5YEP

Crystal structure of SO_3166-SO_3165 from Shewanella oneidensis

Summary for 5YEP

• Entry DOI: 10.2210/pdb5yep/pdb
• Descriptor: Toxin-antitoxin system antidote Mnt family, Toxin-antitoxin system toxin HepN family (2 entities in total)
• Functional Keywords: toxin-antitoxin, hepn-mnt, antitoxin-toxin complex, antitoxin/toxin
• Biological source: Shewanella oneidensis; More
• Total number of polymer chains: 4
• Total formula weight: 64482.91

Authors

Jia, X.,Gao, Z.Q.,Zhang, H.,Dong, Y.H. (deposition date: 2017-09-19, release date: 2018-03-28, Last modification date: 2024-11-06)

Primary citation

Jia, X.,Yao, J.,Gao, Z.,Liu, G.,Dong, Y.H.,Wang, X.,Zhang, H.
Structure-function analyses reveal the molecular architecture and neutralization mechanism of a bacterial HEPN-MNT toxin-antitoxin system.
J. Biol. Chem., 293:6812-6823, 2018

PubMed Abstract: Toxin-antitoxin (TA) loci in bacteria are small genetic modules that regulate various cellular activities, including cell growth and death. The two-gene module encoding a HEPN (higher eukaryotes and prokaryotes nucleotide-binding) domain and a cognate MNT (minimal nucleotidyltransferase) domain have been predicted to represent a novel type II TA system prevalent in archaea and bacteria. However, the neutralization mechanism and cellular targets of the TA family remain unclear. The toxin SO_3166 having a HEPN domain and its cognate antitoxin SO_3165 with an MNT domain constitute a typical type II TA system that regulates cell motility and confers plasmid stability in the bacterium Here, we report the crystal structure and solution conformation of the SO_3166-SO_3165 pair, representing the first complex structures in this TA family. The structures revealed that SO_3165 and SO_3166 form a tight heterooctamer (at a 2:6 ratio), an organization that is very rare in other TA systems. We also observed that SO_3166 dimerization enables the formation of a deep cleft at the HEPN-domain interface harboring a composite R4-6H active site that functions as an RNA-cleaving RNase. SO_3165 bound SO_3166 mainly through its two α-helices (α2 and α4), functioning as molecular recognition elements. Moreover, their insertion into the SO_3166 cleft sterically blocked the R4-6H site or narrowed the cleft to inhibit RNA substrate binding. Structure-based mutagenesis confirmed the important roles of these α-helices in SO_3166 binding and inhibition. Our structure-function analysis provides first insights into the neutralization mechanism of the HEPN-MNT TA family.

PubMed: 29555683
DOI: 10.1074/jbc.RA118.002421

Experimental method

X-RAY DIFFRACTION (3 Å)