6IY8

DmpR-phenol complex of Pseudomonas putida


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.42 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.238 

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This is version 1.2 of the entry. See complete history


Literature

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

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.

(2020) Nat Commun 11: 2728-2728

  • DOI: https://doi.org/10.1038/s41467-020-16562-5
  • Primary Citation of Related Structures:  
    6IY8

  • 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 54 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 54 -dependent transcription.


  • Organizational Affiliation

    Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 305-806, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Positive regulator CapR
A, B, C, D
469Pseudomonas putidaMutation(s): 2 
UniProt
Find proteins for Q7WSM9 (Pseudomonas putida)
Explore Q7WSM9 
Go to UniProtKB:  Q7WSM9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7WSM9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.42 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.238 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.636α = 90
b = 129.998β = 90
c = 110.276γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-10
    Type: Initial release
  • Version 1.1: 2020-06-17
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references, Refinement description