Histidine kinase domain from Erythrobacter litoralis EL346 blue-light activated histidine kinase

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

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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; Structural Biology Initiative, City University of New York Advanced Science Research Center, New York, NY 10031; and Department of Chemistry, City College of New York, New York, NY 10031 Kevin.Gardner@asrc.cuny.edu.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Blue-light-activated histidine kinase 2
A, B, C, D
232Erythrobacter litoralis HTCC2594Mutation(s): 0 
Gene Names: ELI_04860
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.503α = 90
b = 120.503β = 90
c = 192.304γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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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