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Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA

Author

Listed:
  • Nicholas J. Reiter

    (Northwestern University)

  • Amy Osterman

    (Northwestern University)

  • Alfredo Torres-Larios

    (Northwestern University
    Present addresses: Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70-243, México 04510, México (A.T.-L.); Abbott Laboratories, Abbott Park, Illinois 60064-6400, USA (K.K.S.).)

  • Kerren K. Swinger

    (Northwestern University
    Present addresses: Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70-243, México 04510, México (A.T.-L.); Abbott Laboratories, Abbott Park, Illinois 60064-6400, USA (K.K.S.).)

  • Tao Pan

    (University of Chicago)

  • Alfonso Mondragón

    (Northwestern University)

Abstract

Ribonuclease (RNase) P is the universal ribozyme responsible for 5′-end tRNA processing. We report the crystal structure of the Thermotoga maritima RNase P holoenzyme in complex with tRNAPhe. The 154 kDa complex consists of a large catalytic RNA (P RNA), a small protein cofactor and a mature tRNA. The structure shows that RNA–RNA recognition occurs through shape complementarity, specific intermolecular contacts and base-pairing interactions. Soaks with a pre-tRNA 5′ leader sequence with and without metal help to identify the 5′ substrate path and potential catalytic metal ions. The protein binds on top of a universally conserved structural module in P RNA and interacts with the leader, but not with the mature tRNA. The active site is composed of phosphate backbone moieties, a universally conserved uridine nucleobase, and at least two catalytically important metal ions. The active site structure and conserved RNase P–tRNA contacts suggest a universal mechanism of catalysis by RNase P.

Suggested Citation

  • Nicholas J. Reiter & Amy Osterman & Alfredo Torres-Larios & Kerren K. Swinger & Tao Pan & Alfonso Mondragón, 2010. "Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA," Nature, Nature, vol. 468(7325), pages 784-789, December.
    • Handle: RePEc:nat:nature:v:468:y:2010:i:7325:d:10.1038_nature09516
    DOI: 10.1038/nature09516
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    Cited by:

    1. Yangyang Li & Shichen Su & Yanqing Gao & Guoliang Lu & Hehua Liu & Xi Chen & Zhiwei Shao & Yixi Zhang & Qiyuan Shao & Xin Zhao & Jie Yang & Chulei Cao & Jinzhong Lin & Jinbiao Ma & Jianhua Gan, 2022. "Crystal structures and insights into precursor tRNA 5’-end processing by prokaryotic minimal protein-only RNase P," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    2. Jiaqiang Zhu & Wei Huang & Jing Zhao & Loc Huynh & Derek J. Taylor & Michael E. Harris, 2022. "Structural and mechanistic basis for recognition of alternative tRNA precursor substrates by bacterial ribonuclease P," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    3. Meng Xu & Dulmi Senanayaka & Rongwei Zhao & Tafadzwa Chigumira & Astha Tripathi & Jason Tones & Rachel M. Lackner & Anne R. Wondisford & Laurel N. Moneysmith & Alexander Hirschi & Sara Craig & Sahar A, 2024. "TERRA-LSD1 phase separation promotes R-loop formation for telomere maintenance in ALT cancer cells," Nature Communications, Nature, vol. 15(1), pages 1-19, December.

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