ends to generate the 3-OH,2-PO4 and 5-PO4 termini required for sealing by an Nterminal ATP-dependent ligase domain (LIG). Here we report crystal structures of the Trl1-LIG domain from Chaetomium thermophilum at two discrete steps along the reaction pathway: the covalent LIG-(lysyl-N)-AMP Mn2+ intermediate and a LIG ATP (Mn2+)2 Michaelis complex. The structures highlight a two-metal mechanism whereby a pentahydrated metal complex stabilizes the transition state of the ATP phosphate and a second metal bridges the and phosphates to help orient the pyrophosphate leaving group. A LIG-bound sulfate anion is a plausible mimetic of the essential RNA terminal 2-PO4. Trl1-LIG has a distinctive C-terminal domain that instates fungal Trl1 as the founder of an Rnl6 clade of ATP-dependent RNA ligase. We discuss how the Trl1-LIG structure rationalizes the large body of in vivo structure-function data for Saccharomyces cerevisiae Trl1.