An enzyme with a deep trefoil knot for the active-site architecture.
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.
Nureki
Osamu
O
Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Japan.
Shirouzu
Mikako
M
Hashimoto
Kyoko
K
Ishitani
Ryuichiro
R
Terada
Takaho
T
Tamakoshi
Masatada
M
Oshima
Tairo
T
Chijimatsu
Masao
M
Takio
Koji
K
Vassylyev
Dmitry G
DG
Shibata
Takehiko
T
Inoue
Yorinao
Y
Kuramitsu
Seiki
S
Yokoyama
Shigeyuki
S
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
D008780:Methyltransferases; C110074:23S rRNA m1G745 methyltransferase