5YCL

Crystal structure of HigBA complex from Shigella flexneri

Summary for 5YCL

• Entry DOI: 10.2210/pdb5ycl/pdb
• Descriptor: Antitoxin HigA, mRNA interferase HigB (3 entities in total)
• Functional Keywords: toxin, antitoxin system, structural protein
• Biological source: Shigella flexneri; More
• Total number of polymer chains: 4
• Total formula weight: 54388.50

Authors

Youn, W.S.,Seok, S.H.,Seo, M.D. (deposition date: 2017-09-07, release date: 2018-09-19, Last modification date: 2024-11-13)

Primary citation

Yoon, W.S.,Seok, S.H.,Won, H.S.,Cho, T.,Lee, S.J.,Seo, M.D.
Structural changes of antitoxin HigA from Shigella flexneri by binding of its cognate toxin HigB.
Int.J.Biol.Macromol., 130:99-108, 2019

PubMed Abstract: In toxin-antitoxin systems, many antitoxin proteins that neutralize their cognate toxin proteins also bind to DNA to repress transcription, and the DNA-binding affinity of the antitoxin is affected by its toxin. We solved crystal structures of the antitoxin HigA (apo-HigA) and its complex with the toxin HigB (HigBA) from Shigella flexneri. The apo-HigA shows a distinctive V-shaped homodimeric conformation with sequestered N-domains having a novel fold. HigBA appears as a heterotetramer formed by N-terminal dimerization of HigB-bound HigA molecules. The conformational change in HigA upon HigB binding is mediated by rigid-body movements of its C-domains, which accompanied an overall conformational change from wide V-shaped to narrow V-shaped dimer. Consequently, the two putative DNA-binding helices (α7 in each subunit) are repositioned to a conformation more compatible with canonical homodimeric DNA-binding proteins containing HTH motifs. Collectively, this study demonstrates a conformational change in an antitoxin protein, which occurs upon toxin binding and is responsible for regulating antitoxin DNA binding.

PubMed: 30797012
DOI: 10.1016/j.ijbiomac.2019.02.111

Experimental method

X-RAY DIFFRACTION (3.101 Å)