An enzyme with a deep trefoil knot for the active-site architecture

Academic Article


  • Knots in polypeptide chains have been found in very few proteins. Only two proteins are considered to have a shallow 'trefoil' knot, which tucks a few residues at one end of the chain through a loop exposed on the protein surface. Recently, another protein was found by a mathematical algorithm to have a deep 'figure-of-eight' knot which had not been visually identified. In the present study, the crystal structure of a hypothetical RNA 2′-O-ribose methyltransferase from Thermus thermophilus (RrmA) was determined at 2.4 resolution and a deep trefoil knot was found for the first time. The present knot is formed by the threading of a 44-residue polypeptide chain through a 41-residue loop and is better defined than the previously reported knots. Two of the three catalytic residues conserved in the 2′-O-ribose methyltransferase family are located in the knotting loop and in the knotted carboxy-terminal chain, which is the first observation that the enzyme active site is constructed right on the knot. On the other hand, the amino-terminal domain exhibits a geometrical similarity to the ribosomal proteins which recognize an internal loop of RNA.
  • Digital Object Identifier (doi)

    Author List

  • Nureki O; Shirouzu M; Hashimoto K; Ishitani R; Terada T; Tamakoshi M; Oshima T; Chijimatsu M; Takio K; Vassylyev DG
  • Start Page

  • 1129
  • End Page

  • 1137
  • Volume

  • 58
  • Issue

  • 7