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

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Dec 1;62(Pt 12):1196-200. doi: 10.1107/S1744309106046616. Epub 2006 Nov 30.


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 A resolution (PDB code 1vgj). The molecule has a bilobal alpha+beta arrangement with two antiparallel beta-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 A 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Crystallization
  • Crystallography, X-Ray
  • Models, Molecular
  • Polynucleotide Ligases / chemistry*
  • Pyrococcus horikoshii / enzymology*


  • Polynucleotide Ligases

Associated data

  • PDB/1VGJ