title: Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme.
abstract: The tRNA(Gm18) methyltransferase (TrmH) catalyzes the 2'-O methylation of guanosine 18 (Gua18) of tRNA. We solved the crystal structure of Thermus thermophilus TrmH complexed with S-adenosyl-L-methionine at 1.85 A resolution. The catalytic domain contains a deep trefoil knot, which mutational analyses revealed to be crucial for the formation of the catalytic site and the cofactor binding pocket. The tRNA dihydrouridine(D)-arm can be docked onto the dimeric TrmH, so that the tRNA D-stem is clamped by the N- and C-terminal helices from one subunit while the Gua18 is modified by the other subunit. Arg41 from the other subunit enters the catalytic site and forms a hydrogen bond with a bound sulfate ion, an RNA main chain phosphate analog, thus activating its nucleophilic state. Based on Gua18 modeling onto the active site, we propose that once Gua18 binds, the phosphate group activates Arg41, which then deprotonates the 2'-OH group for methylation.
authors.affiliation: Department of Biotechnology, Faculty of Engineering, Ehime University, Matsuyama 790-8577, Japan.
authors.forename: Osamu
authors.initials: O
authors.lastname: Nureki
authors.forename: Kazunori
authors.initials: K
authors.lastname: Watanabe
authors.forename: Shuya
authors.initials: S
authors.lastname: Fukai
authors.forename: Ryohei
authors.initials: R
authors.lastname: Ishii
authors.forename: Yaeta
authors.initials: Y
authors.lastname: Endo
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Hori
authors.forename: Shigeyuki
authors.initials: S
authors.lastname: Yokoyama
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D020134:Catalytic Domain; D003067:Coenzymes / Q000378:metabolism; D019281:Dimerization; D007700:Kinetics; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D012436:S-Adenosylmethionine / Q000378:metabolism; D016963:Thermus thermophilus / Q000201:enzymology / Q000235:genetics / Q000378:metabolism; D012359:tRNA Methyltransferases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D003067:Coenzymes; D012436:S-Adenosylmethionine; D012359:tRNA Methyltransferases