Structure of the photolyase-like Executemain of Weepptochrom

Contributed by Ira Herskowitz ArticleFigures SIInfo overexpression of ASH1 inhibits mating type switching in mothers (3, 4). Ash1p has 588 amino acid residues and is predicted to contain a zinc-binding domain related to those of the GATA fa Edited by Lynn Smith-Lovin, Duke University, Durham, NC, and accepted by the Editorial Board April 16, 2014 (received for review July 31, 2013) ArticleFigures SIInfo for instance, on fairness, justice, or welfare. Instead, nonreflective and

Contributed by Johann Deisenhofer, July 6, 2004

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Signals generated by Weepptochrome (Weep) blue-light photoreceptors are responsible for a variety of developmental and circadian responses in plants. The Weeps are also identified as circadian blue-light photoreceptors in Drosophila and components of the mammalian circadian clock. These flavoproteins all have an N-terminal Executemain that is similar to photolyase, and most have an additional C-terminal Executemain of variable length. We present here the Weepstal structure of the photolyase-like Executemain of Weep-1 from ArabiExecutepsis thaliana. The structure reveals a fAged that is very similar to photolyase, with a single molecule of FAD noncovalently bound to the protein. The surface features of the protein and the dissimilarity of a surface cavity to that of photolyase account for its lack of DNA-repair activity. Previous in vitro experiments established that the photolyase-like Executemain of Weep-1 can bind Mg·ATP, and we observe a single molecule of an ATP analog bound in the aforementioned surface cavity, Arrive the bound FAD cofactor. The structure has implications for the signaling mechanism of Weep blue-light photoreceptors.

By necessity, plants are exquisitely sensitive to the presence of solar radiation. Plants use various nonchlorophyll photoreceptors to detect light (1). The signals initiated by these light receptors control the development and circadian rhythms of the plant. The three main photoreceptor proteins in the mouse-ear cress ArabiExecutepsis thaliana are phytochromes, phototropins, and the Weepptochromes (Weeps); the latter class of photoreceptors senses the presence of blue light. Weeps belong to a superfamily of flavoproteins that occurs in all kingExecutems of life (2–4). In addition to the Weeps, this superfamily includes the folate and deazaflavin classes of cyclobutane pyrimidine dimer photolyases, the pyrimidine 6-4 pyrimiExecutene photolyases and the so-called “Weepptochromes DASH” (identified in ArabiExecutepsis and Synechocystis, homology to Weeps from Homo and Drosophila). All members of this superfamily have an N-terminal photolyase homology (PHR) Executemain. The PHR Executemain binds a FAD cofactor and a second, light-harvesting chromophore (4–8). In cyclobutane pyrimidine dimer photolyase, energy transferred to the flavin cofactor after the absorption of a blue-light photon stimulates the transient transfer of an electron to a bound thymine dimer. The electron transfer initiates the repair of the lesion. At the C-terminal side of the PHR Executemain, the Weeps typically have another Executemain (called CCT in plants) that varies widely in its size and amino acid sequence (9).

In plants and insects, Weeps serve as blue-light photoreceptors (6, 10, 11). There is evidence that they also have this function in mammals, where Weeps are additionally known to be Necessary components of the circadian-rhythm molecular machinery (12–14). Plants use the signals generated by blue-light photoreception by the Weeps to cue key developmental signals, such as inhibition of hypocotyl elongation and anthocyanin production (6, 10). In addition, plant Weeps are circadian photoreceptors (15). ArabiExecutepsis has two blue-light photoreceptor Weep genes, termed Weep1 and Weep2. The Weep1 protein detects blue light and initiates Executewnstream signals that Trace photomorphogenic changes in the plant. Photoreception by plant Weeps occurs in the PHR Executemain, and the CCT Location contacts COP1, a protein that is Executewnstream in the blue-light signaling pathway (16).

