Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 66185.34 
• Atom Count: 4495 
• Residue Count: 560 
• Unique protein chains: 1

2E7Y

High resolution structure of T. maritima tRNase Z

• DOI: 10.2210/pdb2E7Y/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2007-01-15 Released: 2007-09-11 
• 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: 1.97 Å
• R-Value Free: 0.249 
• R-Value Work: 0.204 

Literature

The structure of the flexible arm of Thermotoga maritima tRNase Z differs from those of homologous enzymes

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

(2007) Acta Crystallogr.,Sect.F 63: 637-641

• PubMed: 17671357 
• DOI: 10.1107/S1744309107033623


• PubMed Abstract: 
  

tRNA 3'-processing endoribonuclease (tRNase Z) is one of the enzymes involved in the 3'-end processing of precursor tRNAs and is a member of the metallo-beta-lactamase superfamily. tRNase Z crystal structures have revealed that the enzyme forms a dimer and has a characteristic domain, named a flexible arm or an exosite, which protrudes from the metallo-beta-lactamase core and is involved in tRNA binding. The refined structure of Thermotoga maritima tRNase Z has been determined at 1.97 A resolution, revealing the structure of the flexible arm and the zinc-bound active site. The structure of the flexible arm of T. maritima tRNase Z is distinct from those of the Bacillus subtilis and Escherichia coli tRNase Zs. A comparison of the three tRNase Z structures revealed differences in the dimer orientation, which may be related to the unique cleavage-site specificity of T. maritima tRNase Z.

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Organizational Affiliation: 

RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230-0045, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
PGO	A, B	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.249 
• R-Value Work: 0.204 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 150.299	α = 90.00
b = 172.694	β = 90.00
c = 64.886	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
HKL-2000	data reduction
CNS	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-01-15 
• Released Date: 2007-09-11 
• Deposition Author(s): Ishii, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History 

• Version 1.0: 2007-09-11
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance