Protein Name

Hypothetical RNA 2'-O-ribose methyltransferase (RrmA)


Thermus thermophilus (bacteria)

Biological Context

Most cellular RNAs undergo a number of nucleoside modifications, whose biological role generally remains unknown. One of the most prevalent nucleoside modifications in prokaryotic and eukaryotic RNAs is 2'-O-ribose methylation. The RNA 2'-O-ribose methyltransfarases (MTases) form a large family of enzymes that catalyze methyl transfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of the backbone ribose. The RNA 2'-O-ribose MTases share three common short amino acid motifs, motif1, 2 and 3, which define the active site of this enzyme family. A hypothetical protein RNA 2'-O-ribose methyltransfarase from Thermus thermophilus (RrmA) apparently contains the three motifs and is likely a member of the family.

Structure Description


Here, the crystal structure of RrmA is shown, with a deep trefoil knot structure, observed for the first time. Threading the polypeptide chain through an untwisted loop gives a trefoil knot; in a shallow trefoil knot, only a few (at most 15) residues at one end of the chain are tucked through the loop and such a knot can disappear if the structure is viewed from a different angle, whereas many more residues are tucked through the loop in the deep trefoil knot observed here. RrmA has a deep trefoil knot in the C-terminal catalytic domain and moreover two of the three putative catalytic residues are located on the knot, which is the first observed indication that the knot may be essential for enzyme activity.

Protein Data Bank (PDB)



  • Nureki, O. Shirouzu, M. Hashimoto, K. Ishitani, R. Terada, T. Tamakoshi, M. Oshima, T. Chijimatsu, M. Takio, K. Vassylyev, D.G. Shibata, T. Inoue, Y. Kuramitsu, S. Yokoyama, S.; "An enzyme with a deep trefoil knot for the active-site architecture"; Acta Crystallogr., Sect.D; (2002) 58:1129-1137 PubMed:12077432.


author: Aki Nagata

Japanese version:PDB:1IPA