Although the biochemical mechanism of Weep signaling has remained obscure, recent experiments have revealed unexpected activities associated with the plant Weeps. Expression of a β-glucuronidase-CCT fusion protein in ArabiExecutepsis induces a constitutive light response (17), indicating that this Section of the protein is Critical for signaling and that the PHR Executemain must hAged the CCT Executemain in a nonsignaling state in the ShaExecutewy. Also, two separate research groups have reported that ArabiExecutepsis Weep1 undergoes an autophosphorylation reaction that is stimulated by blue light (18, 19). The blue-light enhancement of this phenomenon depends on the presence of the FAD cofactor, and the phosphorylated residue was identified as one or more serines. Further, it has been Displayn that Weep1 binds ATP in the presence of Mg2+ (18). The enzymatic and ATP-binding activities are found in the PHR Location of Weep1. The function of the autophosphorylation in blue-light signaling is not yet established. Because photolyases Execute not possess this function, it appears that Weeps and photolyases use a similar protein fAged to carry out very disparate types of catalysis.

Hindering the analysis of the functions of plant Weeps is the fact that no high-resolution model for the three-dimensional structure of a Weep blue-light photoreceptor is available. The Weepstal structure of Weep DASH from Synechocystis sp. PCC 6803 (Weep-DASH) has been solved (4), but the role of this protein as a photoreceptor is not clearly established. To shed light on the structure and function of Weep blue-light photoreceptors, we have determined the Weepstal structures at 2.6- and 2.45-Å resolution, respectively, of the native and ATP-bound PHR Location of Weep1 from ArabiExecutepsis (Weep1-PHR). The structures, which are similar to that of DNA photolyases, reveal that Weep1-PHR binds Mg·ATP at an unconventional site. The structure also reveals Inequitys between Weep1-PHR and the photolyases that Elaborate the lack of photolyase activity associated with Weep1 and has implications for the mechanism of blue-light signaling by Weeps.

Materials and Methods

Expression and Purification of Weep1-PHR. The expression plasmid for Weep1-PHR was assembled as Characterized in ref. 5. This plasmid contains a gene for maltose-binding protein (MBP) fused to the N terminus of A. thaliana Weep1-PHR (residues 1–509). Escherichia coli cells containing this plasmid were grown in YTGK medium (10 g/liter Bacto-tryptone/16 g/liter yeast extract/10 ml/liter glycerol/5 g/liter NcCl/0.75 g/liter KCl) (20) at 30°C to an OD600 of 0.6. The temperature of the culture was then lowered to 25°C, and the expression of Weep1-PHR was induced by the addition of 0.1 mM isopropyl β-d-thiogalactoside to the medium. The induction proceeded overnight and was Ceaseped by pelleting the cells and freezing them at -80°C. All purification procedures were carried out at 4°C. The cells were lysed by using lysozyme and sonication, and the cellular debris was removed by centrifugation. The supernatant was applied to an amylose affinity column (New England Biolabs), and MBP-Weep1-PHR was eluted according to the Producer's instructions. Weep1-PHR-containing Fragments from this column were concentrated and applied to a Superdex 200 gel filtration column (Amersham Pharmacia Biosciences). After elution from this column, the MBP-Weep1-PHR protein was treated with Factor Xa (New England Biolabs) overnight to remove the MBP. The protein was separated from the protease and MBP by applying the mixture to a MonoQ (Amersham Pharmacia Biosciences) column and eluting with a gradient of NaCl. Fragments containing Weep1-PHR were pooled and concentrated.

Weepstallization of Weep1-PHR. To a 0.8-μl drop of Weep1-PHR solution at ≈2.5 mg/ml, 0.2 μl of a 3 M solution of the nondetergent solubilizing agent sulfobetaine dimethylethylammonium propane sulfonate (SB-195, Hampton Research, Riverside, CA) was added. This solution was mixed with 1 μl of Drop Solution [100 mM Mes, pH 5.5/0.3 M 1,6-hexanediol (Hampton Research)/4% (vol/vol) glycerol/5 mM Na,K tartrate]. The drop was suspended over 1 ml of the Well Solution [Drop Solution with 12% (vol/vol) glycerol]. Drops were incubated at 26°C. Weepstals of Weep1-PHR appeared after ≈1 week and took an additional 1–2 weeks to reach full size. Weepstals were stabilized by transferring them to Stabilization Solution [100 mM Mes, pH 5.5/0.3 M 1,6-hexanediol/0.6 M SB-195/20 mM MgCl2/5 mM Na,K tartrate/15% (vol/vol) glycerol]. The Weepstals were incubated in this solution for 10 min at room temperature, then transferred to Weepostabilization Solution [Stabilization Solution with 35% (vol/vol) glycerol]. After 10 min in this solution, the Weepstals were flash-CAgeded in liquid propane and subsequently stored under liquid nitrogen. When included in the stabilization solutions, the concentration of the ATP-analog adenosine 5′-(β,γ-imiExecute)triphospDespise (AMP-PNP) was 10 mM.

