9IUW image
Deposition Date 2024-07-22
Release Date 2025-07-30
Last Version Date 2026-02-18
Entry Detail
PDB ID:
9IUW
Title:
Structure of AlaX-M trans-editing enzyme from Pyrococcus furiosus
Biological Source:
Method Details:
Experimental Method:
Resolution:
1.78 Å
R-Value Free:
0.21
R-Value Work:
0.18
R-Value Observed:
0.19
Space Group:
C 1 2 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Partial alanyl-tRNA synthetase matches COOH terminus
Gene (Uniprot):PF0086
Chain IDs:A
Chain Length:214
Number of Molecules:1
Biological Source:Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Ligand Molecules
Primary Citation
A metal ion mediated functional dichotomy encodes plasticity during translation quality control.
Nat Commun 16 3625 3625 (2025)
PMID: 40240361 DOI: 10.1038/s41467-025-58787-2

Abstact

Proofreading during translation of the genetic code is a key process for not only translation quality control but also for its modulation under stress conditions to provide fitness advantage. A major class of proofreading modules represented by editing domains of alanyl-tRNA synthetase (AlaRS-Ed) and threonyl-tRNA synthetase (ThrRS-Ed) features a common fold and an invariant Zn2+ binding motif across life forms. Here, we reveal the structural basis and functional consequence along with the necessity for their operational dichotomy, i.e., the metal ion is ubiquitous in one and inhibitor for the other. The universally conserved Zn2+ in AlaRS-Ed protects its proofreading activity from reactive oxygen species (ROS) to maintain high fidelity Ala-codons translation, necessary for cell survival. On the other hand, mistranslation of Thr-codons is well tolerated by the cells, thereby allowing for a ROS-based modulation of ThrRS-Ed's activity. A single residue rooted over ~3.5 billion years of evolution has been shown to be primarily responsible for the functional divergence. The study presents a remarkable example of how protein quality control is integrated with redox signalling through leveraging the tunability of metal binding sites from the time of last universal common ancestor (LUCA).

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Primary Citation of related structures
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