8X5T

Crystal structure of Thermus thermophilus peptidyl-tRNA hydrolase in complex with adenosine 5'-monophosphate

Summary for 8X5T

• Entry DOI: 10.2210/pdb8x5t/pdb
• Descriptor: Peptidyl-tRNA hydrolase, ADENOSINE MONOPHOSPHATE, L(+)-TARTARIC ACID, ... (5 entities in total)
• Functional Keywords: peptidyl-trna hydrolase, translation
• Biological source: Thermus thermophilus HB8
• Total number of polymer chains: 3
• Total formula weight: 63133.50

Authors

Uehara, Y.,Matsumoto, A.,Nakazawa, T.,Fukuta, A.,Ando, K.,Oka, N.,Uchiumi, T.,Ito, K. (deposition date: 2023-11-19, release date: 2024-11-20, Last modification date: 2025-06-04)

Primary citation

Uehara, Y.,Matsumoto, A.,Nakazawa, T.,Fukuta, A.,Ando, K.,Uchiumi, T.,Oka, N.,Ito, K.
Binding mode between peptidyl-tRNA hydrolase and the peptidyl-A76 moiety of the substrate.
J.Biol.Chem., 301:108385-108385, 2025

PubMed Abstract: Peptidyl-tRNA hydrolase (Pth) hydrolyzes the ester bond between the peptide and the tRNA of peptidyl-tRNA molecules, which are the products of aborted translation, to prevent cell death by recycling tRNA. Numerous studies have attempted to elucidate the substrate recognition mechanism of Pth. However, the binding mode of the peptidyl-A76 (3'-terminal adenosine of tRNA) moiety of the substrate to Pth, especially the A76 moiety, remains unclear. Here, we present the crystal structure of Thermus thermophilus Pth (TtPth) in complex with adenosine 5'-monophosphate (AMP), a mimic of A76. In addition, we show the crystal structure of TtPth in which the active site cleft interacts with the C-terminal three amino acid residues of a crystallographically related neighboring TtPth molecule. Superimposition of these two crystal structures reveals that the C-terminal carboxyl group of the neighboring TtPth molecule and the 3'-hydroxyl group of AMP are located in positions favorable for ester bond formation, and we present a TtPth⋅peptidyl-A76 complex model. The complex model agrees with many previous NMR and kinetic studies, and our site-directed mutagenesis studies support its validity. Based on these facts, we conclude that the complex model properly represents the interaction between Pth and the substrate in the reaction. Furthermore, structural comparisons suggest that the substrate recognition mode is conserved among bacterial Pths. This study provides insights into the molecular mechanism of the reaction and useful information to design new drugs targeting Pth.

PubMed: 40049414
DOI: 10.1016/j.jbc.2025.108385

Experimental method

X-RAY DIFFRACTION (1.6 Å)