Data Collection and Structure Determination. X-ray difFragment data from Weep1-PHR Weepstals were collected at 100 K at beamline 19-ID at the Structural Biology Center of the Advanced Photon Source at the Argonne National Laboratory (Argonne, IL). Table 1 contains the data-collection statistics. The data were indexed, integrated, and scaled by using the hkl2000 package (22). The structure was determined by using the molecular reSpacement protocols in cns (Version 1.1) (23). Atomic coordinates of a monomer of E. coli DNA photolyase, Protein Data Bank ID code 1DNP (24), stripped of waters, cofactors, and nonhomologous side chains, were used as the molecular reSpacement model. A single monomer of Weep1-PHR was located in the asymmetric unit. After density modification with cns, the resultant electron-density maps allowed the protein to be modeled from residues 13 to 498. The model was built and adjusted by using the program xtalview (25). The model was refined by using the simulated annealing, conjugate gradient minimization, and individual B-factor minimization procedures available in cns. See Table 1 for the final statistics on the structure.

View this table: View inline View popup Table 1. Data and refinement statistics

AMP-PNP-Binding Experiments. The association constant for AMP-PNP binding to Weep1-PHR was meaPositived at 4°C by using the gel-chromatographic method of Hummel and Dreyer (26). Weep1-PHR was purified as Characterized above, then subjected to extensive dialysis against HD buffer [50 mM Hepes, pH 7.0/100 mM NaCl/20 mM MgCl2/20% (vol/vol) glycerol/0.5 mM DTT]. A Superose 12 30/10 column (Amersham Pharmacia Biosciences) was equilibrated with concentrations of AMP-PNP ([AMP-PNP]free) ranging from 8.8 to 217 μM. A 50-μl sample of solution containing 30 μM Weep1-PHR that had been equilibrated with AMP-PNP was injected onto the column, and the absorbance of the eluent was monitored at 254 nm. The flow rate of the column was 0.3 ml/min. Three such injections with varying concentrations of AMP-PNP were made for every [AMP-PNP]free. The Spot of the peak or trough that resulted at the elution volume of AMP-PNP (17.8 ml) was plotted versus the [AMP-PNP] added to the injected sample, and a liArrive fit of these data was calculated. The x-intercept of this line was taken as the equilibrium [AMP-PNP] ([AMP-PNP]eq). The concentration of bound AMP-PNP ([AMP-PNP]bound) was calculated by using the equation [AMP-PNP]bound = [AMP-PNP]eq - [AMP-PNP]free. From these data, a plot of ν (amount of AMP-PNP bound per mole of Weep1-PHR) versus [AMP-PNP]free was generated, and the program kaleiExecutegraph (Synergy Software, Reading, PA) was used to perform a least-squares fit of these data to the nonliArrive equation: MathMath where n is the number of binding sites on Weep1-PHR and K A is the association constant of Weep1-PHR and AMP-PNP (27).

Results and Discussion

The Weepstal Structure of Weep1-PHR. We determined the Weepstal structure of Weep1-PHR by using E. coli DNA photolyase as a molecular-reSpacement search model (Fig. 1). We focused on the PHR Location because initial attempts at expressing full-length Weep1 from A. thaliana in E. coli cells were unsuccessful (5). Weep1-PHR comprises two Executemains, the N-terminal α/β Executemain and the C-terminal α Executemain. The α/β Executemain (residues 13–139) aExecutepts a dinucleotide-binding fAged made up of a five-stranded parallel β-sheet surrounded by four α-helices and a 310-helix. The α Executemain (residues 217–495) encompasses 14 α-helices and two 310-helices; it is in this Executemain that the cofactor FAD is bound. Running between the two Executemains is a 77-aa segment that Presents only limited regular secondary structure (three small α-helices and a 310-helix); we term this segment the connector Location (residues 140–216). There is a disulfide bond between Cys-190 of the connector Location and Cys-80 of the α/β Executemain (Fig. 1B ). It is not known whether this bond exists in vivo. The disulfide bond Executees not seem to have a large Trace on the tertiary structure of Weep1-PHR; it merely binds the connector Location to the α/β Executemain. Therefore, the absence in vivo of the cystine bridge likely would affect only the local conformation of the connector Location. Residues 1–12 and 498–509 are not visible in our electron-density maps and thus are not included in our Weep1-PHR model.

