Structure and dynamics of polymyxin-resistance-associated response regulator PmrA in complex with promoter DNA

Yuan-Chao Lou, Tsai-Hsuan Weng, Yi-Chuan Li, Yi-Fen Kao, Wei-Feng Lin, Hwei-Ling Peng, Shan-Ho Chou, Chwan-Deng Hsiao () and Chinpan Chen ()
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Yuan-Chao Lou: Institute of Biomedical Sciences, Academia Sinica
Tsai-Hsuan Weng: Institute of Molecular Biology, Academia Sinica
Yi-Chuan Li: Institute of Molecular Biology, Academia Sinica
Yi-Fen Kao: Institute of Biomedical Sciences, Academia Sinica
Wei-Feng Lin: National Chiao Tung University
Hwei-Ling Peng: National Chiao Tung University
Shan-Ho Chou: Institute of Biochemistry, National Chung Hsing University
Chwan-Deng Hsiao: Institute of Molecular Biology, Academia Sinica
Chinpan Chen: Institute of Biomedical Sciences, Academia Sinica

Nature Communications, 2015, vol. 6, issue 1, 1-12

Abstract: Abstract PmrA, an OmpR/PhoB family response regulator, manages genes for antibiotic resistance. Phosphorylation of OmpR/PhoB response regulator induces the formation of a symmetric dimer in the N-terminal receiver domain (REC), promoting two C-terminal DNA-binding domains (DBDs) to recognize promoter DNA to elicit adaptive responses. Recently, determination of the KdpE–DNA complex structure revealed an REC–DBD interface in the upstream protomer that may be necessary for transcription activation. Here, we report the 3.2-Å-resolution crystal structure of the PmrA–DNA complex, which reveals a similar yet different REC–DBD interface. However, NMR studies show that in the DNA-bound state, two domains tumble separately and an REC–DBD interaction is transiently populated in solution. Reporter gene analyses of PmrA variants with altered interface residues suggest that the interface is not crucial for supporting gene expression. We propose that REC–DBD interdomain dynamics and the DBD–DBD interface help PmrA interact with RNA polymerase holoenzyme to activate downstream gene transcription.

Date: 2015
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DOI: 10.1038/ncomms9838

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