title: An enzyme with a deep trefoil knot for the active-site architecture.
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.
authors.affiliation: Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Japan.
authors.forename: Osamu
authors.initials: O
authors.lastname: Nureki
authors.forename: Mikako
authors.initials: M
authors.lastname: Shirouzu
authors.forename: Kyoko
authors.initials: K
authors.lastname: Hashimoto
authors.forename: Ryuichiro
authors.initials: R
authors.lastname: Ishitani
authors.forename: Takaho
authors.initials: T
authors.lastname: Terada
authors.forename: Masatada
authors.initials: M
authors.lastname: Tamakoshi
authors.forename: Tairo
authors.initials: T
authors.lastname: Oshima
authors.forename: Masao
authors.initials: M
authors.lastname: Chijimatsu
authors.forename: Koji
authors.initials: K
authors.lastname: Takio
authors.forename: Dmitry G
authors.initials: DG
authors.lastname: Vassylyev
authors.forename: Takehiko
authors.initials: T
authors.lastname: Shibata
authors.forename: Yorinao
authors.initials: Y
authors.lastname: Inoue
authors.forename: Seiki
authors.initials: S
authors.lastname: Kuramitsu
authors.forename: Shigeyuki
authors.initials: S
authors.lastname: Yokoyama
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001665:Binding Sites; D020134:Catalytic Domain; D003001:Cloning, Molecular; D008780:Methyltransferases / Q000737:chemistry*; D008958:Models, Molecular; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D016963:Thermus thermophilus / Q000201:enzymology*; D014461:Ultracentrifugation
chemical_list: D008780:Methyltransferases; C110074:23S rRNA m1G745 methyltransferase