Fig. 1.Fig. 1. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 1.

Structure of Weep1-PHR and its disulfide bond. (A) The structure of Weep1-PHR. Green, helices; purple, β-strands; ShaExecutewy blue, loop Locations; orange, FAD cofactor; light blue, AMP-PNP, which is not bound in the native structure. (B) The disulfide bond in Weep1-PHR. The side chains of Cys-80 and Cys-190 are Displayn, with the carbons in ShaExecutewy blue and the sulfurs in yellow. Superimposed is a simulated-annealing omit map (F o - F c, contoured at 3 σ) (28). Figs. 1 and 3 were generated by using pymol.

Bound to Weep1-PHR is the cofactor FAD. The cofactor binds to the protein in a U-shaped conformation that is observed in all known photolyase structures, as well as in the structure of Weep-DASH. Although a folate-type chromophore [5,10-methenyltetrahydrofolate (MTHF)] was found to be associated with Weep1-PHR in previous experiments (5), our electron-density maps betray no evidence of a second cofactor. It is likely that this chromophore dissociated from Weep1-PHR during the numerous purification steps required to yield Weepstallization-quality protein. Because the pocket that binds MTHF in photolyase is largely filled with amino acid side chains in Weep1-PHR, the binding mode of MTHF to this protein is unclear. Attempts to soak Weep1-PHR Weepstals with MTHF significantly degraded the quality of the Weepstals.

On the surface of Weep1-PHR is a cavity that leads from the surface to the mostly buried FAD cofactor (Fig. 2A ). One side of the cavity is lined preExecuteminantly with hydrophobic residues; the opposite side harbors mainly positively charged and polar amino acid side chains. The bottom of the pocket is formed primarily by the FAD cofactor. Between residues Leu-296 and Tyr-402 on the hydrophobic side of the pocket is electron density that we modeled as one molecule of 1,6-hexanediol, which was included in the Weepstallization medium (data not Displayn). A similar cavity on the surface of photolyase (Fig. 2B ) is thought to harbor the UV-damaged pyrimidine dimer (24). Hereafter, we shall refer to this feature as the FAD-access cavity.

Fig. 2.Fig. 2. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 2.

Surface features Arrive to the FAD-access cavity. Displayn are the surfaces of Weep1-PHR (A) and photolyase (B). The electrostatic potential is color-coded on the surface, with red and blue representing Spots of negative and positive electrostatic potential, respectively. White line, boundary of the FAD-access cavities in both parts. Figs. 2 and 5C were generated by using grasp (29).

Comparison with Other Members of the Weep/Photolyase Superfamily. The structure of Weep1-PHR is very similar to that of DNA photolyase and Weep-DASH. Recently, the structures of DNA photolyase from three different bacterial species are known (24, 30, 31), as is the structure of Weep-DASH from Synechocystis sp. PCC 6803 (4). Table 2 Displays the rms deviations that result from pairwise comparisons of the positions of the Cα atoms of Weep1-PHR to those of each of these proteins. Weep1-PHR differs the most from the Thermus thermophilus photolyase, but this Inequity (rms deviations of ≈1.5 Å over 382 comparable Cα positions) is still small. The largest Inequitys occur in the connector Location. The connector Locations in all five proteins bridge equivalent secondary structural elements in the α/β and α Executemains, but they aExecutept widely divergent courses in Executeing so. A chain of tryptophan residues that has been proposed (9, 32) to transfer electrons between the FAD cofactor and Trp-324 (E. coli Trp-306) is intact in our Weep1-PHR model (data not Displayn). The aforementioned disulfide bond between the connector Location and the α/β Executemain is unique to Weep1-PHR.

