6L8E

Crystal structure of heterohexameric YoeB-YefM complex bound to 26bp-DNA

Summary for 6L8E

• Entry DOI: 10.2210/pdb6l8e/pdb
• Descriptor: YefM Antitoxin, YoeB toxin, DNA (26-mer), ... (5 entities in total)
• Functional Keywords: toxin-antitoxin, microbial rnase, yoeb, staphylococcus aureus, toxin, antitoxin-toxin-dna complex, antitoxin/toxin/dna
• Biological source: Staphylococcus aureus subsp. aureus NCTC 8325; More
• Total number of polymer chains: 16
• Total formula weight: 149309.42

Authors

Yue, J.,Xue, L. (deposition date: 2019-11-06, release date: 2020-09-02, Last modification date: 2023-11-22)

Primary citation

Xue, L.,Yue, J.,Ke, J.,Khan, M.H.,Wen, W.,Sun, B.,Zhu, Z.,Niu, L.
Distinct oligomeric structures of the YoeB-YefM complex provide insights into the conditional cooperativity of type II toxin-antitoxin system.
Nucleic Acids Res., 48:10527-10541, 2020

PubMed Abstract: YoeB-YefM, the widespread type II toxin-antitoxin (TA) module, binds to its own promoter to autoregulate its transcription: repress or induce transcription under normal or stress conditions, respectively. It remains unclear how YoeB-YefM regulates its transcription depending on the YoeB to YefM TA ratio. We find that YoeB-YefM complex from S.aureus exists as two distinct oligomeric assemblies: heterotetramer (YoeB-YefM2-YoeB) and heterohexamer (YoeB-YefM2-YefM2-YoeB) with low and high DNA-binding affinities, respectively. Structures of the heterotetramer alone and heterohexamer bound to promoter DNA reveals that YefM C-terminal domain undergoes disorder to order transition upon YoeB binding, which allosterically affects the conformation of N-terminal DNA-binding domain. At TA ratio of 1:2, unsaturated binding of YoeB to the C-terminal regions of YefM dimer forms an optimal heterohexamer for DNA binding, and two YefM dimers with N-terminal domains dock into the adjacent major grooves of DNA to specifically recognize the 5'-TTGTACAN6AGTACAA-3' palindromic sequence, resulting in transcriptional repression. In contrast, at TA ratio of 1:1, binding of two additional YoeB molecules onto the heterohexamer induces the completely ordered conformation of YefM and disassembles the heterohexamer into two heterotetramers, which are unable to bind the promoter DNA optimally due to steric clashes, hence derepresses TA operon transcription.

PubMed: 32845304
DOI: 10.1093/nar/gkaa706

Experimental method

X-RAY DIFFRACTION (2.35 Å)