Crystal structure of tRNA N2,N2-guanosine dimethyltransferase Trm1 from Pyrococcus horikoshii |
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Authors: | Ihsanawati Nishimoto Madoka Higashijima Kyoko Shirouzu Mikako Grosjean Henri Bessho Yoshitaka Yokoyama Shigeyuki |
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Institution: | 1 Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan 2 Institute of Genetics and Microbiology, University Paris-Sud-11, F-91405 Orsay-Cedex, France 3 RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan 4 Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan |
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Abstract: | Trm1 catalyzes a two-step reaction, leading to mono- and dimethylation of guanosine at position 26 in most eukaryotic and archaeal tRNAs. We report the crystal structures of Trm1 from Pyrococcus horikoshii liganded with S-adenosyl-l-methionine or S-adenosyl-l-homocysteine. The protein comprises N-terminal and C-terminal domains with class I methyltransferase and novel folds, respectively. The methyl moiety of S-adenosyl-l-methionine points toward the invariant Phe27 and Phe140 within a narrow pocket, where the target G26 might flip in. Mutagenesis of Phe27 or Phe140 to alanine abolished the enzyme activity, indicating their role in methylating G26. Structural analyses revealed that the movements of Phe140 and the loop preceding Phe27 may be involved in dissociation of the monomethylated tRNA•Trm1 complex prior to the second methylation. Moreover, the catalytic residues Asp138, Pro139, and Phe140 are in a different motif from that in DNA 6-methyladenosine methyltransferases, suggesting a different methyl transfer mechanism in the Trm1 family. |
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Keywords: | AdoMet l-methionine" target="_blank">S-adenosyl-l-methionine AdoHcy l-homocysteine" target="_blank">S-adenosyl-l-homocysteine Trm1 tRNA m22G dimethyltransferase m2G N2-monomethylguanosine m22G N2 N2-dimethylguanosine MTase methyltransferase PDB Protein Data Bank MAD multiple-wavelength anomalous diffraction |
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