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Structural basis for substrate binding, cleavage and allostery in the tRNA maturase RNase Z


Transfer RNAs (tRNAs) are synthesized as part of longer primary transcripts that require processing of both their 3′ and 5′ extremities in every living organism known. The 5′ side is processed (matured) by the ubiquitously conserved endonucleolytic ribozyme, RNase P1, whereas removal of the 3′ tails can be either exonucleolytic2,3 or endonucleolytic4. The endonucleolytic pathway is catalysed by an enzyme known as RNase Z, or 3′ tRNase5,6. RNase Z cleaves precursor tRNAs immediately after the discriminator base (the unpaired nucleotide 3′ to the last base pair of the acceptor stem, used as an identity determinant by many aminoacyl-tRNA synthetases) in most cases6,7,8, yielding a tRNA primed for addition of the CCA motif by nucleotidyl transferase. Here we report the crystal structure of Bacillus subtilis RNase Z at 2.1 Å resolution, and propose a mechanism for tRNA recognition and cleavage. The structure explains the allosteric properties of the enzyme, and also sheds light on the mechanisms of inhibition by the CCA motif and long 5′ extensions. Finally, it highlights the extraordinary adaptability of the metallo-hydrolase domain of the β-lactamase family for the hydrolysis of covalent bonds.

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Figure 1: Ribbon representation of RNase Z at 2.1 Å resolution.
Figure 2: Structural comparison of members of the metallo-β-lactamase family.
Figure 3: Model of RNase Z–tRNA complex and amino acids important for interaction.
Figure 4: Active sites of RNase Z subunits and the proposed cleavage mechanism.


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We thank M. Springer, D. Picot, R. Giégé, F. Allemand, V. Arluison and F. Dardel for discussions, S. Fieulaine and M. Pirocchi for help with the beam-line BM30A at the European Synchrotron Radiation Facility, and J.L. Popot for use of crystallography facilities and X-ray generator at the IBPC. This work was supported by the CNRS (UPR 9073), Université Paris VII-Denis Diderot, PRFMMIP 2001/2003, and ACI Jeunes Chercheurs from the Ministère de l'Education Nationale.

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Correspondence to Ciarán Condon.

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Supplementary information

Supplementary Figure S1

Shows an alignment COGs representing different members of the metallo -lactamase family. (PPT 1058 kb)

Supplementary Figure S2

Shows both the secondary structure features of RNase Z superimposed on its amino acid sequence and the secondary structure topology of the protein. (PPT 52 kb)

Supplementary Figure S3

Shows the crystal packing of RNase Z. (PPT 122 kb)

Supplementary Methods

Describes the seleno-methionine labelling of RNase Z. (RTF 3 kb)

Supplementary Table

Shows data-collection, phasing and refinement statistics for resolution of RNase Z structure. (RTF 304 kb)

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de la Sierra-Gallay, I., Pellegrini, O. & Condon, C. Structural basis for substrate binding, cleavage and allostery in the tRNA maturase RNase Z. Nature 433, 657–661 (2005).

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