Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

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

Macromolecule Content

• Total Structure Weight: 16594.76 
• Atom Count: 1057 
• Residue Count: 142 
• Unique protein chains: 1

3HJ7

Crystal structure of TILS C-terminal domain

• DOI: 10.2210/pdb3HJ7/pdb

• Classification: LIGASE
• Organism(s): Geobacillus kaustophilus (strain HTA426)
• Expression System: Escherichia coli


• Deposited: 2009-05-21 Released: 2009-10-20 
• Deposition Author(s): Nakanishi, K., Bonnefond, L., Kimura, S., Suzuki, T., Ishitani, R., Nureki, O.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.247 
• R-Value Work: 0.218 

Literature

Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase.

Nakanishi, K., Bonnefond, L., Kimura, S., Suzuki, T., Ishitani, R., Nureki, O.

(2009) Nature 461: 1144-1148

• PubMed: 19847269 
• DOI: 10.1038/nature08474
• Primary Citation of Related Structures:  
  3A2K


• PubMed Abstract: 
  

Maturation of precursor transfer RNA (pre-tRNA) includes excision of the 5' leader and 3' trailer sequences, removal of introns and addition of the CCA terminus. Nucleotide modifications are incorporated at different stages of tRNA processing, after the RNA molecule adopts the proper conformation. In bacteria, tRNA(Ile2) lysidine synthetase (TilS) modifies cytidine into lysidine (L; 2-lysyl-cytidine) at the first anticodon of tRNA(Ile2) (refs 4-9). This modification switches tRNA(Ile2) from a methionine-specific to an isoleucine-specific tRNA. However, the aminoacylation of tRNA(Ile2) by methionyl-tRNA synthetase (MetRS), before the modification by TilS, might lead to the misincorporation of methionine in response to isoleucine codons. The mechanism used by bacteria to avoid this pitfall is unknown. Here we show that the TilS enzyme specifically recognizes and modifies tRNA(Ile2) in its precursor form, thereby avoiding translation errors. We identified the lysidine modification in pre-tRNA(Ile2) isolated from RNase-E-deficient Escherichia coli and did not detect mature tRNA(Ile2) lacking this modification. Our kinetic analyses revealed that TilS can modify both types of RNA molecule with comparable efficiencies. X-ray crystallography and mutational analyses revealed that TilS specifically recognizes the entire L-shape structure in pre-tRNA(Ile2) through extensive interactions coupled with sequential domain movements. Our results demonstrate how TilS prevents the recognition of tRNA(Ile2) by MetRS and achieves high specificity for its substrate. These two key points form the basis for maintaining the fidelity of isoleucine codon translation in bacteria. Our findings also provide a rationale for the necessity of incorporating specific modifications at the precursor level during tRNA biogenesis.

---

Organizational Affiliation: 

Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa 225-8501, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
tRNA(Ile)-lysidine synthase	A	142	Geobacillus kaustophilus (strain HTA426)	Mutation(s): 0  Gene Names: tilS EC: 6.3.4.19
Find proteins for Q5L3T3 (Geobacillus kaustophilus (strain HTA426)) Go to UniProtKB:  Q5L3T3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.247 
• R-Value Work: 0.218 
• Space Group: P 6₄ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 72.880	α = 90.00
b = 72.880	β = 90.00
c = 172.740	γ = 120.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
PHENIX	refinement
DENZO	data reduction
MOLREP	phasing
HKL-2000	data collection
SCALEPACK	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-05-21 
• Released Date: 2009-10-20 
• Deposition Author(s): Nakanishi, K., Bonnefond, L., Kimura, S., Suzuki, T., Ishitani, R., Nureki, O.

Revision History 

• Version 1.0: 2009-10-20
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2017-11-01
  Type: Refinement description