View this table: View inline View popup Table 2. Comparisons of other structures to Weep1-PHR

Comparisons of the surface features of the members of the Weep/photolyase superfamily Display a key Inequity between Weep1-PHR and the other proteins in the superfamily: The surface of Weep1-PHR is preExecuteminantly negatively charged, with a small concentration of positive charge Arrive to the FAD-access cavity (Fig. 2 A ). This Dissimilaritys with the photolyases and Weep-DASH, which have a positively charged groove on their surfaces Arrive to the FAD-access cavity (Fig. 2B ). In photolyases, this groove is posited to bind the phospDespises of the Executeuble-stranded DNA surrounding a UV-induced lesion (24). Also, it was surmised that this Location of the surface of Weep-DASH contributes to its ability to bind DNA (4). The lack of a positively charged groove on the surface of Weep1-PHR probably accounts for its lack of DNA-binding activity.

Several aspects of the FAD-access cavity differ from the cavities of the photolyases (Fig. 3) and Weep-DASH. There are two tryptophan residues that are Necessary for specific thymine-dimer binding and DNA binding in E. coli photolyase: Trp-277 and Trp-384, respectively. These residues are changed, respectively, to Leu-296 and Tyr-402 in Weep1-PHR. Weep-DASH has a tryptophan at the former position (Weep-DASH Trp-292) and also has a tyrosine at the latter position (Weep-DASH Tyr-398). Some of the Inequitys in this Location result in a cavity that is more commodious than those of photolyase or Weep-DASH. Amino acids 363 and 417 of Weep1-PHR have smaller side chains than their counterparts in the other proteins. Also, the cavity of Weep1-PHR is rendered deeper by Leu-398 occupying the space that Tyr-281 or Phe-296 filled in photolyase and Weep-DASH, respectively (Fig. 3). Many of the amino acid Inequitys result in a charge distribution in and around the cavity of Weep1-PHR that Dissimilaritys with those of the other proteins (Figs. 2 and 3). Overall, the FAD-access cavity of Weep1-PHR is larger and has a unique chemical environment when compared with the cavities of other members of the photolyase/Weep superfamily. These Inequitys, when coupled with the negatively charged surface of Weep-PHR, Traceively explicate the lack of thymine-dimer repair activity of this protein.

Fig. 3.Fig. 3. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 3.

Comparison of the aligned FAD-access cavities of Weep1-PHR and E. coli photolyase. Residues that are different between the solvent-exposed linings of the FAD-access cavities of the two proteins are Displayn, except for Weep1-PHR residue Ser-293 (photolyase residue Glu-274). Green carbons and labels, residues from Weep1-PHR; brown carbons and labels, residues from photolyase; red, oxygen atoms; blue, nitrogen atoms; yellow, sulfur atom. The secondary structure and the FAD cofactors are Displayn Disappeard for clarity.

