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.
Bibliographical noteFunding Information:
This research was partly supported by the Marine Biotechnology Programme of the Korea Institute of Marine Science and Technology Promotion (KIMST), the Ministry of Oceans and Fisheries (MOF) (No. 20170488), the National Research Fund (NRF-2018R1A2A2A05021648) and the KRIBB Research Initiative. S.-G.L. supported partly by the grant from the National Research Foundation (2018R1A2B3004755). S.K. was partly funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 753528. C.J. was funded by the Foundation for Fundamental Research on Matter (Projectruimte 15PR3188).
© 2020, The Author(s).