9JRY

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

Summary for 9JRY

• Entry DOI: 10.2210/pdb9jry/pdb
• Descriptor: FiDCB, 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 (2 entities in total)
• Functional Keywords: cyanobacteria, dual-cysteine bacteriophytochrome, signaling protein
• Biological source: Fischerella sp. PCC 9605
• Total number of polymer chains: 2
• Total formula weight: 120308.66

Authors

Yang, H.W.,Park, Y.-I.,Song, J.-J. (deposition date: 2024-09-29, release date: 2025-01-22, Last modification date: 2025-03-19)

Primary citation

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.
Dual-Cys bacteriophytochromes: intermediates in cyanobacterial phytochrome evolution?
Febs J., 292:1197-1216, 2025

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 and C3 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.

PubMed: 39801362
DOI: 10.1111/febs.17395

Experimental method

X-RAY DIFFRACTION (3.35 Å)