Crystal structure and mutational study of a unique SpoU family archaeal methylase that forms 2'-O-methylcytidine at position 56 of tRNA

J Mol Biol. 2008 Jan 25;375(4):1064-75. doi: 10.1016/j.jmb.2007.11.023. Epub 2007 Nov 17.


The conserved cytidine residue at position 56 of tRNA contributes to the maintenance of the L-shaped tertiary structure. aTrm56 catalyzes the 2'-O-methylation of the cytidine residue in archaeal tRNA, using S-adenosyl-L-methionine. Based on the amino acid sequence, aTrm56 is the most distant member of the SpoU family. Here, we determined the crystal structure of Pyrococcus horikoshii aTrm56 complexed with S-adenosyl-L-methionine at 2.48 A resolution. aTrm56 consists of the SPOUT domain, which contains the characteristic deep trefoil knot, and a unique C-terminal beta-hairpin. aTrm56 forms a dimer. The S-adenosyl-L-methionine binding and dimerization of aTrm56 were similar to those of the other SpoU members. A structure-based sequence alignment revealed that aTrm56 conserves only motif II, among the four signature motifs. However, an essential Arg16 residue is located at a novel position within motif I. Biochemical assays showed that aTrm56 prefers the L-shaped tRNA to the lambda form as its substrate.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Binding Sites
  • Crystallography, X-Ray
  • Cytidine / analogs & derivatives*
  • Cytidine / chemistry*
  • Dimerization
  • Hydrogen Bonding
  • Hydrophobic and Hydrophilic Interactions
  • Methylation
  • Models, Chemical
  • Models, Molecular
  • Molecular Sequence Data
  • Mutation
  • Protein Binding
  • Protein Conformation
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Pyrococcus horikoshii / enzymology
  • RNA, Archaeal / chemistry*
  • RNA, Archaeal / genetics
  • RNA, Archaeal / metabolism
  • RNA, Transfer / chemistry*
  • RNA, Transfer / metabolism
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / metabolism
  • S-Adenosylmethionine / metabolism
  • Sequence Homology, Amino Acid
  • tRNA Methyltransferases / chemistry*
  • tRNA Methyltransferases / genetics*
  • tRNA Methyltransferases / metabolism


  • RNA, Archaeal
  • Recombinant Proteins
  • Cytidine
  • S-Adenosylmethionine
  • RNA, Transfer
  • tRNA Methyltransferases

Associated data

  • PDB/2YY8