9U9G

Crystal structure of antitoxin HipB from Pseudomonas fluorescens 2P24

Summary for 9U9G

• Entry DOI: 10.2210/pdb9u9g/pdb
• Descriptor: XRE family transcriptional regulator, HipB (2 entities in total)
• Functional Keywords: antitoxin, homodimer
• Biological source: Pseudomonas fluorescens
• Total number of polymer chains: 4
• Total formula weight: 66456.28

Authors

Song, Y.J.,Zhang, S.P.,Bao, R.,He, Y.X. (deposition date: 2025-03-27, release date: 2026-04-01)

Primary citation

Zhang, S.P.,Song, Y.J.,Ye, Y.P.,Ye, Z.R.,Yang, F.L.,Niu, B.,Bai, F.H.,Fan, C.H.,Wan, L.X.,He, M.,Wang, Y.,Bao, R.,He, Y.X.
Neutralization Mechanism of a HipA-like Toxin Targeting Isoleucyl-tRNA Synthetase.
J.Mol.Biol., 438:169563-169563, 2026

PubMed Abstract: The HipA toxin from type II HipBA toxin-antitoxin (TA) system targets and inactivates specific cellular components to inhibit bacterial growth. While the molecular targets and neutralization mechanisms of several HipBA-like systems have been well characterized, their structural and functional diversity remains poorly understood. Here, we investigate a HipBA-like module from Pseudomonas fluorescens (HipBA), where the HipB antitoxin features a long, disordered C-terminal region in the absence of HipA. Using X-ray crystallography, AlphaFold modeling and mutagenesis assays, we show that upon binding to HipA, part of this C-terminal region forms two α-helices that are essential for both the interaction with and neutralization of the HipA toxin. Importantly, HipB binding blocks the ATP binding sites of HipA, potentially by inducing a conformational change in the HipA N1 subdomain via its C-terminal α6 helix. Finally, we also discovered that HipA (clade VI in the "Hip tree"), specifically phosphorylates isoleucyl-tRNA synthetase at Ser604, strongly inhibiting its aminoacylation activity. Collectively, our findings reveal the critical role of the HipB C-terminal region in toxin binding and neutralization, while also highlighting the evolutionarily divergent substrate preferences of HipA-like toxins.

PubMed: 41297663
DOI: 10.1016/j.jmb.2025.169563

Experimental method

X-RAY DIFFRACTION (2.15 Å)