1WW1 | pdb_00001ww1

Crystal structure of tRNase Z from Thermotoga maritima

• PDB DOI: https://doi.org/10.2210/pdb1WW1/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-12-30 Released: 2005-02-22 
• Deposition Author(s): Ishii, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.279 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Literature

Crystal Structure of the tRNA 3' Processing Endoribonuclease tRNase Z from Thermotoga maritima

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

(2005) J Biological Chem 280: 14138-14144

• PubMed: 15701599 
• DOI: https://doi.org/10.1074/jbc.M500355200
• Primary Citation Related Structures: 
  1WW1


• PubMed 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.

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Organizational Affiliation: 
• Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 65.56 kDa 
• Atom Count: 4,055 
• Modeled Residue Count: 488 
• Deposited Residue Count: 560 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNase Z	A, B	280	Thermotoga maritima MSB8	Mutation(s): 0  EC: 3.1.26.11
UniProt
Find proteins for Q9WZW8 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZW8  Go to UniProtKB:  Q9WZW8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.279 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.902	α = 90
b = 73.642	β = 90
c = 91.994	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-22 
Deposition Author(s): Ishii, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-02-22
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations