PXD062828

PXD062828 is an original dataset announced via ProteomeXchange.

Title	Neutralization mechanism of a HipA-like toxin targeting isoleucyl-tRNA synthetase
Description	HipAB is a type II toxin-antitoxin (TA) system that targets and inactivates specific aminoacyl-tRNA synthetases in response to various stresses. While the molecular targets and neutralization mechanisms of several HipAB-like TA systems have been well characterized, their structural and functional diversity remains less understood. In this study, we investigated a HipAB-like module (HipABpf) from Pseudomonas fluorescens, where the HipBpf antitoxin features a long, disordered C-terminal region in the absence of HipApf. Using a combination of X-ray crystallography, AlphaFold modeling and mutagenesis assays, we show that upon binding to HipApf, part of this C-terminal region forms two α-helices that are essential for both the interaction with and neutralization of the HipApf toxin. Importantly, HipBpf binding blocks the ATP binding sites of HipApf, potentially by inducing a conformational change in the HipApf N1 subdomain via its C-terminal α6 helix. We also discovered that HipApf phosphorylates the isoleucyl-tRNA synthetase at Ser604, strongly inhibiting its aminoacylation activity. Finally, we demonstrated that the HipABpf system plays a role in coping with oxidative stress and carbon starvation. Taken together, our findings reveal the critical role of the HipBpf C-terminal region in toxin binding and neutralization, while also highlighting the evolutionarily divergent substrate preferences of HipA-like toxins.
HostingRepository	iProX
AnnounceDate	2025-04-11
AnnouncementXML	Submission_2026-03-04_23:10:35.956.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Siping Zhang
SpeciesList	scientific name: Escherichia coli K-12; NCBI TaxID: 83333;
ModificationList	phosphorylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-10 20:40:52	ID requested
1	2025-04-10 20:41:04	announced
⏵ 2	2026-03-04 23:10:36	announced	2026-03-05: Add info.

Zhang SP, Song YJ, Ye YP, Ye ZR, Yang FL, Niu B, Bai FH, Fan CH, Wan LX, He M, Wang Y, Bao R, He YX, Neutralization Mechanism of a HipA-like Toxin Targeting Isoleucyl-tRNA Synthetase. J Mol Biol, 438(2):169563(2026) [pubmed]

submitter keyword: HipAB system,Pseudomonas fluorescens,Phosphorylation,Neutralization mechanism

Yongxing He
contact affiliation	Lanzhou University
contact email	heyx@lzu.edu.cn
lab head
Siping Zhang
contact affiliation	Lanzhou University
contact email	zhangsp2015@lzu.edu.cn
dataset submitter

iProX dataset URI