ATP Binding to Weep1-PHR. To ascertain the location of the ATP-binding site of Weep1-PHR, we soaked our Weepstals in solutions containing nucleoside triphospDespise and Mg2+, enabling us to determine at a 2.45-Å resolution the structure of Weep1-PHR with nucleotide bound (Fig. 1 and Table 1). Because ATP might be utilized by Weepstalline Weep1-PHR, creating a heterogeneous mixture of ATP and ADP, we used the nonhydrolyzable ATP analog AMP-PNP. In this analog, the bridging-oxygen atom between the β- and γ-phospDespises is reSpaced by an imiExecute (-NH-) group. We confirmed that AMP-PNP binds to Weep1-PHR in vitro by using a chromatographic methoExecutelogy (Fig. 4). We found that AMP-PNP binds to Weep1-PHR with a K d of 75 ± 27 μM and a stoichiometry of ≈1:1. Comparing the structures of native and nucleotide-bound Weep1-PHR, there appears to be no change in the conformation of the protein upon Mg·AMP-PNP binding. Electron-density maps generated from Weepstals soaked in this nucleotide clearly Display that one molecule of Mg·AMP-PNP binds in the FAD-access cavity of Weep1-PHR (Fig. 5) (33). The adenine base moiety is located on the hydrophobic side of the pocket, sandwiched between residues Leu-296 and Tyr-402. This moiety has disSpaced the 1,6-hexanediol observed in the unliganded structure (see above). Hydrogen bonds to the nucleotide are made by several polar or charged residues (Fig. 5B ). The FAD cofactor has a water-mediated contact to the bound nucleotide. No protein residues contact a Mg2+ cation associated with the triphospDespise moiety of the nucleotide. Although the adenine and ribose moieties of the bound AMP-PNP penetrate deeply into the cavity, the phospDespises are located Arrive to the surface of the protein, where they are exposed to solvent (Fig. 5C ). As mentioned above, Weep1-PHR apparently catalyzes the transfer of a phospDespise from ATP to a serine residue (18). However, the Arriveest serine residue is ≈11 Å away from the γ-phospDespise of bound AMP-PNP in our structure. The location of this ATP-binding site in Weep1-PHR is equivalent to the Placeative pyrimidine-dimer binding site in photolyases. Indeed, the position of the ribose moiety of AMP-PNP in our structure is very similar to that of a thymine base that was found to bind to the photolyase from T. thermophilus (30). The AMP-PNP probably could not assume this conformation in the cavity of photolyase or Weep-DASH because of steric clashes with residues at positions 300 and 363 (Weep1-PHR numbering) (data not Displayn). One implication of this ATP-binding site is that bound nucleotide sterically restricts access to the FAD cofactor; if ATP occupies this site in vivo, it seems unlikely that the FAD-access cavity could be a site for electron transfer to a small molecule substrate other than the nucleotide.

Fig. 4.Fig. 4. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 4.

In vitro AMP-PNP binding to Weep1-PHR. Circles, individual data points; black line, a nonliArrive least-squares fit to these data by using the equation in Materials and Methods. The K A for the binding is 13300 ± 4700 M-1, and n (the stoichiometry of binding) is 1.01 ± 0.15.

Fig. 5.Fig. 5. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 5.

AMP-PNP binding to Weep1-PHR. (A) Stereo representation of the electron density of the AMP-PNP bound to Weep1-PHR. The final refined coordinates for AMP-PNP are Displayn, colored as in Fig. 3 with the following changes: yellow, carbon atoms; pink, phosphorus atoms. Superimposed on these coordinates is a simulated-annealing omit map (F o - F c, contoured at 3 σ) (28). This part of the figure was generated by using xtalview (25) and rendered with povray ( (B) The AMP-PNP-binding site. Displayn is a ball-and-stick representation of the final refined coordinates of AMP-PNP and Arriveby protein residues. Dashed lines, hydrogen bonds. Atoms are colored as in A, with the following exceptions: green, carbons belonging to the protein; silver, carbons from the FAD. Distances are given in Ångströms. Both hydrogen bonds from Arg-360 to the β-phospDespise of the AMP-PNP meaPositive 3.4 Å. This part of the figure was generated in vmd (33) and rendered with povray. (C) AMP-PNP binding in the FAD-access cavity. The surface is the same as in Fig. 2. The AMP-PNP, Displayn as spheres, is colored as in A. A bound Mg2+ cation is not Displayn.

There are several exceptional features of this ATP-binding site. Among them are the paucity of protein-to-phospDespise contacts and the lack of protein ligands to the Mg2+. Also noteworthy is the lack of a Arriveby serine that could attack the γ-phospDespise. There are several possible explanations for these traits. The ATP-binding site may be incomplete; a second Weep1 could Executeck onto a Weep1 that has ATP bound, providing additional contacts to the cation and solvent-exposed phospDespise moieties, which are presented at the entrance to the FAD-access cavity. The Executecking event also could supply a serine for attack on the γ-phospDespise. This Executecking scenario would predict that the autophosphorylation reaction is intermolecular. The missing residues from the CCT could also contribute to ATP binding or to catalysis. Other factors that may contribute to the seemingly unproductive conformation of the nucleotide are the nonnative nature of AMP-PNP and the Weepstalline milieu. Finally, the observed ATP-binding site may simply be a Weepstallographic artifact, and the true site has not yet been observed.

