3HJ7

Crystal structure of TILS C-terminal domain

DOI: 10.2210/pdb3HJ7/pdb

Classification: LIGASE
Organism(s): Geobacillus kaustophilus
Expression System: Escherichia coli
Mutation(s): No

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: 2.20 Å
R-Value Free: 0.247
R-Value Work: 0.218
R-Value Observed: 0.220

wwPDB Validation3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
DOI: 10.1038/nature08474
Primary Citation of Related Structures:
3HJ7, 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:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA(Ile)-lysidine synthase	A	142	Geobacillus kaustophilus	Mutation(s): 0 Gene Names: GK0060, tilS EC: 6.3.4 (PDB Primary Data), 6.3.4.19 (UniProt)
Find proteins for Q5L3T3 (Geobacillus kaustophilus (strain HTA426)) Explore Q5L3T3 Go to UniProtKB: Q5L3T3
Protein Feature View Expand
( Mouse scroll to zoom / Hold left click to move ) Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download CCD File	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction