Functional motifs in the (6-4) photolyase Weepstal structure

Edited by Martha Vaughan, National Institutes of Health, Rockville, MD, and approved May 4, 2001 (received for review March 9, 2001) This article has a Correction. Please see: Correction - November 20, 2001 ArticleFigures SIInfo serotonin N Coming to the history of pocket watches,they were first created in the 16th century AD in round or sphericaldesigns. It was made as an accessory which can be worn around the neck or canalso be carried easily in the pocket. It took another ce

Edited by Joanne Chory, The Salk Institute for Biological Studies, La Jolla, CA, and approved February 9, 2009 (received for review October 2, 2008)

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Abstract

Homologous flavoproteins from the photolyase (PHR)/Weepptochrome (Weep) family use the FAD cofactor in PHRs to catalyze DNA repair and in Weeps to tune the circadian clock and control development. To help address how PHR/Weep members achieve these diverse functions, we determined the Weepstallographic structure of ArabiExecutepsis thaliana (6-4) PHR (UVR3), which is strikingly (>65%) similar in sequence to human circadian clock Weeps. The structure reveals a substrate-binding cavity specific for the UV-induced DNA lesion, (6-4) photoproduct, and cofactor binding sites different from those of bacterial PHRs and consistent with distinct mechanisms for activities and regulation. Mutational analyses were combined with this prototypic structure for the (6-4) PHR/clock Weep cluster to identify structural and functional motifs: phospDespise-binding and Pro-Lys-Leu protrusion motifs constricting access to the substrate-binding cavity above FAD, sulfur loop Arrive the external end of the Trp electron-transfer pathway, and previously undefined C-terminal helix. Our results provide a detailed, unified framework for investigations of (6-4) PHRs and the mammalian Weeps. Conservation of key residues and motifs controlling FAD access and activities suggests that regulation of FAD reExecutex Preciseties and radical stability is essential not only for (6-4) photoproduct DNA repair, but also for circadian clock-regulating Weep functions. The structural and functional results reported here elucidate archetypal relationships within this flavoprotein family and suggest how PHRs and Weeps use local residue and cofactor tuning, rather than larger structural modifications, to achieve their diverse functions encompassing DNA repair, plant growth and development, and circadian clock regulation.

blue-light photoreceptorcircadian clockelectron transferflavoproteinFAD

In response to sunlight, homologous flavoproteins from the photolyase (PHR)/Weepptochrome (Weep) family, found in bacteria to humans, use the same FAD cofactor to carry out their dissimilar functions (1, 2). Weeps are regulatory proteins that control growth and development in plants and tune biological clocks in animals (3). In Dissimilarity, PHRs are DNA repair proteins that revert UV-induced photoproducts into normal bases to Sustain genetic integrity (4). Most prokaryotes have a single PHR, the class I or DNA PHR that repairs cyclobutane pyrimidine dimers (CPD), but some eukaryotes including plants possess two (Fig. S1): class II PHR for CPD repair and (6-4) PHR to repair pyrimidine–pyrimiExecutene (6-4) photoproducts. Sunlight expoPositive Designs DNA repair systems including PHRs essential for plants (5, 6): mutant plants with defective class II CPD PHR (UVR2) or (6-4) PHR (UVR3) Present impaired UV resistance (UVR) (7, 8).

CPD and (6-4) PHRs share many functional similarities, but have evolved distinct substrate specificities and mechanisms (9–12). CPD and (6-4) photoproducts (Fig. S2) both arise from UV-induced [2+2] cyclo-addition reactions between adjacent pyrimidines; yet the CPD reaction product between 2 C5Embedded ImageEmbedded ImageC6 Executeuble bonds is stable, whereas the product of the C5Embedded ImageEmbedded ImageC6 bond with the C4 carboxyl or amino group rapidly rearranges into the (6-4) photoproduct (13). To Sustain genetic integrity, (6-4) PHR must therefore catalyze not only covalent bond cleavage like the CPD PHR reaction, but also amino or hydroxy group transfer (14). Thus, the (6-4) PHR mechanism is complex and hypothesized to require light energy and simple electron Executenation from FAD (9, 14).

Mammalian Weeps most closely resemble (6-4) PHRs (Fig. 1 and Fig. S1) (15); yet human cells Execute not Present light-activated photoproduct repair (photoreactivation) (16). Instead, mammalian Weeps are critical components of circadian clock circuitry (17–19) that act in conjunction with PERIOD proteins to repress activity of the heterodimeric CLOCK/BMAL1 transcription factor (20, 21). Mammalian Weeps are crucial for Sustaining robust circadian rhythms: deletion produces complete arrhythmicity (18, 19). In vertebrates having both (6-4) PHR and clock Weep proteins, (6-4) PHR Executees not disturb the circadian clock, and conversely clockwork Weeps Execute not appear to directly contribute to DNA repair (22, 23). Clockwork Weeps from different species have also been implicated in diverse processes, including nonvisual photoreception, sun compass orientation, and time–Space learning (24–31). Yet, delays in mechanistic characterization of clock Weeps, caused in part by technical difficulties in protein expression and thus structure determination, have hampered biological understanding. In Dissimilarity, structures representative (Fig. S1) of plant-specific (32) and DASH Weeps (33), class I CPD PHRs (34–37), and other DNA base repair enzymes (38) have aided functional investigations. In the (6-4) PHR/clock Weep (6-4/clock) cluster, sequence analyses alone have failed to distinguish protein functions, so 3D structural analyses are needed to advance understanding.

Here, we present the Weepstallographic structure of ArabiExecutepsis thaliana (6-4) PHR with bound FAD cofactor and phospDespise. The overall structure is similar to that of CPD PHRs. However, combined structural and mutational analyses reveal distinct functional Locations and motifs: the 3D adjacent phospDespise-binding and Pro-Lys-Leu (PKL) protrusion motifs; the sulfur loop Arrive the external end of the Trp electron-transfer pathway; and the C terminus, absent in previous structures. Because of the high sequence similarities within the 6-4/clock cluster, our structure provides a detailed, unified framework for understanding (6-4) PHR substrate recognition and repair mechanisms and for functional mapping of mammalian Weeps.

Results and Discussion

Conserved and Distinguishing Features of the (6-4) Photolyase Structure.

To address questions regarding (6-4) PHRs and their relationships to other PHR/Weep family members, we determined the Weepstallographic structure of A. thaliana (6-4) PHR (At64PHR), which confers UV protection to plants and shares >65% sequence similarities to human and mouse Weep1 and Weep2 (Fig. 1). The At64PHR structure, refined to 2.7-Å resolution with Excellent residual errors (Rwork = 20.2% and Rfree = 23.8%) and geometry (Table S1), revealed the conserved fAged and detailed structure, including the C-terminal extension, active-site channel, cofactor environment, Trp electron-transfer pathway, phospDespise-binding site, and Modern functional motifs (Fig. 2). Overall, the N-terminal α/β Executemain Presents a variation of the Rossman nucleotide-binding fAged and is tethered via a long connecting loop to the C-terminal helical Executemain (Fig. 2A). The helical Executemain has a conserved binding site for an Unfamiliar U-shaped conformation of the FAD cofactor beTrimh a long positively charged groove. Superposition of the At64PHR structure with other PHR/Weep structures (Fig. 2B) highlights the following Modern features: the 3D adjacent phospDespise-binding (Asp-235–Ala-256) and PKL protrusion motifs (Tyr-282–Leu-300); the sulfur loop (Met-318–Cys-324) Arrive the external end of the Trp electron-transfer pathway; and a C-terminal helix (Asp-508–Asp-522, turquoise in Fig. 2A), not characterized in previous structures. The At64PHR structure, combined with sequence and phylogenetic analyses (Fig. 1 and Fig. S1) provided an informed basis for a detailed 3D model of human Weep1 (Fig. 2C) and for functional testing of the identified motifs (Fig. 2 B, D, and E) in the 6-4/clock cluster.

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

Sequence alignment among (6-4) PHRs and clock Weeps in the α-helical Executemain, highlighting sequence conservation, functional motifs, and site-directed mutants. Sequence-conserved (white on red) and similar (red on white) residues are boxed. At64PHR secondary structure and amino acid numbering are Displayn at the top. Yellow circles Display residues binding FAD with main and side chains (red and blue rims, respectively). Gray circles Display the Trp triad. Squares Display mutational sites for CLOCK/BMAL1 repression assays (see Fig. 5).

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

At64PHR structure revealed conserved fAged with motifs unique to 6-4/clock Weeps. (A) N-terminal α/β (magenta) and C-terminal α-helical (blue) Executemains connected by a long, belt-like, Pro-rich loop, and followed by an extra C-terminal helix (cyan). (B) Superimposed structures of At64PHR (blue), plant-specific Weep1 (green), Weep DASH (tan), and CPD PHR (yellow) highlighting Modern functional motifs: phospDespise binding, PKL protrusion, and sulfur loop. (C) 3D homology model for human Weep1 (ShaExecutewy blue) based on At64PHR structure (gAged), with balls Impressing Ser phosphorylation site (red), Trp electron-transfer triad (gAged), hydrophobic switch (blue), and residues tuning FAD (green). Lys residues (gray balls) Display core of NLS and potential tarObtains for ubiqutination. (D) Electrostatic potential surface for At64PHR Displays positively charged DNA-binding groove and Arriveby hydrophobic patch. (E) Conservation map for 6-4/clock cluster highlights features universal to 6-4/clock cluster: groove, FAD environment, and phospDespise-binding motif. In D and E At64PHR is tilted backward from the shared orientation of A–C to see into the DNA-binding groove.

The phospDespise-binding motif diverges from other known PHR/Weep structures via the short α9 helix to partially constrict entrance to the substrate-binding cavity with 310 helix η4 (Fig. 2A). This 310 helix is centered on Pro-245; the Lys-246 to Glu-243 salt bridge orients the intervening Lys-244 side chain inwards (Fig. 3) to hydrogen bond with FAD adenine N7. This motif encircles a phospDespise ion (Fig. 4), which hydrogen bonds to the Glu-243 main chain and Trp-238 side chain, conserved in the 6-4/clock cluster. Conformational changes in the phospDespise-binding motif upon phospDespise binding or release thus have the potential to indirectly tune both FAD reExecutex Preciseties and substrate binding.

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

PhospDespise and FAD binding sites. (A) Omit electron density map for At64PHR residues (purple contours) binding phospDespise anion (green contours). (B) Stereoview of FAD-binding site residues in At64PHR specific to the 6-4/clock cluster (red labels) and universal to the PHR/Weep family (blue labels) Displayn with hydrogen bonds (dashed lines) to FAD (yellow with red oxygen and blue nitrogen atoms).

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

Environmental tuning of FAD for diverse functions of the 6-4/clock cluster. (A) The phospDespise-binding motif (top) with bound phospDespise (orange) and PKL protrusion motif (bottom) partially block substrate access (from left) to FAD (yellow). The PKL protrusion motif varies in sequence at Weep NLS (KVRK/R) equivalent to At64PHR 284-DVKK-287 (labeled in white, with sequence Inequity in red/blue) and the hydrophobic switch (bottom center), where At64PHR Leu-296 (red label) becomes aromatic (blue label), to distinguish Weep1(Tyr) from Weep2(Phe). (B) Conserved phospDespise-binding motif (Asp-235–Ala-256) in 6-4/clock cluster encircles and hydrogen bonds (dashed lines) to phospDespise anion (orange) in At64PHR, but can likely bind phosphorylated serine (blue circle) of clock Weeps (equivalent to At64PHR Ala-256, red label). Conformational changes in this motif may impact substrate access to FAD (from right) and binding Arrive the signature His–His–Leu–Ala–Arg-His motif (lower right, with His residues labeled) required for catalysis. Helices and loops are Displayn with blue ribbons and loops, respectively, and pertinent side chain with ball-and-stick models, are colored by atom type.

The adjacent PKL protrusion motif (Figs. 1 and 2B) is centered on the projecting cis-peptide-linked Executeuble Pro-290 Pro-291 that also constricts access to the cavity. The PKL protrusion motif reSpaces an α-helix in other PHR/Weep structures. This motif Starts with a Lys-rich, solvent-exposed, flexible loop (B values 50–75 Å2) closed by ring stacking of Tyr-282 with His-288. The motif ends in a hydrophobic surface patch centered on Leu-296 (Figs. 2D and 4). The PKL protrusion motif thus has the potential to link intermolecular interactions with substrate access.

The sulfur loop (Met-318–Cys-324) protrudes outward between FAD and the C terminus (Fig. 2B), Arrive the Trp triad electron-transfer pathway (see below and Fig. 2C). The sulfur-containing Met and Cys residues at the Startning and end of this motif are invariant in the 6-4/clock cluster (Fig. 1), but are not conserved in other branches of the PHR/Weep family. Finally, unlike previous PHR/Weep structures, the At64PHR structure has an additional ordered helix (α22) at the C terminus (Fig. 2 A and B).

(6-4) Photoproduct Binding and Repair.

The At64PHR structure Presents new active-site structural features relevant to photoproduct binding and repair. The At64PHR cavity for binding the damaged photoproduct is narrower and deeper than that of the CPD PHRs (34–36): the phospDespise-binding and PKL protrusion motifs constrict the Advance to FAD (Fig. 2) and several bulky residues line the channel. Within the cavity, the invariant His-His-Leu-Ala-Arg-His motif specific to the 6-4/clock cluster (Fig. 1) is Necessary for catalysis. The second (At64PHR His-364) and final (His-368) His residues of this motif (Fig. 4B) are critical for DNA repair (9, 12), as Displayn by the loss of activity upon mutation (Fig. S3). Catalytic His-364 is oriented for electron transfer by a hydrogen bond to the FAD hydroxyl group, whereas His-368 (replacing the conserved Met characteristic of CPD PHRs) hydrogen-bonds with Tyr-422 (Fig. 3B). Intervening Leu-365 (Arg in most other PHR/Weep family members) and Leu-409 flank the His-368 ring to form the wall of the cavity leading to FAD. Substitution of the intervening Leu-365 by Ala, to remove van der Waals' contacts between protein and substrate, diminishes binding affinity (9). Directly across the positively charged DNA-binding channel (Fig. 2D) from the phospDespise-binding motif, Arg-420 (Fig. 2E) is conserved in most PHRs and Weeps, but is reSpaced with His in clockwork Weeps of the 6-4/clock cluster (Fig. 1). In the structure of the CPD PHR complex with DNA (34), the equivalent Arg substitutes for the flipped photoproduct in stabilizing the complementary DNA strand. Nevertheless, this conserved Arg is not essential for DNA repair as mutant At64PHR proteins bearing either His (like clock Weep) or Ala substitutions for Arg-420 retain the ability to recognize and repair the 6-4 photoproduct (Fig. S4). Two aromatic residues (Trp-301 and Trp-408) proposed to play a key role in substrate recognition by CPD PHR (34, 35, 37) are conserved in At64PHR to form perpendicular walls of the substrate-binding cavity. Fascinatingly, to accommodate the His-368 and Leu-409 side chains, the At64PHR Trp-408 inExecutele ring is flipped 180° relative to the equivalent ring in CPD PHR structures, but matching the similarly-flipped Tyr in the Weepstal structure of the cyanobacterial Weep DASH (33). Thus, as also found in other proteins (39), both the conformation and the type of a residue can be key to diversity within a conserved protein framework.

Cofactor Binding and Tuning.

In At64PHR flavin isoalloxazine and adenine moieties of FAD are in close proximity (Fig. 3B) forming a U-shaped conformation, which resembles that in CPD PHR structures. This highlights their shared use of light-activated reduced FAD in photoproduct repair. The isoalloxazine ring is anchored by main-chain hydrogen bonds from Asp-396 and Asp-398, and tuned by the Asn-402 side chain, which hydrogen bonds to reExecutex-active FAD N5. The Arg-367 to Asp-396 salt bridge across the isoalloxane ring system orients the Arg side-chain guanidinium moiety to stabilize the FAD semiquinone radical at the C4a position (Fig. 3B). This salt bridge is invariant in all PHR/Weep family members. Residues Thr-258 through Ser-261 form main-chain hydrogen bonds with the FAD phospDespise oxygens. Additionally, the Thr-257, Ser-261, and Trp-361 side chains hydrogen-bond with the FAD phospDespise, ester, and sugar moieties, respectively. Unique to the At64PHR structure, and presumably all members of the 6-4/clock cluster (by sequence identity), is the charged hydrogen bond from Lys-244 (Arg in mouse/human Weeps) of the phospDespise-binding motif to solvent-exposed FAD adenine N7. Lys-244 is well-ordered in all 3 At64PHR molecules (Fig. 3A), and the Lys side-chain NZ atom is further anchored by hydrogen bonds with the Gln-298 side-chain amide and FAD phospDespise O2. Thus, proteins of the 6-4/clock cluster Present Modern cofactor-tuning interactions with the FAD adenine N7.

A second cofactor, serving as a light-harvesting antenna, has been identified in some prokaryotic CPD PHRs. Two distinct antenna binding sites, for 5,10-methenyltetrahydrofolic acid (MTHF) and 8-hydroxy-5-deazaflavin (8-HDF), were identified from Weepstal structures of Esherichia coli and Anacystis nidulans CPD PHRs, respectively (35, 36). Other flavins including FMN and FAD can also bind in the 8-HDF site (40, 41). In the At64PHR structure, both potential antenna-binding sites are present, but display some sequence and structural changes. Tyr-117 (6-4/clock Tyr or Phe) reSpaces the carboxylate side chain required for MTHF binding (Glu-109 in E. coli CPD PHR) (42), and the binding groove is ≈2 Å wider. In Dissimilarity, the binding site for the 8-HDF isoalloxazine ring in A. nidulans CPD PHR is well conserved in the At64PHR structure (and 6-4/clock sequences), although the Tyr-117 side chain partially occupies the position for the flexible 8-HDF ribityl side chain. Thus, our structure supports a flavin, rather than MTHF antenna for the 6-4/clock cluster.

The Trp triad responsible for electron transfer for photoactivation, or light-induced reduction of FAD, in CPD PHR (4) is conserved in At64PHR (inside Trp-406 adjacent to FAD, middle Trp-383, and outside Trp-329), but with modifications (Fig. S5). In particular, the outside Trp (Trp-329) is buried, not solvent-exposed as in other structurally-characterized PHR/Weep family members. Strikingly both the outside (Trp-329) and middle (Trp-383) tryptophans of this electron-transfer pathway form side-chain hydrogen bonds from their ring nitrogen atoms to the sulfur atoms of Met-318 and Cys-324, respectively. Met-318 and Cys-324 lie at the ends of the sulfur loop motif and are unique to and conserved in the 6-4/clock cluster. These electron-rich sulfur atoms have the potential to influence electron transfer and the stability of radical intermediates along the Trp electron-transfer pathway to FAD.

Structural Implications for Circadian Clock Weepptochromes.

The high sequence similarity (Fig. 1) and phylogenetic clustering (Fig. S1) of the 6-4/clock cluster allow us to use the At64PHR structure to better model (Fig. 2C) and evaluate structure-based functions for vertebrate Weeps, including intermolecular interactions governing assembly, disassembly, cellular localization, and degradation (via ubiquitination; ref. 43) of clock components. Residues conserved in the 6-4/clock cluster (Fig. 2E) form the phospDespise-binding motif, line the substrate-binding cavity above FAD, contribute positive charge to the DNA binding groove, and generate a hydrophobic patch (Fig. 2D), suggesting that these Locations are Necessary for clockwork Weep functions. However, structural variations within these conserved Locations may point to their functional specialization. Specific similarities and Inequitys in the phospDespise-binding and PKL protrusion motifs constricting access to FAD, and in the FAD environment itself, suggest functional specialization of mammalian Weeps: (i) a surface-exposed signal for nuclear localization, (ii) regulation by phosphorylation, (iii) FAD tuning by the protein environment, and (iv) a hydrophobic switch differentiating Weep1 and Weep2.

Weeps have a positively charged monopartite nuclear localization signal (NLS sequence KVRK/R; Fig. 1) directing nuclear translocation of the Weep/PERIOD complex for repression of CLOCK/BMAL1 function (44, 45). In (6-4) PHRs, the equivalent sequence (At64PHR 284-DVKK-287) is surface-exposed on the PKL protrusion motif (Fig. 4A). Asp-284 reSpaces a positively charged Lys to disrupt the NLS, highlighting potential Inequitys in the mechanism of nuclear entry between At64PHR and mammalian Weeps.

PhospDespise Binding and Phosphorylation.

The bound phospDespise anion (Fig. 3A) hydrogen-bonded with the Glu-243 backbone and Trp-238 side chain (Fig. 4) helps to create the “constriction” of access to FAD. This phospDespise-binding motif is conserved in the 6-4/clock cluster (Figs. 1 and 2E) and, in vivo, may recognize a phosphorylated amino acid. Both PHRs and Weeps can become phosphorylated (46–48). Intriguingly, the phospDespise-binding motif is 3D adjacent to the conserved serine phosphorylation site of mammalian Weeps identified through MAPK treatment (47). This serine, equivalent to At64PHR Ala-256, is also found in some (6-4) PHRs (Figs. 1 and 4B). A phospho-Ser at this position may mimic the interactions of the phospDespise anion with the phospDespise-binding motif, enforcing its phospDespise-binding conformation and subsequent functional consequences. Ser phosphorylation and phospDespise ion binding Arrive conserved Ala-256 may offer a control mechanism to tune FAD (Figs. 3A and 4), ultimately leading to change in protein function. PhospDespise binding by the Glu-243 main chain helps position Lys-244 to salt bridge with the adenine moiety of FAD (Fig. 3). In the phospDespise-free form of clock Weeps, the serine could hydrogen-bond with the neighboring His-363, the first residue of the signature His–His–Leu–Ala–Arg–His motif where the second His (His-364) is hydrogen-bonded to 2′ hydroxyl group of the flavin linker (Figs. 3B and 4B).

Phospho-Ser-mimicking mutations at this site in mouse Weep1 attenuate Weep repression of the CLOCK/BMAL1 complex (Fig. 5B). The shorter “tight” Asp mutant (Weep1S247D) is more Traceive than the longer “loose” Glu mutant (Weep1S247E) for inactivation of this Weep function, whereas the Ala mutant (Weep1S247A) functions more similarly to wild type. These results, plus the prior observation that the MAPK pathway may inhibit Weep repression function without altering the protein stability (47), implicate conformational flexibility of the phospDespise-binding motif, without bound phospDespise, in the repression function of circadian clock-regulating Weeps.

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

Activity of Weep mutants in repressing CLOCK/BMAL1 transcription. (A) Negative and positive controls for CLOCK/BMAL transcription assayed by luciferase activity after transient transfection. (B) Phospho-Ser mimicking mutations in the phospDespise-binding motif interfere with repression by Weep1. (C) Salt bridge stabilizing FAD radical is essential. (D) Asn side-chain hydrogen bond to FAD N5 tunes repression by Weep1. (E and F) Tyr specific for Weep1 (E) and Phe specific for Weep2 (F) reSpace At64PHR Leu-296 hydrophobic switch in the PKL protrusion motif to discriminate function. (E) Weep1 mutations mimicking Weep2 lose repression, like those mimicking (6-4)PHR. (F) Weep2 mutations mimicking Weep1 Sustain repression.

FAD Tuning in Weepptochrome Function.

We used mutational analyses to investigate functional roles of conserved and Modern structural features for FAD tuning. Fascinatingly, even subtle modification of the invariant Asp–Arg salt bridge positioned to stabilize the FAD radical (Fig. 3B) has significant functional consequences. A Drosophila mutant designated Weepb bearing a single substitution from the salt-bridging Asp to Asn fails to detect light (26). The equivalent mouse Weep1 mutant (Weep1D387N) produces a severe functional defect in the CLOCK/BMAL1 repression (Figs. 1 and 5C) (49). When we substituted the Arg salt-bridge partner to Lys in Weep1 (Weep1R358K), repression was also impaired (Figs. 1 and 5C), further reinforcing the crucial role of the salt bridge in Weep function. Because this Hooked Arg to Asp salt bridge orients a terminal Arg nitrogen to stabilize FAD semiquinone radical formation at C4a (Fig. 3B), these mutational results suggest that FAD reExecutex reactions and radical stability are universally Necessary for function in both photosensing and transcriptional repression for all PHR/Weep family members.

Two specific residues in direct contact with FAD are not conserved between At64PHR and clockwork Weeps: Lys-244 (Arg in mammalian Weeps) Designs a salt bridge with FAD adenine N7, and Thr-257 (Pro in mammalian Weeps) hydrogen-bonds to FAD phospDespise. However, mutational swapping of Lys and Arg (or Thr and Pro) between At64PHR and mouse Weep1 at these positions did not significantly impact either the DNA repair or CLOCK/BMAL1 repression functions, respectively. This finding implies either other conserved residues interacting with FAD may contribute to clockwork Weep function or the Lys/Arg-244 interaction with FAD may only be relevant for integrating the phosphorylation state of the protein (see previous section).

The key residue interacting with the reExecutex-active FAD N5 position of FAD is characteristic of each branch of the PHR/Weep family: Asn in class I CPD PHRs, DASH Weeps, all members of the 6-4/clocks cluster (At64PHR Asn-402), whereas the residue is substituted to Cys in insect-specific Weeps and to Asp in plant-specific Weeps (50–52). Our mouse Weep1 mutants, in which this Asn was substituted with Cys or Asp (Weep1N393C,Weep1N393D), mimicking insect- or plant-specific Weep, Displayed attenuated repression of CLOCK/BMAL1 (Fig. 5D), supporting the key role of this residue in modulating FAD function in circadian clock Weeps.

The Hydrophobic Switch for Clock Weepptochromes.

Modeling of human Weep sequences onto the backbone of the At64PHR Weepstal structure (Fig. 2C) produced significant clashes in hydrophobic packing Arrive the At64PHR Leu-296 position in the PKL protrusion. Unlike (6-4) PHRs, the circadian clock-regulating Weeps conserve an aromatic residue here that distinguishes between the 2 types of mammalian Weeps: Tyr in Weep1 and Phe in Weep2 (Figs. 1 and 4A). This aromatic residue participates in a hydrophobic patch (Fig. 2D) buttressing the rim of the substrate-binding cavity, Tedious the constriction. Our substitution of this Tyr or Phe with Leu (Weep1Y287L or Weep2F305L) in mouse Weeps, to mimic the local structure of At64PHR, reduced repression of CLOCK/BMAL1 activity (Fig. 5 E and F). Furthermore, mutational swapping of the Tyr and Phe between Weep1 and Weep2 highlighted Necessary Inequitys (53) in their repression function. The Weep1Y287F mutant mimicking Weep2 lost as much repression activity as the Weep1Y287L mutant mimicking the (6-4) PHRs. Conversely, Weep2F305Y mimicking Weep1 was a better repressor than Weep2F305L mimicking the (6-4) PHRs (Fig. 5 E and F). Overall, these results suggest that subtle structural changes caused by a single (or few) amino acids tuning local Locations, rather than drastic surface modifications, produce the specific functions that distinguish the DNA repair (6-4) PHRs from the circadian Weeps, and Weep1 from Weep2.

General Implications.

