Crystal Structure of the 2′-5′ RNA Ligase from Thermus thermophilus HB8

The 2′-5′ RNA ligase family members are bacterial and archaeal RNA ligases that ligate 5′ and 3′ half-tRNA molecules with 2′,3′-cyclic phosphate and 5′-hydroxyl termini, respectively, to the product containing the 2′-5′ phosphodiester linkage. Here, the crystal structure of the 2′-5′ RNA ligase protein from an extreme thermophile, Thermus thermophilus HB8, was solved at 2.5 Å resolution. The structure of the 2′-5′ RNA ligase superimposes well on that of the Arabidopsis thaliana cyclic phosphodiesterase (CPDase), which hydrolyzes ADP-ribose 1″,2″-cyclic phosphate (a product of the tRNA splicing reaction) to the monoester ADP-ribose 1″-phosphate. Although the sequence identity between the two proteins is remarkably low (9.3%), the 2′-5′ RNA ligase and CPDase structures have two HX(T/S)X motifs in their corresponding positions. The HX(T/S)X motifs play important roles in the CPDase activity, and are conserved in both the CPDases and 2′-5′ RNA ligases. Therefore, the catalytic mechanism of the 2′-5′ RNA ligase may be similar to that of the CPDase. On the other hand, the electrostatic potential of the cavity of the 2′-5′ RNA ligase is positive, but that of the CPDase is negative. Furthermore, in the CPDase, two loops with low B-factors cover the cavity. In contrast, in the 2′-5′ RNA ligase, the corresponding loops form an open conformation and are flexible. These characteristics may be due to the differences in the substrates, tRNA and ADP-ribose 1″,2″-cyclic phosphate.