1D5W | pdb_00001d5w

PHOSPHORYLATED FIXJ RECEIVER DOMAIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.244 (Depositor) 
  • R-Value Work: 
    0.217 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Conformational changes induced by phosphorylation of the FixJ receiver domain.

Birck, C.Mourey, L.Gouet, P.Fabry, B.Schumacher, J.Rousseau, P.Kahn, D.Samama, J.P.

(1999) Structure 7: 1505-1515

  • DOI: https://doi.org/10.1016/s0969-2126(00)88341-0
  • Primary Citation Related Structures: 
    1D5W

  • PubMed Abstract: 

    A variety of bacterial adaptative cellular responses to environmental stimuli are mediated by two-component signal transduction pathways. In these phosphorelay cascades, histidine kinases transphosphorylate a conserved aspartate in the receiver domain, a conserved module in the response regulator superfamily. The main effect of this phosphorylation is to alter the conformation of the response regulator in order to modulate its biological function. The response regulator FixJ displays a typical modular arrangement, with a phosphorylatable N-terminal receiver domain and a C-terminal DNA-binding domain. In the symbiotic bacterium Sinorhizobium meliloti, phosphorylation of this response regulator activates transcription of nitrogen-fixation genes. The crystal structures of the phosphorylated and of the unphosphorylated N-terminal receiver domain of FixJ (FixJN) were solved at 2.3 A and 2.4 A resolution, respectively. They reveal the environment of the phosphoaspartate in the active site and the specific conformational changes leading to activation of the response regulator. Phosphorylation of the conserved aspartate induces major structural changes in the beta 4-alpha 4 loop, and in the signaling surface alpha 4-beta 5 that mediates dimerization of the phosphorylated full-length response regulator. A site-directed mutant at this protein-protein interface decreases the affinity of the phosphorylated response regulator for the fixK promoter tenfold. The cascade of phosphorylation-induced conformational changes in FixJN illustrates the role of conserved residues in stabilizing the phosphoryl group in the active site, triggering the structural transition and achieving the post-phosphorylation signaling events. We propose that these phosphorylation-induced conformational changes underly the activation of response regulators in general.


  • Organizational Affiliation
    • Groupe de Cristallographie Biologique, CNRS-IPBS, Toulouse, France.

Macromolecule Content 

  • Total Structure Weight: 42.26 kDa 
  • Atom Count: 2,978 
  • Modeled Residue Count: 367 
  • Deposited Residue Count: 378 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TRANSCRIPTIONAL REGULATORY PROTEIN FIXJ
A, B, C
126Sinorhizobium melilotiMutation(s): 3 
UniProt
Find proteins for P10958 (Rhizobium meliloti (strain 1021))
Explore P10958 
Go to UniProtKB:  P10958
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10958
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.244 (Depositor) 
  • R-Value Work:  0.217 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.15α = 90
b = 91.3β = 112.45
c = 59.88γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-10-11
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-08-22
    Changes: Other
  • Version 1.4: 2021-11-03
    Changes: Database references, Derived calculations