3VV4

Crystal structure of cyanobacteriochrome TePixJ GAF domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


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Literature

Structures of cyanobacteriochromes from phototaxis regulators AnPixJ and TePixJ reveal general and specific photoconversion mechanism

Narikawa, R.Ishizuka, T.Muraki, N.Shiba, T.Kurisu, G.Ikeuchi, M.

(2013) Proc Natl Acad Sci U S A 110: 918-923

  • DOI: 10.1073/pnas.1212098110
  • Primary Citation of Related Structures:  
    3W2Z, 3VV4

  • PubMed Abstract: 
  • Cyanobacteriochromes are cyanobacterial tetrapyrrole-binding photoreceptors that share a bilin-binding GAF domain with photoreceptors of the phytochrome family. Cyanobacteriochromes are divided into many subclasses with distinct spectral properties. Among them, putative phototaxis regulators PixJs of Anabaena sp ...

    Cyanobacteriochromes are cyanobacterial tetrapyrrole-binding photoreceptors that share a bilin-binding GAF domain with photoreceptors of the phytochrome family. Cyanobacteriochromes are divided into many subclasses with distinct spectral properties. Among them, putative phototaxis regulators PixJs of Anabaena sp. PCC 7120 and Thermosynechococcus elongatus BP-1 (denoted as AnPixJ and TePixJ, respectively) are representative of subclasses showing red-green-type and blue/green-type reversible photoconversion, respectively. Here, we determined crystal structures for the AnPixJ GAF domain in its red-absorbing 15Z state (Pr) and the TePixJ GAF domain in its green-absorbing 15E state (Pg). The overall structure of these proteins is similar to each other and also similar to known phytochromes. Critical differences found are as follows: (i) the chromophore of AnPixJ Pr is phycocyanobilin in a C5-Z,syn/C10-Z,syn/C15-Z,anti configuration and that of TePixJ Pg is phycoviolobilin in a C10-Z,syn/C15-E,anti configuration, (ii) a side chain of the key aspartic acid is hydrogen bonded to the tetrapyrrole rings A, B and C in AnPixJ Pr and to the pyrrole ring D in TePixJ Pg, (iii) additional protein-chromophore interactions are provided by subclass-specific residues including tryptophan in AnPixJ and cysteine in TePixJ. Possible structural changes following the photoisomerization of the chromophore between C15-Z and C15-E are discussed based on the X-ray structures at 1.8 and 2.0-Å resolution, respectively, in two distinct configurations.


    Organizational Affiliation

    Department of Life Sciences Biology, Graduate School of Art and Sciences, University of Tokyo, Komaba, Meguro, Tokyo 153-8902, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methyl-accepting chemotaxis proteinA, B196Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: tll0569
UniProt
Find proteins for Q8DLC7 (Thermosynechococcus elongatus (strain BP-1))
Explore Q8DLC7 
Go to UniProtKB:  Q8DLC7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PVG
Query on PVG

Download Ideal Coordinates CCD File 
C [auth A], G [auth B]Phycoviolobilin, green light-absorbing form
C33 H40 N4 O6
YWHXTEHCIWOHBT-STWNLGFLSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], F [auth A], H [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.868α = 90
b = 72.868β = 90
c = 166.667γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-30
    Type: Initial release