4R3A

Erythrobacter litoralis EL346 blue-light activated histidine kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.290 
  • R-Value Observed: 0.294 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Full-length structure of a monomeric histidine kinase reveals basis for sensory regulation.

Rivera-Cancel, G.Ko, W.H.Tomchick, D.R.Correa, F.Gardner, K.H.

(2014) Proc Natl Acad Sci U S A 111: 17839-17844

  • DOI: https://doi.org/10.1073/pnas.1413983111
  • Primary Citation of Related Structures:  
    4R38, 4R39, 4R3A

  • PubMed Abstract: 

    Although histidine kinases (HKs) are critical sensors of external stimuli in prokaryotes, the mechanisms by which their sensor domains control enzymatic activity remain unclear. Here, we report the full-length structure of a blue light-activated HK from Erythrobacter litoralis HTCC2594 (EL346) and the results of biochemical and biophysical studies that explain how it is activated by light. Contrary to the standard view that signaling occurs within HK dimers, EL346 functions as a monomer. Its structure reveals that the light-oxygen-voltage (LOV) sensor domain both controls kinase activity and prevents dimerization by binding one side of a dimerization/histidine phosphotransfer-like (DHpL) domain. The DHpL domain also contacts the catalytic/ATP-binding (CA) domain, keeping EL346 in an inhibited conformation in the dark. Upon light stimulation, interdomain interactions weaken to facilitate activation. Our data suggest that the LOV domain controls kinase activity by affecting the stability of the DHpL/CA interface, releasing the CA domain from an inhibited conformation upon photoactivation. We suggest parallels between EL346 and dimeric HKs, with sensor-induced movements in the DHp similarly remodeling the DHp/CA interface as part of activation.


  • Organizational Affiliation

    Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-8816;


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Blue-light-activated histidine kinase 2
A, B
352Erythrobacter litoralis HTCC2594Mutation(s): 0 
Gene Names: ELI_04860
EC: 2.7.13.3
UniProt
Find proteins for Q2NB77 (Erythrobacter litoralis (strain HTCC2594))
Explore Q2NB77 
Go to UniProtKB:  Q2NB77
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2NB77
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.290 
  • R-Value Observed: 0.294 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.882α = 90
b = 98.882β = 90
c = 422.255γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2014-12-31
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description