An enzyme with a deep trefoil knot for the active-site architecture
Acta Crystallographica Section D
Volume 58, Issue 7, pages 1129–1137, July 2002
How to Cite
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. and Yokoyama, S. (2002), An enzyme with a deep trefoil knot for the active-site architecture. Acta Crystallographica Section D, 58: 1129–1137. doi: 10.1107/S0907444902006601
- knots in polypeptide;
- Thermus thermophilus HB8.
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 Å 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.