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Abstract Agp1 BONA WL-PCM a canonical biliverdin-binding bacteriophytochrome from the soil bacterium Agrobacterium BONA WL-PCM that acts as a light-regulated histidine kinase. Crystal structures of the photosensory core modules PCMs of homologous phytochromes have provided a consistent picture of the structural changes that these proteins undergo during photoconversion between the parent red light-absorbing state Pr and the far-red light-absorbing state Pfr. We present the crystal structures of the PCM of Agp1 at 2. Whereas in the mutant structure the dimer subunits are in anti-parallel orientation, the wild-type structure contains parallel subunits. The resolution of the mutant structure enabled us to detect a sterically strained conformation of the chromophore at ring A that we attribute to the tight interaction with Pro of the conserved PRXSF motif in the tongue.


Based on this observation and on data from mutants where residues in the tongue region were replaced by alanine, we discuss the crucial roles of those residues in Pr-to-Pfr photoconversion. In plants, phytochromes have evolved to the dominating BONA WL-PCM, controlling processes such as seed germination, seedling development, shade avoidance, or flower induction.

DNA sequencing led to the discovery of phytochromes also in cryptophytes, heterokonts, green algae, fungi, and many bacteria 1— 4where they modulate diverse physiological processes in response to light conditions, hence enabling organisms to adapt to their environment. In Agrobacterium fabrum C58 formerly Agrobacterium tumefaciens C58the species of this study, phytochromes control bacterial conjugation 5. At the C terminus, most bacterial phytochromes have a histidine kinase HK module that consists of a dimerization and histidine phosphotransfer domain and a catalytic and ATP binding domain 7— 9. In phytochromes and cyanobacteriochromes, the natural bilin chromophore is covalently attached to the protein via a characteristic Cys residue. Fungal and most bacterial phytochromes incorporate a biliverdin BV chromophore that is bound to a Cys residue at the N terminus of the PAS domain 15— Most cyanobacterial phytochromes and cyanobacteriochromes incorporate a phycocyanobilin PCB chromophore, which is bound to a Cys in the GAF domain.

In prototypical phytochromes, the dark state is Pr, but some bacterial phytochromes termed bathy phytochromes have a thermodynamically stable Pfr state 19— A wealth of structural knowledge of phytochromes has accumulated because of the BONA WL-PCM structural determination of the chromophore binding domain CBD of Deinococcus radiodurans phytochrome DrBphP, which contains the PAS and the GAF domains These two phytochromes were crystallized in their thermodynamically stable states Pr and Pfr, respectively.

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The arrangement of two protein subunits in the crystals is parallel in the case of PaBphP and anti-parallel in the case of Cph1. Similarities between two different types of phytochromes as represented by Cph1 and PaBphP already indicated conserved structural features of phytochromes in general that are also valid for phytochrome structures described later, such as the conserved topologies in the PAS, GAF, and PHY domains and effective solvent shields that surround the bilin moieties 21 Comparison of the Cph1 Pr and PaBphP Pfr structures revealed also numerous differences that were shown later to be generally valid for the respective photochromic states of phytochromes. These differences might reflect general differences between Pr and Pfr and thereby provide information about protein conformational changes during photoconversion. This result speaks against a rearrangement of secondary structure in the tongue in PaBphP.

This model BONA WL-PCM a large scale conformational change during photoconversion from Pr to Pfr at the tongue of the GAF2 domain in group II phytochromes, which structurally plays a similar role as the PHY domain in canonical phytochromes.

Further detailed insights into structural changes during photoconversion were provided by x-ray crystallographic and small angle x-ray scattering studies on the PCM of DrBphP by Takala et al. Although the former group could crystallize this PCM in the Pr state and as an illuminated form that was enriched in Pfr, the BONA WL-PCM group managed to obtain crystal structures of the wild-type BONA WL-PCM in the Pr form and of the Pfr form after introducing a single site substitution in the middle of the tongue of the PHY domain.

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Although the Pfr subunit arrangements are significantly different in both studies and demand further investigation, the rearrangement of secondary structure in the tongue of the PHY domain during photoconversion seems to be a universal feature of bacterial phytochromes. The PHY domain connects directly to the HK of bacterial phytochromes and is the domain most relevant for intramolecular signal transduction from the PCM to the C terminus. BONA WL-PCM

How these and other protein conformational changes are induced by light triggered isomerization of the chromophore from ZZZssa to ZZEssa stereochemistry and how the signal is transmitted to the HK are questions that are still not answered on the structural level. The phytochromes Agp1 and Agp2 from Agrobacterium have been extensively used as model systems for biochemical and BONA WL-PCM studies related to chromophore protein interaction, light-induced conformational changes, or HK regulation, and it is desired to combine results from these studies with structural data 732— Here, we describe how we employed the surface entropy reduction SER strategy that was devised by Derewenda and co-workers 39— 41 and how we obtained crystals of high diffraction quality. The SER mutant crystals contain dimer subunits in anti-parallel arrangement, whereas dimer subunits are oriented parallel in the wild-type Agp1-PCM crystals.

In addition to the crystal structures, we present biochemical analyses on Agp1 single-site mutants where highly conserved residues in the tongue of the PHY domain were substituted by alanine. BONA WL-PCM evidence from previously BONA WL-PCM work and our data suggests that these residues play similar roles in stabilizing the photochromic forms in both prototypical and bathy phytochromes.


The crystallographic phase problem was solved by a combination of molecular replacement using as search model the PAS-GAF fragment of the prototypical bacteriophytochrome DrBphP 22 and single wavelength anomalous dispersion Crystallographic refinement at 3. These crystals belong to the same space group and have similar unit cell parameters as those of the locked chromophore adduct, indicating the same type of crystal packing Table 1. Crystallographic refinement ended up with the same problems as observed with the locked chromophore adduct, even if solving the phase problem was solely based on molecular replacement, using in addition the PAS-GAF bidomain of DrBphP 22 and the PHY domain of the cyanobacterial phytochrome Cph1 23 as search models. BONA Computech Co., Ltd., established in Taiwan inhas been known as a professional VGA add-on card manufacturer in the.

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