PDBsum entry: 1ww1

Hydrolase

PDB id: 1ww1

Contents

Protein chains

250 a.a. *

238 a.a. *

Metals

_ZN ×2

Waters ×49

* Residue conservation analysis

PDB id:

1ww1

Name:

Hydrolase

Title:

Crystal structure of trnase z from thermotoga maritima

Structure:

Trnase z. Chain: a, b. Synonym: hypothetical protein tm0864. Engineered: yes

Source:

Thermotoga maritima. Organism_taxid: 243274. Strain: msb8. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.60Å R-factor: 0.225 R-free: 0.279

Authors:

R.Ishii,S.Yokoyama,Riken Structural Genomics/proteomics Init (Rsgi)

Key ref:

R.Ishii et al. (2005). Crystal structure of the tRNA 3' processing endoribonuclease tRNase Z from Thermotoga maritima. J Biol Chem, 280, 14138-14144. PubMed id: 15701599 DOI: 10.1074/jbc.M500355200

Date:

30-Dec-04 Release date: 22-Feb-05

Protein chain

Q9WZW8  (Q9WZW8_THEMA) -  Putative uncharacterized protein

Seq: 280 a.a.

Struc: 250 a.a.

Protein chain

Q9WZW8  (Q9WZW8_THEMA) -  Putative uncharacterized protein

Seq: 280 a.a.

Struc: 238 a.a.

 Gene Ontology (GO) functional annotation 

• Biochemical function: hydrolase activity (2 terms)

DOI no: 10.1074/jbc.M500355200

J Biol Chem 280:14138-14144 (2005)

PubMed id: 15701599

Crystal structure of the tRNA 3' processing endoribonuclease tRNase Z from Thermotoga maritima.

R.Ishii, A.Minagawa, H.Takaku, M.Takagi, M.Nashimoto, S.Yokoyama.

ABSTRACT

The maturation of the tRNA 3' end is catalyzed by a tRNA 3' processing endoribonuclease named tRNase Z (RNase Z or 3'-tRNase) in eukaryotes, Archaea, and some bacteria. The tRNase Z generally cuts the 3' extra sequence from the precursor tRNA after the discriminator nucleotide. In contrast, Thermotoga maritima tRNase Z cleaves the precursor tRNA precisely after the CCA sequence. In this study, we determined the crystal structure of T. maritima tRNase Z at 2.6-A resolution. The tRNase Z has a four-layer alphabeta/betaalpha sandwich fold, which is classified as a metallo-beta-lactamase fold, and forms a dimer. The active site is located at one edge of the beta-sandwich and is composed of conserved motifs. Based on the structure, we constructed a docking model with the tRNAs that suggests how tRNase Z may recognize the substrate tRNAs.

Selected figure(s)

Figure 1.
FIG. 1. Ribbon diagram displaying the overall structure of T. maritima tRNase Z (stereoview). A, the T. maritima tRNase Z subunit structure. The -helices, -strands, and 3[10] helices are colored yellow, cyan, and orange, respectively. The conserved motifs of the metallo- -lactamase superfamily are represented by ball-and-stick models and are colored red. The disordered regions are represented by dashed lines. B, the T. maritima tRNase Z dimer structure. The two subunits are colored pink and green. The non-crystallographic symmetry 2-fold axis is perpendicular to the paper. All of the graphic figures in the present study were drawn with CueMol (cuemol.sourceforge.jp/en/).

Figure 4.
FIG. 4. Comparison of the active site of T. maritima tRNase Z with that of B. fragilis metallo- -lactamase (stereoview). A, the active site of T. maritima tRNase Z. The conserved motifs, except for motif III, which is disordered, are represented by ball-and-stick models. Secondary structures are colored as in Fig. 1A. The side chain of Thr-47, which interacts with Asp-25, and the bound zinc ion are also depicted. B, the superposition of the active site of T. maritima tRNase Z (magenta) and that of B. fragilis metallo- -lactamase (cyan). The side chains involved in the conserved motifs are depicted as ball-and-stick representations. The zinc ion(s) (colored gold in T. maritima tRNase Z and gray in B. fragilis metallo- -lactamase, respectively) and the water molecules (red) are depicted as spheres.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 14138-14144) copyright 2005.

Figures were selected by an automated process.