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Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase

Author

Listed:
  • Kazunori Watanabe

    (Institute of Biological Resources and Functions, National Institute of Advanced Industrial Sciences and Technology, 1-1-1, Higashi, Tsukuba-shi, Ibaraki 305-8566, Japan)

  • Yukimatsu Toh

    (Institute of Biological Resources and Functions, National Institute of Advanced Industrial Sciences and Technology, 1-1-1, Higashi, Tsukuba-shi, Ibaraki 305-8566, Japan)

  • Kyoko Suto

    (Institute of Biological Resources and Functions, National Institute of Advanced Industrial Sciences and Technology, 1-1-1, Higashi, Tsukuba-shi, Ibaraki 305-8566, Japan)

  • Yoshihiro Shimizu

    (Graduate School of Frontier Sciences, University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan)

  • Natsuhisa Oka

    (Graduate School of Frontier Sciences, University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan)

  • Takeshi Wada

    (Graduate School of Frontier Sciences, University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan)

  • Kozo Tomita

    (Institute of Biological Resources and Functions, National Institute of Advanced Industrial Sciences and Technology, 1-1-1, Higashi, Tsukuba-shi, Ibaraki 305-8566, Japan)

Abstract

Eubacterial leucyl/phenylalanyl-tRNA protein transferase (LF-transferase) catalyses peptide-bond formation by using Leu-tRNALeu (or Phe-tRNAPhe) and an amino-terminal Arg (or Lys) of a protein, as donor and acceptor substrates, respectively. However, the catalytic mechanism of peptide-bond formation by LF-transferase remained obscure. Here we determine the structures of complexes of LF-transferase and phenylalanyl adenosine, with and without a short peptide bearing an N-terminal Arg. Combining the two separate structures into one structure as well as mutation studies reveal the mechanism for peptide-bond formation by LF-transferase. The electron relay from Asp 186 to Gln 188 helps Gln 188 to attract a proton from the α-amino group of the N-terminal Arg of the acceptor peptide. This generates the attacking nucleophile for the carbonyl carbon of the aminoacyl bond of the aminoacyl-tRNA, thus facilitating peptide-bond formation. The protein-based mechanism for peptide-bond formation by LF-transferase is similar to the reverse reaction of the acylation step observed in the peptide hydrolysis reaction by serine proteases.

Suggested Citation

  • Kazunori Watanabe & Yukimatsu Toh & Kyoko Suto & Yoshihiro Shimizu & Natsuhisa Oka & Takeshi Wada & Kozo Tomita, 2007. "Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase," Nature, Nature, vol. 449(7164), pages 867-871, October.
    • Handle: RePEc:nat:nature:v:449:y:2007:i:7164:d:10.1038_nature06167
    DOI: 10.1038/nature06167
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    Cited by:

    1. Thilini Abeywansha & Wei Huang & Xuan Ye & Allison Nawrocki & Xin Lan & Eckhard Jankowsky & Derek J. Taylor & Yi Zhang, 2023. "The structural basis of tRNA recognition by arginyl-tRNA-protein transferase," Nature Communications, Nature, vol. 14(1), pages 1-12, December.

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