TY - JOUR
T1 - Structural basis for the substrate recognition and catalysis of peptidyl-tRNA hydrolase
AU - Ito, Kosuke
AU - Murakami, Ryo
AU - Mochizuki, Masahiro
AU - Qi, Hao
AU - Shimizu, Yoshihiro
AU - Miura, Kin Ichiro
AU - Ueda, Takuya
AU - Uchiumi, Toshio
N1 - Funding Information:
Grant-in-Aid for Young Scientists (Start-up) [20870018 to K.I.] and Grant-in-Aid for Young Scientists (B) [21770108 to K.I.] from the Japan Society for the Promotion of Science (JSPS); the Uchida Energy Science Promotion Foundation grant [22-1-10 to K.I.]; UNION TOOL CO grant (to K.I.); Grant for the Promotion of Niigata University Research Projects [22C017 to K.I.]; Grants-in-Aid for Education and Research at the Institute of Science and Technology from Niigata University (to K.I.). Funding for open access charge: Niigata University.
PY - 2012/11
Y1 - 2012/11
N2 - 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.
AB - 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.
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U2 - 10.1093/nar/gks790
DO - 10.1093/nar/gks790
M3 - Article
C2 - 22923517
AN - SCOPUS:84869022853
SN - 0305-1048
VL - 40
SP - 10521
EP - 10531
JO - Nucleic acids research
JF - Nucleic acids research
IS - 20
ER -