4GLQ

Crystal Structure of the blue-light absorbing form of the Thermosynechococcus elongatus PixJ GAF-domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.772 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

A Photo-Labile Thioether Linkage to Phycoviolobilin Provides the Foundation for the Blue/Green Photocycles in DXCF-Cyanobacteriochromes.

Burgie, E.S.Walker, J.M.Phillips Jr, G.N.Vierstra, R.D.

(2013) Structure 21: 88-97

  • DOI: 10.1016/j.str.2012.11.001
  • Primary Citation of Related Structures:  4FOF

  • PubMed Abstract: 
  • The phytochrome superfamily encompasses a diverse collection of photochromic photoreceptors in plants and microorganisms that employ a covalently linked bilin cradled in a cGMP-phosphodiesterase/adenylyl-cyclase/FhlA (GAF) domain to detect light. Whe ...

    The phytochrome superfamily encompasses a diverse collection of photochromic photoreceptors in plants and microorganisms that employ a covalently linked bilin cradled in a cGMP-phosphodiesterase/adenylyl-cyclase/FhlA (GAF) domain to detect light. Whereas most interconvert between red- and far-red-light-absorbing states, cyanobacteria also express variants called cyanobacteriochromes (CBCRs) that modify bilin absorption to collectively perceive the entire visible spectrum. Here, we present two X-ray crystallographic structures of the GAF domain from the blue/green photochromic CBCR PixJ from Thermosynechococcus elongatus. These structures confirm the hypothesis that CBCRs variably manipulate the chromophore π-conjugation system through isomerization and a second thioether linkage, in this case involving the bilin C10 carbon and Cys494 within a DXCF sequence characteristic of blue/green CBCRs. Biochemical studies support a mechanism for photoconversion whereby the second linkage ruptures on route to the green-light-absorbing state. Collectively, the TePixJ(GAF) models illustrate the remarkable structural and photochemical versatility among phytochromes and CBCRs in driving light perception.


    Organizational Affiliation

    Department of Genetics, 425-G Henry Mall, University of Wisconsin-Madison, Madison, WI 53706, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methyl-accepting chemotaxis protein
A
171Thermosynechococcus elongatus (strain BP-1)N/A
Find proteins for Q8DLC7 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DLC7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VRB
Query on VRB

Download SDF File 
Download CCD File 
A
Phycoviolobilin, blue light-absorbing form
3-[5-[(3-ethyl-4-methyl-5-oxidanylidene-1,2-dihydropyrrol-2-yl)methyl]-2-[[5-[(Z)-(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid
C33 H42 N4 O6
KTSIPBCNIBDFRK-JTNIOKRPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.772 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.155 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 47.040α = 90.00
b = 47.040β = 90.00
c = 125.966γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data collection
PDB_EXTRACTdata extraction
PHENIXrefinement
DENZOdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-02-06
    Type: Database references
  • Version 1.2: 2013-02-13
    Type: Database references
  • Version 1.3: 2013-05-15
    Type: Non-polymer description
  • Version 1.4: 2017-11-15
    Type: Database references, Refinement description, Structure summary