Ryo Murakami

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Publications (2)8.53 Total impact

  • Article: Structural basis for the substrate recognition and catalysis of peptidyl-tRNA hydrolase.
    Kosuke Ito, Ryo Murakami, Masahiro Mochizuki, Hao Qi, Yoshihiro Shimizu, Kin-Ichiro Miura, Takuya Ueda, Toshio Uchiumi
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    ABSTRACT: Peptidyl-tRNA hydrolase (Pth) cleaves the ester bond between the peptide and the tRNA of peptidyl-tRNA molecules, which are produced by aborted translation, to recycle tRNA for further rounds of protein synthesis. Pth is ubiquitous in nature, and its enzymatic activity is essential for bacterial viability. We have determined the crystal structure of Escherichia coli Pth in complex with the tRNA CCA-acceptor-TΨC domain, the enzyme-binding region of the tRNA moiety of the substrate, at 2.4 Å resolution. In combination with site-directed mutagenesis studies, the structure identified the amino acid residues involved in tRNA recognition. The structure also revealed that Pth interacts with the tRNA moiety through the backbone phosphates and riboses, and no base-specific interactions were observed, except for the interaction with the highly conserved base G53. This feature enables Pth to accept the diverse sequences of the elongator-tRNAs as substrate components. Furthermore, we propose an authentic Pth:peptidyl-tRNA complex model and a detailed mechanism for the hydrolysis reaction, based on the present crystal structure and the previous studies' results.
    Nucleic Acids Research 08/2012; · 8.03 Impact Factor
  • Article: Crystallization and preliminary X-ray analysis of peptidyl-tRNA hydrolase from Escherichia coli in complex with the acceptor-TΨC domain of tRNA.
    Kosuke Ito, Hao Qi, Yoshihiro Shimizu, Ryo Murakami, Kin-ichiro Miura, Takuya Ueda, Toshio Uchiumi
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    ABSTRACT: Peptidyl-tRNA hydrolase (Pth) cleaves the ester bond between the peptide and the tRNA of peptidyl-tRNA molecules, which are the product of aborted translation. In the present work, Pth from Escherichia coli was crystallized with the acceptor-TΨC domain of tRNA using 1,4-butanediol as a precipitant. The crystals belonged to the hexagonal space group P6(1), with unit-cell parameters a = b = 55.1, c = 413.1 Å, and diffracted X-rays beyond 2.4 Å resolution. The asymmetric unit is expected to contain two complexes of Pth and the acceptor-TΨC domain of tRNA (V(M) = 2.8 Å(3) Da(-1)), with a solvent content of 60.8%. The structure is being solved by molecular replacement.
    Acta Crystallographica Section F Structural Biology and Crystallization Communications 12/2011; 67(Pt 12):1566-9. · 0.51 Impact Factor
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