6IY8

DmpR-phenol complex of Pseudomonas putida

Summary for 6IY8

• Entry DOI: 10.2210/pdb6iy8/pdb
• Descriptor: Positive regulator CapR, PHENOL, ZINC ION (3 entities in total)
• Functional Keywords: phenol, transcription, dmpr, capr, atpase, gene regulation
• Biological source: Pseudomonas putida
• Total number of polymer chains: 4
• Total formula weight: 213024.13

Authors

Park, K.H.,Woo, E.J. (deposition date: 2018-12-13, release date: 2020-06-10, Last modification date: 2024-03-27)

Primary citation

Park, K.H.,Kim, S.,Lee, S.J.,Cho, J.E.,Patil, V.V.,Dumbrepatil, A.B.,Song, H.N.,Ahn, W.C.,Joo, C.,Lee, S.G.,Shingler, V.,Woo, E.J.
Tetrameric architecture of an active phenol-bound form of the AAA+transcriptional regulator DmpR.
Nat Commun, 11:2728-2728, 2020

PubMed 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 σ 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 σ-dependent transcription.

PubMed: 32483114
DOI: 10.1038/s41467-020-16562-5

Experimental method

X-RAY DIFFRACTION (3.42 Å)