Small-Angle X-ray Scattering Reveals the Solution Structure of a Bacteriophytochrome in the Catalytically Active Pr State

Evans, Katie; Grossmann, J. Günter; Fordham-Skelton, Anthony P.; Papiz, Miroslav Z.

doi:10.1016/j.jmb.2006.09.045

Cited by 37 publications

(36 citation statements)

References 43 publications

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“…Histidine phosphorylation in HKs is based on a parallel arrangement of both protein domains, as also had been shown for the ortholog protein Cph1 from Synechocystis PCC6803 (15,16). In addition, a bacteriophytochrome has recently been characterized as a homodimer via the small-angle scattering technique, acknowledging the commonly proposed dimeric arrangement also for this protein class (17). This assumption would also be in accordance with a parallel arrangement of the two chromophore-binding domains in a phytochrome homodimer.…”

Section: Discussionsupporting

confidence: 56%

A Non-hydrolyzable ATP Derivative Generates a Stable Complex in a Light-inducible Two-component System

Sharda¹,

Koay²,

Kim

et al. 2009

Journal of Biological Chemistry

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Section: Discussionsupporting

confidence: 56%

A Non-hydrolyzable ATP Derivative Generates a Stable Complex in a Light-inducible Two-component System

Sharda¹,

Koay²,

Kim

et al. 2009

Journal of Biological Chemistry

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“…Clearly, a reexamination of the quaternary structures of various Phy types is needed to address this issue. For example, the Y-shaped quaternary structures revealed by small angle x-ray scattering (30,31) and electron microscopy (32) of higher plant and bacterial Phys have been interpreted solely on the basis of C-terminal contacts.…”

Section: Discussionmentioning

confidence: 99%

High Resolution Structure of Deinococcus Bacteriophytochrome Yields New Insights into Phytochrome Architecture and Evolution

Wagner

Zhang

Brunzelle

et al. 2007

Journal of Biological Chemistry

224

440

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Phytochromes are red/far red light photochromic photoreceptors that direct many photosensory behaviors in the bacterial, fungal, and plant kingdoms. They consist of an N-terminal domain that covalently binds a bilin chromophore and a C-terminal region that transmits the light signal, often through a histidine kinase relay. Using x-ray crystallography, we recently solved the first three-dimensional structure of a phytochrome, using the chromophore-binding domain of Deinococcus radiodurans bacterial phytochrome assembled with its chromophore, biliverdin IX␣. Now, by engineering the crystallization interface, we have achieved a significantly higher resolution model. This 1.45 Å resolution structure helps identify an extensive buried surface between crystal symmetry mates that may promote dimerization in vivo. It also reveals that upon ligation of the C3 2 carbon of biliverdin to Cys 24 , the chromophore A-ring assumes a chiral center at C2, thus becoming 2(R),3(E)-phytochromobilin, a chemistry more similar to that proposed for the attached chromophores of cyanobacterial and plant phytochromes than previously appreciated. The evolution of bacterial phytochromes to those found in cyanobacteria and higher plants must have involved greater fitness using more reduced bilins, such as phycocyanobilin, combined with a switch of the attachment site from a cysteine near the N terminus to one conserved within the cGMP phosphodiesterase/ adenyl cyclase/FhlA domain. From analysis of site-directed mutants in the D. radiodurans phytochrome, we show that this bilin preference was partially driven by the change in binding site, which ultimately may have helped photosynthetic organisms optimize shade detection. Collectively, these three-dimensional structural results better clarify bilin/protein interactions and help explain how higher plant phytochromes evolved from prokaryotic progenitors. Phytochromes (Phys)3 comprise a ubiquitous superfamily of photoreceptors present in the plant, fungal, and bacterial kingdoms. They play critical roles in various light-regulated processes, ranging from phototaxis and pigmentation in bacteria to seed germination, chloroplast development, shade avoidance, and flowering in higher plants (1, 2). Phys are homodimeric complexes with each polypeptide containing an N-terminal chromophore-binding domain (CBD) that autocatalytically attaches via a thioether linkage a single linear tetrapyrrole (or bilin) chromophore, a PHY domain that is important for spectral integrity, and a C-terminal domain that promotes dimerization and often signal transmission (3). Through unique interactions among the bilin and the CBD and PHY domains, Phys can exist as two metastable conformers, a red light (R)-absorbing Pr form and a far red light (FR)-absorbing Pfr form. By photoconverting between Pr and Pfr, Phys act as unique light-regulated switches in various signal transduction cascades. In bacteria and fungi, a canonical histidine kinase (HK) domain is typically present downstream of the PHY domain, thus allowing these P...

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“…Included are x-ray crystallographic and/or solution 2D-NMR structures of the GAF domain from PAS-less Phys Anders et al, 2013), a Phy that photoconverts from Pr to the Pnr state (Yang et al, 2007), and CBCRs (Burgie et al, 2013;Narikawa et al, 2013;Cornilescu et al, 2014), crystal structures of the entire PSM region (PAS-GAF-PHY) from canonical Phys (Essen et al, 2008;Burgie et al, 2014b;Takala et al, 2014) and bathyPhys (Yang et al, 2008;Bellini and Papiz, 2012), and even images of entire Phy dimers by small-angle x-ray scattering (Evans et al, 2006) and single-particle electron microscopy (SPEM) (Li et al, 2010). Particularly informative have been paired structures of the dark-adapted and photoactivated states (Ulijasz et al, 2010;Cornilescu et al, 2014;Takala et al, 2014), comparisons of canonical and bathy-Phys (Yang et al, 2009), and solid-state NMR analyses of the bilin and temperature-scanning cryocrystallography following sample irradiation (Song et al, 2011;Yang et al, 2011) that have collectively illuminated the structural changes associated with photointerconversion.…”

Section: D Structures Of Bacterial Physmentioning

confidence: 99%

Phytochromes: An Atomic Perspective on Photoactivation and Signaling

2014

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Small-Angle X-ray Scattering Reveals the Solution Structure of a Bacteriophytochrome in the Catalytically Active Pr State

Cited by 37 publications

References 43 publications

A Non-hydrolyzable ATP Derivative Generates a Stable Complex in a Light-inducible Two-component System

A Non-hydrolyzable ATP Derivative Generates a Stable Complex in a Light-inducible Two-component System

High Resolution Structure of Deinococcus Bacteriophytochrome Yields New Insights into Phytochrome Architecture and Evolution

Phytochromes: An Atomic Perspective on Photoactivation and Signaling

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