The structure of Pyrococcus horikoshii 2′-5′ RNA ligase at 1.94 Å resolution reveals a possible open form with a wider active-site cleft

Bacterial and archaeal 2′-5′ RNA ligases, members of the 2H phosphoesterase superfamily, catalyze the linkage of the 5′ and 3′ exons via a 2′-5′-phosphodiester bond during tRNA-precursor splicing. The crystal structure of the 2′-5′ RNA ligase PH0099 from Pyrococcus horikoshii OT3 was solved at 1.94 Å resolution (PDB code 1vgj). The molecule has a bilobal α+β arrangement with two antiparallel β-sheets constituting a V-shaped active-site cleft, as found in other members of the 2H phosphoesterase superfamily. The present structure was significantly different from that determined previously at 2.4 Å resolution (PDB code 1vdx) in the active-site cleft; the entrance to the cleft is wider and the active site is easily accessible to the substrate (RNA precursor) in our structure. Structural comparison with the 2′-5′ RNA ligase from Thermus thermophilus HB8 also revealed differences in the RNA precursor-binding region. The structural differences in the active-site residues (tetrapeptide motifs H-X-T/S-X) between the members of the 2H phosphoesterase superfamily are discussed.