6SAX

Chromophore binding domain of bacteriophytochrome linked diguanylyl cyclase from Idiomarina species A28L (Pr-state monomer).

Summary for 6SAX

• Entry DOI: 10.2210/pdb6sax/pdb
• Related: 5llw 5lly 6et7
• Descriptor: Diguanylate cyclase (GGDEF) domain-containing protein, 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid (3 entities in total)
• Functional Keywords: bacteriophytochrome, biliverdin, monomer, protein, fluorescent protein
• Biological source: Idiomarina sp. A28L
• Total number of polymer chains: 2
• Total formula weight: 72970.87

Authors

Gourinchas, G.,Winkler, A. (deposition date: 2019-07-18, release date: 2019-12-11, Last modification date: 2024-11-13)

Primary citation

Buhrke, D.,Gourinchas, G.,Muller, M.,Michael, N.,Hildebrandt, P.,Winkler, A.
Distinct chromophore-protein environments enable asymmetric activation of a bacteriophytochrome-activated diguanylate cyclase.
J.Biol.Chem., 295:539-551, 2020

PubMed Abstract: Sensing of red and far-red light by bacteriophytochromes involves intricate interactions between their bilin chromophore and the protein environment. The light-triggered rearrangements of the cofactor configuration and eventually the protein conformation enable bacteriophytochromes to interact with various protein effector domains for biological modulation of diverse physiological functions. Excitation of the holoproteins by red or far-red light promotes the photoconversion to their far-red light-absorbing Pfr state or the red light-absorbing Pr state, respectively. Because prototypical bacteriophytochromes have a parallel dimer architecture, it is generally assumed that symmetric activation with two Pfr state protomers constitutes the signaling-active species. However, the bacteriophytochrome from species A28L (PadC) has recently been reported to enable long-range signal transduction also in asymmetric dimers containing only one Pfr protomer. By combining crystallography, hydrogen-deuterium exchange coupled to MS, and vibrational spectroscopy, we show here that Pfr of PadC is in equilibrium with an intermediate "Pfr-like" state that combines features of Pfr and Meta-R states observed in other bacteriophytochromes. We also show that structural rearrangements in the N-terminal segment (NTS) can stabilize this Pfr-like state and that the PHY-tongue conformation of PadC is partially uncoupled from the initial changes in the NTS. This uncoupling enables structural asymmetry of the overall homodimeric assembly and allows signal transduction to the covalently linked physiological diguanylate cyclase output module in which asymmetry might play a role in the enzyme-catalyzed reaction. The functional differences to other phytochrome systems identified here highlight opportunities for using additional red-light sensors in artificial sensor-effector systems.

PubMed: 31801828
DOI: 10.1074/jbc.RA119.011915

Experimental method

X-RAY DIFFRACTION (2.4 Å)