Tetrameric architecture of an active phenol-bound form of the AAA+ transcriptional regulator DmpR

Kwang-Hyun Park, Sungchul Kim, Su-Jin Lee, Jee-Eun Cho, Vinod Vikas Patil, Arti Baban Dumbrepatil, Hyung-Nam Song, Woo-Chan Ahn, Chirlmin Joo (), Seung-Goo Lee, Victoria Shingler and Eui-Jeon Woo ()
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Kwang-Hyun Park: Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB)
Sungchul Kim: Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology
Su-Jin Lee: Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB)
Jee-Eun Cho: Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB)
Vinod Vikas Patil: Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB)
Arti Baban Dumbrepatil: Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB)
Hyung-Nam Song: Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB)
Woo-Chan Ahn: Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB)
Chirlmin Joo: Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology
Seung-Goo Lee: Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB)
Victoria Shingler: Umeå University
Eui-Jeon Woo: Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB)

Nature Communications, 2020, vol. 11, issue 1, 1-12

Abstract: Abstract The Pseudomonas putida phenol-responsive regulator DmpR is a bacterial enhancer binding protein (bEBP) from the AAA+ ATPase family. Even though it was discovered more than two decades ago and has been widely used for aromatic hydrocarbon sensing, the activation mechanism of DmpR has remained elusive. Here, we show that phenol-bound DmpR forms a tetramer composed of two head-to-head dimers in a head-to-tail arrangement. The DmpR-phenol complex exhibits altered conformations within the C-termini of the sensory domains and shows an asymmetric orientation and angle in its coiled-coil linkers. The structural changes within the phenol binding sites and the downstream ATPase domains suggest that the effector binding signal is propagated through the coiled-coil helixes. The tetrameric DmpR-phenol complex interacts with the σ54 subunit of RNA polymerase in presence of an ATP analogue, indicating that DmpR-like bEBPs tetramers utilize a mechanistic mode distinct from that of hexameric AAA+ ATPases to activate σ54-dependent transcription.

Date: 2020
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DOI: 10.1038/s41467-020-16562-5

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