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

Acta Crystallogr D Biol Crystallogr. 2002 Jul;58(Pt 7):1129-37. doi: 10.1107/s0907444902006601. Epub 2002 Jun 20.

Abstract

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 A 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Binding Sites
  • Catalytic Domain
  • Cloning, Molecular
  • Methyltransferases / chemistry*
  • Models, Molecular
  • Models, Theoretical
  • Molecular Sequence Data
  • Open Reading Frames
  • Protein Structure, Tertiary
  • Sequence Homology, Amino Acid
  • Thermus thermophilus / enzymology*
  • Ultracentrifugation

Substances

  • Methyltransferases
  • 23S rRNA m1G745 methyltransferase