8W26

X-ray crystal structure of the GAF-PHY domains of SyB-Cph1

Summary for 8W26

• Entry DOI: 10.2210/pdb8w26/pdb
• Descriptor: histidine kinase, PHYCOCYANOBILIN, 1,2-ETHANEDIOL, ... (5 entities in total)
• Functional Keywords: histidine kinase, phytochrome, pas-less, cyanobacteria, gene regulation
• Biological source: Synechococcus sp. JA-2-3B'a(2-13)
• Total number of polymer chains: 1
• Total formula weight: 49784.38

Authors

Burgie, E.S.,Vierstra, R.D. (deposition date: 2024-02-20, release date: 2024-05-22, Last modification date: 2024-12-25)

Primary citation

Burgie, E.S.,Mickles, A.J.,Luo, F.,Miller, M.D.,Vierstra, R.D.
Crystal structure of the photosensory module from a PAS-less cyanobacterial phytochrome as Pr shows a mix of dark-adapted and photoactivated features.
J.Biol.Chem., 300:107369-107369, 2024

PubMed Abstract: Phytochromes (Phys) are a diverse collection of photoreceptors that regulate numerous physiological and developmental processes in microorganisms and plants through photointerconversion between red-light-absorbing Pr and far-red light-absorbing Pfr states. Light is detected by an N-terminal photo-sensing module (PSM) sequentially comprised of Period/ARNT/Sim (PAS), cGMP-phosphodiesterase/adenylyl cyclase/FhlA (GAF), and Phy-specific (PHY) domains, with the bilin chromophore covalently-bound within the GAF domain. Phys sense light via the Pr/Pfr ratio measured by the light-induced rotation of the bilin D-pyrrole ring that triggers conformational changes within the PSM, which for microbial Phys reaches into an output region. A key step is a β-stranded to α-helical reconfiguration of a hairpin loop extending from the PHY domain to contact the GAF domain. Besides canonical Phys, cyanobacteria express several variants, including a PAS-less subfamily that harbors just the GAF and PHY domains for light detection. Prior 2D-NMR studies of a model PAS-less Phy from Synechococcus_sp._JA-2-3B'a(2-13) (SyB-Cph1) proposed a unique photoconversion mechanism involving an A-pyrrole ring rotation while magic-angle-spinning NMR probing the chromophore proposed the prototypic D-ring flip. To help solve this conundrum, we determined the crystallographic structure of the GAF-PHY region from SyB-Cph1 as Pr. Surprisingly, this structure differs from canonical Phys by having a Pr ZZZsyn,syn,anti bilin configuration but shifted to the activated position in the binding pocket with consequent folding of the hairpin loop to α-helical, an architecture common for Pfr. Collectively, the PSM of SyB-Cph1 as Pr displayed a mix of dark-adapted and photoactivated features whose co-planar A-C pyrrole rings support a D-ring flip mechanism.

PubMed: 38750792
DOI: 10.1016/j.jbc.2024.107369

Experimental method

X-RAY DIFFRACTION (2.6 Å)