8K9O | pdb_00008k9o

Crystal structure of Cyanobacteriochrome RcaE GAF domain in Pg state

• PDB DOI: https://doi.org/10.2210/pdb8K9O/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Microchaete diplosiphon
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-08-01 Released: 2024-05-15 
• Deposition Author(s): Nagae, T., Hirose, Y., Mishima, M.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.231 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.198 (DCC) 

Starting Model: experimental

Literature

Green/red light-sensing mechanism in the chromatic acclimation photosensor.

Nagae, T., Fujita, Y., Tsuchida, T., Kamo, T., Seto, R., Hamada, M., Aoyama, H., Sato-Tomita, A., Fujisawa, T., Eki, T., Miyanoiri, Y., Ito, Y., Soeta, T., Ukaji, Y., Unno, M., Mishima, M., Hirose, Y.

(2024) Sci Adv 10: eadn8386-eadn8386

• PubMed: 38865454 
• DOI: https://doi.org/10.1126/sciadv.adn8386
• Primary Citation Related Structures: 
  8K9O


• PubMed Abstract: 
  

  Certain cyanobacteria alter their photosynthetic light absorption between green and red, a phenomenon called complementary chromatic acclimation. The acclimation is regulated by a cyanobacteriochrome-class photosensor that reversibly photoconverts between green-absorbing (Pg) and red-absorbing (Pr) states. Here, we elucidated the structural basis of the green/red photocycle. In the Pg state, the bilin chromophore adopted the extended C15- Z , anti structure within a hydrophobic pocket. Upon photoconversion to the Pr state, the bilin is isomerized to the cyclic C15- E , syn structure, forming a water channel in the pocket. The solvation/desolvation of the bilin causes changes in the protonation state and the stability of π-conjugation at the B ring, leading to a large absorption shift. These results advance our understanding of the enormous spectral diversity of the phytochrome superfamily.

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Organizational Affiliation: 
• Department of Molecular Biophysics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan.
Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan.
Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan.
Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Honjomachi, Saga 840-8502, Japan.
Division of Biophysics, Department of Physiology, Jichi Medical University, Yakushiji, Shimotsuke, Tochigi 329-0498, Japan.
Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 22.63 kDa 
• Atom Count: 1,567 
• Modeled Residue Count: 179 
• Deposited Residue Count: 194 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
histidine kinase	A	194	Microchaete diplosiphon	Mutation(s): 0  Gene Names: rcaE EC: 2.7.13.3
UniProt
Find proteins for Q47897 (Microchaete diplosiphon) Explore Q47897  Go to UniProtKB:  Q47897

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CYC (Subject of Investigation/LOI)	B [auth A]	PHYCOCYANOBILIN C33 H40 N4 O6 VXTXPYZGDQPMHK-GMXXPEQVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.231 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.198 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.273	α = 90
b = 64.273	β = 90
c = 84.116	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-15 
Deposition Author(s): Nagae, T., Hirose, Y., Mishima, M.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	22H02562
Japan Society for the Promotion of Science (JSPS)	Japan	19K06707
Other private	Japan	--

Revision History  

• Version 1.0: 2024-05-15
  Type: Initial release
  
• Version 1.1: 2024-06-26
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Structure summary