4GCZ

Structure of a blue-light photoreceptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Full-length structure of a sensor histidine kinase pinpoints coaxial coiled coils as signal transducers and modulators.

Diensthuber, R.P.Bommer, M.Gleichmann, T.Moglich, A.

(2013) Structure 21: 1127-1136

  • DOI: 10.1016/j.str.2013.04.024

  • PubMed Abstract: 
  • Two-component systems (TCSs), which comprise sensor histidine kinases (SHK) and response-regulator proteins, represent the predominant strategy by which prokaryotes sense and respond to a changing environment. Despite paramount biological importance, ...

    Two-component systems (TCSs), which comprise sensor histidine kinases (SHK) and response-regulator proteins, represent the predominant strategy by which prokaryotes sense and respond to a changing environment. Despite paramount biological importance, a dearth exists of intact SHK structures containing both sensor and effector modules. Here, we report the full-length crystal structure of the engineered, dimeric, blue-light-regulated SHK YF1 at 2.3 Å resolution, in which two N-terminal light-oxygen-voltage (LOV) photosensors are connected by a coiled coil to the C-terminal effector modules. A second coaxial coiled coil derived from the N-termini of the LOV photosensors and inserted between them crucially modulates light regulation: single mutations within this coiled coil attenuate or even invert the signal response of the TCS. Structural motifs identified in YF1 recur in signal receptors, and the underlying signaling principles and mechanisms may be widely shared between soluble and transmembrane, prokaryotic, and eukaryotic signal receptors of diverse biological activity.


    Organizational Affiliation

    Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany. ralph.diensthuber@hu-berlin.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Blue-light photoreceptor, Sensor protein fixL
A, B
385Bacillus subtilis (strain 168)Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
This entity is chimeric
Gene Names: pfyP (ytvA), fixL
EC: 2.7.13.3
Find proteins for O34627 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O34627
Find proteins for P23222 (Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110))
Go to UniProtKB:  P23222
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FMN
Query on FMN

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Download CCD File 
A, B
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
ADP
Query on ADP

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Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.179 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 105.216α = 90.00
b = 105.216β = 90.00
c = 441.958γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
MxCuBEdata collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2013-07-10
    Type: Database references
  • Version 1.2: 2013-07-24
    Type: Database references
  • Version 1.3: 2017-08-23
    Type: Advisory, Refinement description, Source and taxonomy