9JRY | pdb_00009jry

Crystal structure of FiDCB, a dual-cysteine cyanobacterial phytochrome of Fischerella sp. PCC 9605

• PDB DOI: https://doi.org/10.2210/pdb9JRY/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Fischerella sp. PCC 9605
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-29 Released: 2025-01-22 
• Deposition Author(s): Yang, H.W., Park, Y.-I., Song, J.-J.
• Funding Organization(s): Other government, National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free: 
  0.297 (Depositor), 0.296 (DCC) 
• R-Value Work: 
  0.280 (Depositor), 0.280 (DCC) 
• R-Value Observed: 
  0.282 (Depositor) 

Starting Model: experimental

Literature

Dual-Cys bacteriophytochromes: intermediates in cyanobacterial phytochrome evolution?

Yang, H.W., Song, J.Y., Song, J.J., Kim, Y.W., Rockwell, N.C., Kim, W., Kim, H., Lagarias, J.C., Park, Y.I.

(2025) FEBS J 292: 1197-1216

• PubMed: 39801362 
• DOI: https://doi.org/10.1111/febs.17395
• Primary Citation Related Structures: 
  9JRY


• PubMed Abstract: 
  

  Previous studies have identified three families of knotted phytochrome photoreceptors in cyanobacteria. We describe a fourth type: 'hybrid' phytochromes with putative bilin-binding cysteine residues in both their N-terminal 'knot' extensions and cGMP-phosphodiesterase/adenylate cyclase/FhlA (GAF) domains, which we designate as dual-cysteine bacteriophytochromes (DCBs). Recombinant expression of DCBs in Escherichia coli yields photoactive phycocyanobilin (PCB) adducts with red/far-red photocycles similar to those of the GAF-Cys-containing cyanobacterial phytochromes (Cph1s). Incorporation of the PCB precursor, biliverdin IXα (BV), gave multiple populations, one of which appears similar to those of cyanobacterial bacteriophytochromes (cBphPs). A crystal structure of FiDCB bound to BV exhibits two thioether linkages between the GAF- and 'PAS-knot'-Cys residues and the C3 ¹ and C3 ² atoms of BV. When expressed in Synechocystis sp. PCC 6803, DCBs incorporate PCB rather than BV. DCBs can be converted to photoactive cBphP-, Cph1-, and tandem-cysteine cyanobacterial phytochrome (TCCP) analogs by removal and/or addition of a cysteine residue by site-directed mutagenesis. This structural plasticity contrasts with our inability to generate functional photosensor analogs by analogous site-directed mutagenesis of TCCP and Cph1 representatives. Phylogenetic analysis demonstrates that DCBs do not form a monophyletic clade and also suggest that Cph1 and TCCP families independently emerged from different lineages of cBphPs, possibly via DCB intermediates.

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Organizational Affiliation: 
• Department of Biological Sciences, Chungnam National University, Daejeon, Korea.
Department of Biological Science and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea.
Department of Molecular and Cellular Biology, University of California, Davis, CA, USA.
Department of Convergent Bioscience and Informatics, Chungnam National University, Daejeon, Korea.
Department of Bio-AI Convergence, Chungnam National University, Daejeon, Korea.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 120.31 kDa 
• Atom Count: 7,430 
• Modeled Residue Count: 914 
• Deposited Residue Count: 1,042 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FiDCB	A, B	521	Fischerella sp. PCC 9605	Mutation(s): 0  EC: 2.7.13.3
UniProt
Find proteins for Q9R6X3 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)) Explore Q9R6X3  Go to UniProtKB:  Q9R6X3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BLR (Subject of Investigation/LOI)	C [auth A], D [auth B]	3-[5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[[5-[(Z)-(3-ethenyl-4-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 H36 N4 O6 BPYKTIZUTYGOLE-IFADSCNNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free:  0.297 (Depositor), 0.296 (DCC) 
• R-Value Work:  0.280 (Depositor), 0.280 (DCC) 
• R-Value Observed: 0.282 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.551	α = 90
b = 147.131	β = 99.145
c = 88.076	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Yang, H.W., Park, Y.-I., Song, J.-J.

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Funding Organization	Location	Grant Number
Other government		KGM1002311
National Research Foundation (NRF, Korea)	Korea, Republic Of	2020M3A9G710393422

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release
  
• Version 1.1: 2025-03-19
  Changes: Database references