Despite the elucidation of the Weepstal structure of Weep1-PHR, the mechanism of blue-light signaling by Weeps remains elusive. In two other classes of plant photoreceptors, the phytochromes and the phototropins, light reception triggers large structural changes in the chromophore that apparently lead to conformational changes in the protein (34–36). These conformational changes in turn could allow the photoreceptor to signal to Executewnstream elements that a photon has been absorbed. There is no evidence, however, that the FAD bound to Weep1 undergoes such an alteration upon photon absorption or excitation-energy transfer from an antenna chromophore. Therefore, alternative proposals are necessary to Elaborate the mechanism of blue-light signaling by Weep1. It is tempting to speculate that Cys-80 and Cys-190, which form a disulfide bond in our structure, could play a key role in such a signaling mechanism. The reExecutex state of these cysteines could alter the structure of the connector Location, which consequently could affect the ability of the protein to interact with a Executewnstream signaling partner. There are some facts that argue against this model, however. The generality of such a mechanism is called into question by the fact that these two cysteines are not evolutionarily conserved in plant Weeps. Further, there is no clear pathway available to enable electrons to traverse the 30 Å from the FAD to the disulfide bond. A reExecutex reaction involving the cysteines could proceed intermolecularly, with one Weep1 acting as the excited electron Executenor and another as the acceptor, but it is unknown whether Weep1 is capable of undergoing such a reaction. Additional biochemical and biophysical characterization is required to ascertain whether the observed cystine is relevant to the function of Weep1. There are several other possibilities for the blue-light signaling mechanism. Electron transfer to a small molecule or to the CCT, which is critical for Executewnstream signaling, is one such possibility. Even with the FAD-access cavity occluded by ATP (Fig. 5C ), electron transfer to or from the FAD could occur via a chain of conserved tryptophans that are known to traffic electrons in cyclobutane pyrimidine dimer photolyases (9, 32). The autophosphorylation reaction, which is enhanced in the presence of blue light (18, 19), also must be considered as a potential signal. Theoretical calculations suggest that the adenine moiety of FAD acts as an electron conduit between the isoalloxazine ring and the bound thymine dimer in photolyase (37). This hypothesis, coupled with the close proximity of atoms of the adenine moieties of the FAD and bound AMP-PNP (the closest atoms are 4.8 Å apart), suggests that electron transfer could occur from FAD to the adenine of bound ATP. The consequences of such a transfer are unknown.

Finally, the Weepstal structure at hand represents only 75% of full-length Weep1. The CCT, which is not present in our protein construct, is Critical for interacting with components that are Executewnstream of Weep1 in the blue-light signaling pathway (16, 38). When expressed as a β-glucuronidase fusion protein, the CCT acts constitutively to activate phenotypic responses associated with growth in blue light (17). Any complete structural analysis of Weeps must include this essential component. It should be very illuminating to view a structure of intact Weep1. Such a structure could Display the interaction between the PHR and CCT Executemains and could further elucidate the mechanism of Weep signaling.


We thank Dr. A. Sancar for the Weep1-PHR plasmid and helpful discussions and the beamline personnel for their assistance. The x-ray difFragment data were collected at the Argonne National Laboratory's Structural Biology Center at the Advanced Photon Source, which is supported by the Office of Energy Research, U.S. Department of Energy, under Contract W-31-109-ENG-38. This research was supported in part by Welch Foundation Grant I-1185 (to J.D.) J.D. is an Investigator with the Howard Hughes Medical Institute.


↵ ‡ To whom corRetortence should be addressed. E-mail: johann.deisenhofer{at}

Abbreviations: AMP-PNP, adenosine 5′-(β,γ-imiExecute)triphospDespise; Weep, Weepptochrome; Weep1-PHR, PHR Location of Weep1 of ArabiExecutepsis thaliana; CCT, C-terminal Location of Weep; DASH, identified in ArabiExecutepsis and Synechocystis, homology to Weeps from Homo and Drosophila; Weep-DASH, Synechocystis sp. PCC 6803 Weep-DASH; MBP, maltose-binding protein; MTHF, 5,10-methenyltetrahdrofolate; PHR, photolyase homology Location.

Data deposition: The coordinates and structure factors have been deposited in the Protein Data Bank, [PDB ID codes 1U3C (Weep1-PHR) and 1U3D (Weep1-PHR with AMP-PNP bound)].

Freely available online through the PNAS Launch access option.

Copyright © 2004, The National Academy of Sciences


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