Protein Name

RNase Z / tRNA(Thr) complex


Bacillus subtilis

Biological Context

Various kinds of ribonucleases, such as RNase P, RNase T and RNase Z, are involved in removing unnecessary regions of a precursor tRNA during its maturation process (processing). RNase Z is an enzyme which catalyzes cleavage of tRNA 3' terminus and thus is essential to make a functionally mature tRNA. The 3’ region of a mature tRNA plays an important role in binding of the amino acid (aminoacylation) and a CCA motif is conserved there (Fig. 1). RNase Z recognizes a discriminator nucleotide in the precursor tRNA and removes unnecessary regions downstream thereof. A CCA-adding enzyme then connects the CCA motif next to the discriminator nucleotide at the 3' terminus, resulting in the mature tRNA.

Deletion of the gene encoding RNase Z is lethal in Bacillus subtilis and Saccharomyces cerevisiae, and mutations in RNase Z in humans have been linked to prostate-cancer susceptibility.

Structure Description


The crystal structure of RNase Z bound to tRNA (Thr) was solved at 2.9-Å resolution. RNase Z functions as a dimer and is thus able to bind two tRNAs simultaneously (Fig. 2). RNase Z monomer consists of a metallo-β-lactamase domain and a flexible arm. It catches a tRNA with the arm and catalyzes the processing reaction at the β-lactamase domain with a Zn ion. Two RNase Z works cooperatively after dimer formation: one subunit recognizes a tRNA and the other subunit cleaves it. Most of the contacts between protein and tRNA are in the sugar-phosphate backbone rather than the bases of the tRNA. This allows RNase Z to recognize a wide variety of tRNA sequences.

The crystal structure of tRNA-free RNase Z has already been solved and also forms a dimer (xPSSS:1Y44). The structure of the two subunits, active A subunit and inactive B subunit, shows different conformational states of the enzyme. In addition, the structure of tRNA-bound RNase Z complex shows symmetrical properties. The superimposition of both structures reveals that the tRNA-free inactive B subunit changes its conformation to A subunit-like active state upon tRNA binding. It seems that the dimer cooperation enables the coincidental catalytic activity for two tRNAs.

It is expected that detection of additional tRNA structures with other processing enzymes will uncover the whole tRNA maturation mechanism.

tRNA (Fig. 1) Secondary structure model of tRNAs

Transfer RNAs form a cloverleaf secondary structure with 3 loops; D loop (d), T loop (t), and anticodon loop (a). The 3' end of tRNAs has a CCA sequence, important for binding to an amino acid.
structure (Fig. 1) Cristal structure of RNase Z bound to tRNA (Thr)

Blue, RNase Z; green, tRNA (Thr); yellow sphere, Zn ion. The position of tRNA (Thr) anticodon arm is unknown. RNase Z is functional in a dimer form, thus the crystallographic symmetrical part is shown as orange.

Protein Data Bank (PDB)



Li de la Sierra-Gallay, I. Mathy, N. Pellegrini, O. Condon, C.; "Structure of the ubiquitous 3' processing enzyme RNase Z bound to transfer RNA."; Nat.Struct.Mol.Biol.; (2006) 13:376-377 PubMed:16518398.


author: Naoya Fujita

Japanese version:PDB:2FK6