7E1F

Native-DBD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of phosphorylation-induced activation of the response regulator VbrR.

Hong, S.Guo, J.Zhang, X.Zhou, X.Zhang, P.Yu, F.

(2023) Acta Biochim Biophys Sin (Shanghai) 

  • DOI: https://doi.org/10.3724/abbs.2022200
  • Primary Citation of Related Structures:  
    7E1B, 7E1D, 7E1F, 7E1H

  • PubMed Abstract: 

    Two-component systems typically consist of a paired histidine kinase and response regulator and couple environmental changes to adaptive responses. The response regulator VbrR from Vibrio parahaemolyticus , a member of the OmpR/PhoB family, regulates virulence and antibiotic resistance genes. The activation mechanism of VbrR remains unclear. Here, we report the crystal structures of full-length VbrR in complex with DNA in the active conformation and the N-terminal receiver domain (RD) and the C-terminal DNA-binding domain (DBD) in both active and inactive conformations. Structural and biochemical analyses suggest that unphosphorylated VbrR adopts mainly as inactive dimers through the DBD at the autoinhibitory state. The RD undergoes a monomer-to-dimer transition upon phosphorylation, which further induces the transition of DBD from an autoinhibitory dimer to an active dimer and enables its binding with target DNA. Our study suggests a new model for phosphorylation-induced activation of response regulators and sheds light on the pathogenesis of V . parahaemolyticus .


  • Organizational Affiliation

    National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-binding response regulatorA [auth B],
B [auth A]
96Vibrio parahaemolyticusMutation(s): 0 
Gene Names: C9I78_18460CA163_10520CGH73_12770CGI34_20580CGI42_14750D5E78_24805F0L89_03250F0L99_22745WR32_19050
UniProt
Find proteins for A0A0L8SKF9 (Vibrio parahaemolyticus)
Explore A0A0L8SKF9 
Go to UniProtKB:  A0A0L8SKF9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0L8SKF9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.455α = 90
b = 52.135β = 90
c = 96.961γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32025020, 31971120

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-09
    Type: Initial release
  • Version 1.1: 2023-02-15
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Data collection, Refinement description