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Structural basis for template-independent RNA polymerization

Nature volume 430, pages 700704 (05 August 2004) | Download Citation

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Abstract

The 3′-terminal CCA nucleotide sequence (positions 74–76) of transfer RNA is essential for amino acid attachment1 and interaction with the ribosome2,3,4 during protein synthesis. The CCA sequence is synthesized de novo and/or repaired by a template-independent RNA polymerase, ‘CCA-adding enzyme’, using CTP and ATP as substrates5. Despite structural and biochemical studies5,6,7,8, the mechanism by which the CCA-adding enzyme synthesizes the defined sequence without a nucleic acid template remains elusive. Here we present the crystal structure of Aquifex aeolicus CCA-adding enzyme, bound to a primer tRNA lacking the terminal adenosine and an incoming ATP analogue, at 2.8 Å resolution. The enzyme enfolds the acceptor T helix of the tRNA molecule. In the catalytic pocket, C75 is adjacent to ATP, and their base moieties are stacked. The complementary pocket for recognizing C74-C75 of tRNA forms a ‘protein template’ for the penultimate two nucleotides, mimicking the nucleotide template used by template-dependent polymerases. These results are supported by systematic analyses of mutants. Our structure represents the ‘pre-insertion’ stage of selecting the incoming nucleotide and provides the structural basis for the mechanism underlying template-independent RNA polymerization.

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Acknowledgements

We thank A. M. Weiner for the Aa.LC plasmids; and M. Kawamoto and H. Sakai for help with data collection at SPring-8. This work was supported by Kurata Memorial Hitachi Science and Technology Foundation, Takeda Science Foundation, Foundation of Advanced Technology Institute and a Grant-in-aid for Young Scientists (to K.T.); by Asahi Glass Foundation (to S.F.); by a grant from the Ministry of Education, Culture, Sports, Science and Technology (to N.T.); and by a PRESTO Program grant from Japan Science and Technology and a Naito Foundation grant (to O.N.).

Author information

Author notes

    • Kozo Tomita
    •  & Shuya Fukai

    These authors contributed equally to this work.

Affiliations

  1. Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba-shi, Ibaragi 305-8666, Japan

    • Kozo Tomita
  2. Department of Integrated Bioscience, Graduate School of Frontier Science, University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan

    • Kozo Tomita
    • , Takuya Ueda
    •  & Nono Takeuchi
  3. Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501, Japan

    • Shuya Fukai
    •  & Osamu Nureki
  4. Department of Biotechnology, Graduate School of Agricultural and Life Sciences, the University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan

    • Ryuichiro Ishitani
  5. Cellular Signaling Laboratory, RIKEN Harima Institute at SPring-8, 1-1-1 Kouto Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan

    • Dmitry G. Vassylyev
  6. PRESTO, JST, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan

    • Osamu Nureki

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The authors declare that they have no competing financial interests.

Corresponding author

Correspondence to Osamu Nureki.

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    Supplementary Table 1

    Data collection and refinement statistics

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https://doi.org/10.1038/nature02712

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