The structure of a complete phytochrome sensory module in the Pr ground state

Abstract

Phytochromes are red/far-red photochromic biliprotein photoreceptors, which in plants regulate seed germination, stem extension, flowering time, and many other light effects. However, the structure/functional basis of the phytochrome photoswitch is still unclear. Here, we report the ground state structure of the complete sensory module of Cph1 phytochrome from the cyanobacterium Synechocystis 6803. Although the phycocyanobilin (PCB) chromophore is attached to Cys-259 as expected, paralleling the situation in plant phytochromes but contrasting to that in bacteriophytochromes, the ZZZssa conformation does not correspond to that expected from Raman spectroscopy. We show that the PHY domain, previously considered unique to phytochromes, is structurally a member of the GAF (cGMP phosphodiesterase/adenylyl cyclase/FhlA) family. Indeed, the tandem-GAF dumbbell revealed for phytochrome sensory modules is remarkably similar to the regulatory domains of cyclic nucleotide (cNMP) phosphodiesterases and adenylyl cyclases. A unique feature of the phytochrome structure is a long, tongue-like protrusion from the PHY domain that seals the chromophore pocket and stabilizes the photoactivated far-red-absorbing state (Pfr). The tongue carries a conserved PRxSF motif, from which an arginine finger points into the chromophore pocket close to ring D forming a salt bridge with a conserved aspartate residue. The structure that we present provides a framework for light-driven signal transmission in phytochromes.biliprotein ͉ photochromicity ͉ photoreceptor ͉ protein structure ͉ sensory histidine protein kinase

Structure of the Cyanobacterial Phytochrome 2 Photosensor Implies a Tryptophan Switch for Phytochrome Signaling

“…The different output domains, especially the GGDEF*-EAL module downstream of the SynCph2(1-2) sensor, imply that the antiparallel association of the photosensory domains could be functionally relevant in SynCph2 and not just a crystallization artifact as found for SynCph1 (8). For example, FimX from Pseudomonas aeruginosa, a twitching motility regulator, also carries GGDEF-EAL domains.…”

“…Two models were considered in this work: (a) the crystal structure of SynCph2 (1)(2) itself and (b) a modified structure of SynCph2(1-2) with a planar PCB chromophore as found in the structure of the SynCph1 photosensory module (8).…”

“…Our structural and mutagenesis data on SynCph2 indicate that the conserved PRXSF, W(G/A)G, and WXE motifs of the tongue region are crucial for P fr formation. Other structural elements, which contribute to the bilin-binding site of a canonical phytochrome such as SynCph1 (8,9), are either missing (N terminus) or replaced like the subsite for ring B and C propionates. The W(G/A)G and WXE motifs are shared by Group I and II phytochromes and affect P r 3 P fr photoconversion due to their distance and link to the bilin binding pocket via a conserved H-bonding network.…”

“…CBCRs cover a broad range of the visible/near UV spectrum but are restricted to cyanobacteria. Whereas, the photosensory modules of several prokaryotic phytochromes from Groups I (8,9) and III (13,14) have been characterized structurally, little is known about Cph2 homologues in Group II.…”

“…1A). The succeeding PHY domain belongs also to the GAF superfamily and stabilizes the chromophore, by sealing it from solvent access, through its tongue-like extension (8,9). Together, the GAF domain, N terminus, and tongue region form a complex, tripartite pocket enclosing the bilin chromophore.…”