Crystal structure of the 2′-5′ RNA ligase from Thermus thermophilus HB8

Miyuki Kato, Mikako Shirouzu, Takaho Terada, Hiroto Yamaguchi, Kazutaka Murayama, Hiroaki Sakai, Seiki Kuramitsu, Shigeyuki Yokoyama

Research output: Contribution to journalArticlepeer-review

32 Citations (Scopus)


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 2.5Å 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.

Original languageEnglish
Pages (from-to)903-911
Number of pages9
JournalJournal of Molecular Biology
Issue number5
Publication statusPublished - 2003 Jun 20
Externally publishedYes


  • 2′-5′ RNA ligase
  • CPDase
  • Crystal structure
  • Thermus thermophilus
  • tRNA splicing

ASJC Scopus subject areas

  • Molecular Biology
  • Biophysics
  • Structural Biology


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