4GLQ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.159 

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Ligand Structure Quality Assessment 


This is version 1.7 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: https://doi.org/10.1016/j.str.2012.11.001
  • Primary Citation of Related Structures:  
    4FOF, 4GLQ

  • 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. 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methyl-accepting chemotaxis protein171Thermosynechococcus vestitus BP-1Mutation(s): 1 
Gene Names: tll0569
UniProt
Find proteins for Q8DLC7 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DLC7 
Go to UniProtKB:  Q8DLC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DLC7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VRB
Query on VRB

Download Ideal Coordinates CCD File 
B [auth A]Phycoviolobilin, blue light-absorbing form
C33 H42 N4 O6
KTSIPBCNIBDFRK-JTNIOKRPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.159 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.04α = 90
b = 47.04β = 90
c = 125.966γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-02-06
    Changes: Database references
  • Version 1.2: 2013-02-13
    Changes: Database references
  • Version 1.3: 2013-05-15
    Changes: Non-polymer description
  • Version 1.4: 2017-11-15
    Changes: Database references, Refinement description, Structure summary
  • Version 1.5: 2020-09-23
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.6: 2024-03-13
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.7: 2024-04-03
    Changes: Refinement description