8X5T | pdb_00008x5t

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

PDB DOI: https://doi.org/10.2210/pdb8X5T/pdb

Classification: TRANSLATION
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli B
Mutation(s): No

Deposited: 2023-11-19 Released: 2024-11-20
Deposition Author(s): Uehara, Y., Matsumoto, A., Nakazawa, T., Fukuta, A., Ando, K., Oka, N., Uchiumi, T., Ito, K.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.168 (Depositor), 0.180 (DCC)
R-Value Work:
0.144 (Depositor), 0.159 (DCC)
R-Value Observed:
0.145 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Binding mode between peptidyl-tRNA hydrolase and the peptidyl-A76 moiety of the substrate.

Uehara, Y., Matsumoto, A., Nakazawa, T., Fukuta, A., Ando, K., Uchiumi, T., Oka, N., Ito, K.

(2025) J Biological Chem 301: 108385-108385

PubMed: 40049414 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.jbc.2025.108385
Primary Citation of Related Structures:
8X5T, 8X5U

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.

Organizational Affiliation

Department of Biology, Faculty of Science, Niigata University, Niigata, Japan.

Macromolecule Content

Total Structure Weight: 63.13 kDa
Atom Count: 5,000
Modeled Residue Count: 554
Deposited Residue Count: 561
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-tRNA hydrolase	A, B, C	187	Thermus thermophilus HB8	Mutation(s): 0 Gene Names: pth, TTHA1588 EC: 3.1.1.29
UniProt
Find proteins for Q5SHZ2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHZ2 Go to UniProtKB: Q5SHZ2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SHZ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP (Subject of Investigation/LOI) Query on AMP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
TLA Query on TLA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	G [auth A], I [auth B], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B]