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Comparative Study
. 2017 Jun 2;45(10):6209-6216.
doi: 10.1093/nar/gkx216.

The crystal structure of Trz1, the long form RNase Z from yeast

Miao Ma  1 , Ines Li de la Sierra-Gallay  1 , Noureddine Lazar  1 , Olivier Pellegrini  2 , Dominique Durand  1 , Anita Marchfelder  3 , Ciarán Condon  2 , Herman van Tilbeurgh  1
Affiliations
Comparative Study

The crystal structure of Trz1, the long form RNase Z from yeast

Miao Ma et al. Nucleic Acids Res. .

Abstract

tRNAs are synthesized as precursor RNAs that have to undergo processing steps to become functional. Yeast Trz1 is a key endoribonuclease involved in the 3΄ maturation of tRNAs in all domains of life. It is a member of the β-lactamase family of RNases, characterized by an HxHxDH sequence motif involved in coordination of catalytic Zn-ions. The RNase Z family consists of two subfamilies: the short (250-400 residues) and the long forms (about double in size). Short form RNase Z enzymes act as homodimers: one subunit embraces tRNA with a protruding arm, while the other provides the catalytic site. The long form is thought to contain two fused β-lactamase domains within a single polypeptide. Only structures of short form RNase Z enzymes are known. Here we present the 3.1 Å crystal structure of the long-form Trz1 from Saccharomyces cerevisiae. Trz1 is organized into two β-lactamase domains connected by a long linker. The N-terminal domain has lost its catalytic residues, but retains the long flexible arm that is important for tRNA binding, while it is the other way around in the C-terminal domain. Trz1 likely evolved from a duplication and fusion of the gene encoding the monomeric short form RNase Z.

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Figures

Figure 1.
Figure 1.
Structure of Trz1. (A) Cartoon presentation of the Trz1 structure. The N-terminal domain (NTD) and C-terminal domain (CTD) are shown in green and cyan, respectively, and the linker is shown in purple. Two zinc ions are shown as yellow spheres and the phosphate ion is shown as sticks (present in the active site). The region corresponding to the unresolved flexible arm protruding from the NTD is shown as a dashed line and the loop replacing the flexible arm in the CTD is in red (labeled with an asterisk). (B) The CTD of Trz1 superimposed on BsuTrz (transparent gray, PDB code: 1y44). The core of the CTD is shown in cyan and the extensions are in orange. The conserved tRNA recognition elements α17 and loop PxKxRN and the nearby AxDx loop in the CTD are in blue. The NTD of Trz1 is shown as a green ribbon and the linker region is shown in purple. (C) The NTD of Trz1 superimposed on BsuTrz (transparent gray). The β-lactamase core of the NTD is shown in green and the extensions are in yellow. The CTD of Trz1 is shown as blue ribbon. (D) Superimposition of the NTD (green) and CTD (cyan) of Trz1 (linker in purple).
Figure 2.
Figure 2.
Active site motifs. (A) Stereo views of the Ψ-histidine motif in NTD (upper panels) and Zn-binding His-motif in CTD (lower panels). (B) Structure based sequence alignment of the conserved motifs in C- and NTDs: PxKxRN loop, motif I to V and AxDx motif. RNase ZL sequences from Saccharomyces cerevisiae (Sce = Trz1), Caenorhabditis elegans (Cel), Drosophila melanogaster (Dme), Mus musculus (Mmu) and Homo sapiens (Hsa) are represented.
Figure 3.
Figure 3.
Model of Trz1 in complex with tRNA. (A) This model was generated by superimposition of Trz1 onto the BsuTrz/tRNA complex (PDB code: 2FK6). The N- and C-terminal halves and linker of Trz1 are shown in green/cyan and purple, respectively. For clarity, BsuTrz was omitted in the figure and only the tRNA (orange) is shown. Arrows indicate the position of the flexible arm and acceptor stem. The active center residues of Trz1 are shown as pink sticks, and zinc ions as yellow spheres. The α17 helix and the ‘PxKxRN’ and AxDx loops are shown in blue. (B) Sequence conservation projected onto the surface of Trz1 as generated with default parameters by the consurf webserver (http://consurf.tau.ac.il). The complex is shown in the same orientation as for panel A. (C) Zoom on the superimposition of the active site residues of Trz1 and BsuTrz. Only Trz1 residues are labeled and BsuTrz residues are shown as gray sticks. (D) Zoom on the active site of the Trz1/tRNA complex. The tRNA is shown as orange sticks and the uracil 73 is labeled.
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