title: Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
abstract: The deep trefoil knot architecture is unique to the SpoU and tRNA methyltransferase D (TrmD) (SPOUT) family of methyltransferases (MTases) in all three domains of life. In bacteria, TrmD catalyzes the N(1)-methylguanosine (m(1)G) modification at position 37 in transfer RNAs (tRNAs) with the (36)GG(37) sequence, using S-adenosyl-l-methionine (AdoMet) as the methyl donor. The m(1)G37-modified tRNA functions properly to prevent +1 frameshift errors on the ribosome. Here we report the crystal structure of the TrmD homodimer in complex with a substrate tRNA and an AdoMet analog. Our structural analysis revealed the mechanism by which TrmD binds the substrate tRNA in an AdoMet-dependent manner. The trefoil-knot center, which is structurally conserved among SPOUT MTases, accommodates the adenosine moiety of AdoMet by loosening/retightening of the knot. The TrmD-specific regions surrounding the trefoil knot recognize the methionine moiety of AdoMet, and thereby establish the entire TrmD structure for global interactions with tRNA and sequential and specific accommodations of G37 and G36, resulting in the synthesis of m(1)G37-tRNA.
authors.affiliation: RIKEN Systems and Structural Biology Center, Tsurumi-ku, Yokohama 230-0045, Japan; Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Tsurumi-ku, Yokohama 230-0045, Japan;
authors.forename: Takuhiro
authors.initials: T
authors.lastname: Ito
authors.affiliation: Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107;
authors.forename: Isao
authors.initials: I
authors.lastname: Masuda
authors.affiliation: RIKEN Systems and Structural Biology Center, Tsurumi-ku, Yokohama 230-0045, Japan; Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan;
authors.forename: Ken-ichi
authors.initials: K
authors.lastname: Yoshida
authors.affiliation: RIKEN Systems and Structural Biology Center, Tsurumi-ku, Yokohama 230-0045, Japan; Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan;
authors.forename: Sakurako
authors.initials: S
authors.lastname: Goto-Ito
authors.affiliation: RIKEN Systems and Structural Biology Center, Tsurumi-ku, Yokohama 230-0045, Japan; Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Tsurumi-ku, Yokohama 230-0045, Japan;
authors.forename: Shun-ichi
authors.initials: S
authors.lastname: Sekine
authors.affiliation: Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-747, Republic of Korea;
authors.forename: Se Won
authors.initials: SW
authors.lastname: Suh
authors.affiliation: Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107;
authors.forename: Ya-Ming
authors.initials: YM
authors.lastname: Hou
authors.affiliation: RIKEN Systems and Structural Biology Center, Tsurumi-ku, Yokohama 230-0045, Japan; Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; RIKEN Structural Biology Laboratory, Tsurumi-ku, Yokohama 230-0045, Japan yokoyama@riken.jp.
authors.forename: Shigeyuki
authors.initials: S
authors.lastname: Yokoyama
mesh_terms: D000241:Adenosine / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D000595:Amino Acid Sequence; D000926:Anticodon / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites; D055162:Biocatalysis; D018360:Crystallography, X-Ray; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism*; D006147:Guanine / Q000378:metabolism; D006193:Haemophilus influenzae / Q000201:enzymology*; D007700:Kinetics; D008745:Methylation; D008958:Models, Molecular; D008969:Molecular Sequence Data; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012436:S-Adenosylmethionine; D016415:Sequence Alignment; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D020124:Thermotoga maritima / Q000201:enzymology*; D012359:tRNA Methyltransferases / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D000926:Anticodon; D029968:Escherichia coli Proteins; D006147:Guanine; D012436:S-Adenosylmethionine; D012343:RNA, Transfer; C489297:TrmD protein, E coli; D012359:tRNA Methyltransferases; D000241:Adenosine; C006235:sinefungin
keywords: RNA modification; SPOUT methyltransferase; TrmD; X-ray crystallography