A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome

• Published in: Nature 2005-11, Vol.438 (7066), p.325-331
• Main Authors: Brunzelle, Joseph S, Vierstra, Richard D, Wagner, Jeremiah R, Forest, Katrina T
• Format: Article
• Language: English
• Subjects: Amino acids; Bacteriology; Bile Pigments - metabolism; Biliverdine - metabolism; Binding Sites; Biochemistry; Biological and medical sciences; Botany; Crystallization; Deinococcus - chemistry; Deinococcus radiodurans; Eukaryotes; Evolution, Molecular; Flowers & plants; Fundamental and applied biological sciences. Psychology; Histidine Kinase; Humanities and Social Sciences; Light; Light Signal Transduction - radiation effects; Microbiology; Models, Molecular; Morphology, structure, chemical composition; multidisciplinary; Photoreception; Photosynthesis; Phytochrome - chemistry; Phytochrome - metabolism; Phytochrome - radiation effects; Pigmentation; Protein Folding; Protein Kinases - metabolism; Protein Structure, Tertiary; Proteins; Science; Science (multidisciplinary)
• ISSN: 0028-0836; 1476-4687; 1476-4679
• DOI: 10.1038/nature04118

Phytochromes are red/far-red light photoreceptors that direct photosensory responses across the bacterial, fungal and plant kingdoms. These include photosynthetic potential and pigmentation in bacteria as well as chloroplast development and photomorphogenesis in plants. Phytochromes consist of an amino-terminal region that covalently binds a single bilin chromophore, followed by a carboxy-terminal dimerization domain that often transmits the light signal through a histidine kinase relay. Here we describe the three-dimensional structure of the chromophore-binding domain of Deinococcus radiodurans phytochrome assembled with its chromophore biliverdin in the Pr ground state. Our model, refined to 2.5 Å resolution, reaffirms Cys 24 as the chromophore attachment site, locates key amino acids that form a solvent-shielded bilin-binding pocket, and reveals an unusually formed deep trefoil knot that stabilizes this region. The structure provides the first three-dimensional glimpse into the photochromic behaviour of these photoreceptors and helps to explain the evolution of higher plant phytochromes from prokaryotic precursors. Phytochromes: knot now Conserved from bacteria to fungi and higher plants, phytochromes are agriculturally important light-sensing proteins that have been studied from genetic and biochemical perspectives for decades. Three-dimensional structural information on them has proven elusive, but now the structure of a phytochrome from the bacterium Deinococcus radiodurans has been determined. It reveals possible chromophore attachment and light-signalling mechanisms. The protein fold of the molecule is surprising: the light-sensing region is shaped like a knot, perhaps in order to add rigidity and stability to the structure.