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Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA

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.

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Figure 1: Crystal structure of the T. maritima RNase P holoenzyme in complex with tRNA.
Figure 2: tRNA recognition by RNase P is mediated by RNA–RNA interactions.
Figure 3: Protein–RNA contacts within the RNase P holoenzyme.
Figure 4: Pre-tRNA leader–protein interactions in the RNase P holoenzyme.
Figure 5: Structure of the RNase P active site environment.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Coordinates for theRNase P holoenzyme–tRNA complex, with and without 5′ tRNA leader sequence, have been deposited into the RCSB Protein Data Bank (accession code 3OKB and 3OK7, respectively).

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Acknowledgements

We thank E. Sontheimer and O. Uhlenbeck for comments and suggestions, N. Pace for the gift of the T. maritima RNase P protein plasmid, Obiter Research, A. Davis and M. E. Duban for advice and preparation of iridium hexammine, and A. Samelson for discussions and assistance. In addition, we are grateful for data collection assistance from S. Anderson, Z. Wawrzak, and staff at LS-CAT. Research was supported by the NIH. N.J.R. is an NRSA postdoctoral fellow.

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A.M. directed the work. A.T.-L. and A.M. conceived the project. All authors performed and designed experiments. N.J.R. obtained crystallographic data. N.J.R. and A.M. analysed the crystallographic data. N.J.R. and A.M. wrote the paper with contributions from all authors.

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Correspondence to Alfonso Mondragón.

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Reiter, N., Osterman, A., Torres-Larios, A. et al. Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA. Nature 468, 784–789 (2010). https://doi.org/10.1038/nature09516

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