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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.USA 111: 17839-17844

  • DOI: 10.1073/pnas.1413983111
  • Primary Citation of Related Structures:  

  • 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 f ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Blue-light-activated histidine kinase 2
A, B
352Erythrobacter litoralis (strain HTCC2594)Mutation(s): 0 
EC: 2.7.13.3
Find proteins for Q2NB77 (Erythrobacter litoralis (strain HTCC2594))
Go to UniProtKB:  Q2NB77
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RBF
Query on RBF

Download SDF File 
Download CCD File 
A, B
RIBOFLAVIN
RIBOFLAVINE; VITAMIN B2
C17 H20 N4 O6
AUNGANRZJHBGPY-SCRDCRAPSA-N
 Ligand Interaction
ANP
Query on ANP

Download SDF File 
Download CCD File 
A, B
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.290 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 98.882α = 90.00
b = 98.882β = 90.00
c = 422.255γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
HKL-3000data scaling
DENZOdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2014-12-31
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description