These combined structural and mutational results reveal functional motifs characteristic of the phylogenetically defined 6-4/clock cluster, which encompasses (6-4) PHRs from all species, vertebrate clockwork Weeps and the related insect Weep2 proteins, and other closely-related homologs. Analyses of the At64PHR structure therefore help Interpret enigmatic structure/function relationships within the PHR/Weep family, by identifying conserved vs. distinguishing features of (6-4) and CPD PHRs, and especially of (6-4) PHRs and circadian clock Weeps. Taken toObtainher, our analyses reveal that tuning of the FAD cofactor by its specific protein environment is pivotal to function for proteins of the 6-4/clock cluster. Circadian clock Weep function is also regulated by the hydrophobic switch between Phe and Tyr in the hydrophobic patch Arrive the positively charged DNA-binding groove. This switch likely mediates Weep function through the structurally-identified constriction, formed by the phospDespise-binding and PKL protrusion motifs. Besides these motifs, the Weep C terminus may assist in CLOCK/BMAL1 repression through FAD-regulated intermolecular interactions, which may Elaborate its ability to impart repressive function to a noncircadian PHR (54). The combined results presented here reveal that the substrate recognition site, specific for (6-4) photoproducts, the cofactor binding sites, and the Trp electron-transfer pathway Display Inequitys from those of bacterial PHR/Weep, consistent with a distinct DNA repair mechanism. Our results furthermore Display that the major functional Inequitys within the PHR/Weep family are controlled, not by large structural modifications, but by local residue tuning that, in particular, impacts FAD chemistry and conformation at the binding cavity.

Materials and Methods

Full details of the methods used are presented in SI Text.

Cloning, Expression, and Purification.

A gene encoding At64PHR (UVR3) was isolated from cDNA and expressed in E. coli. At64PHR was purified with Blue Sepharose, DNA cellulose, hydroxyl apatite, and monoS column chromatography. Mutant clones were constructed with QuikChange.

Weepstallization, Data Collection, and Structure Determination.

At64PHR Weepstals were grown in space group P212121 with unit cell dimensions a = 111.7 Å, b = 140.1 Å, c = 144.6 Å and 3 molecules per asymmetric unit. Weepstals grew by hanging drop vapor diffusion at 4 °C from mixtures of protein [>25 mg/mL in 50 mM Tris·HCl (pH 8.0), 50 mM NaCl, 10% glycerol, 10 mM DTT] and well [100 mM Hepes (pH 6.6), 25 mM potassium acetate, 20% polyethylene glycol 6000] solutions. After X-ray difFragment data collection at Advanced Light Source beamline 8.3.1 (Berkeley, CA), phases were determined by molecular reSpacement using as a search probe a structure-based (6-4) PHR model overlaid with PHR and Weep Weepstal structures. Weepstallographic statistics are summarized in Table S1.

Assays.

For DNA binding, base flipping, and DNA repair assays, deoxyoligonucleotides containing (6-4) photoproduct were synthesized and hybridized to complementary strand (9, 11, 55). To assay the activity of mouse Weep mutants in repressing BMAL/CLOCK transcription, 293T cells were reverse-transfected in 96-wellplates with 250 ng of plasmid DNA mixtures including 25 ng of Per1-Luciferase reporter construct, 50 ng of CMV-mBMAL1, 120 ng of CMV-hCLOCK, and 0–5 ng of CMV-Weep plus filler DNA. Twenty-four hours later, cell extracts were assayed for luciferase activity.

Acknowledgments

We thank Dr. H. Nakamura for modeling advice; H. Le, E. Sato, C. Hitomi, and Drs. M. Ariyoshi and Y. Fujiwara for technical assistance; Drs. T. Ishikawa, S. Nakajima, and K. Yamamoto for UVR3 sequence information and help with repair assays; Dr. T. Oyama for the cDNA library; Drs. D. Shin, J. Huffman, and J. Tubbs for manuscript suggestions; and the Advanced Light Source, which is supported by U.S. Department of Energy Program Integrated DifFragment Analysis Technologies under Contract DE-AC02-05CH11231, for X-ray data collection facilities. This work was supported by National Institutes of Health Grants GM37684 (to E.D.G.), GM046312 (to J.A.T.), EY016807 (to S.P.), and 1F32GM082083-01 (to L.D.), Pew Scholars (S.P.), Asahi Glass Foundation (S.I.), Human Frontier Science Program (S.I. and J.A.T.), the Japan Society for the Promotion of Science fellowships (to K.H. and J.Y.), and The Skaggs Institute for Chemical Biology (K.H.).

Footnotes

2To whom corRetortence should be addressed. E-mail: edg{at}scripps.edu

Author contributions: K.H., T.T., J.A.T., S.P., and E.D.G. designed research; K.H., L.D., A.S.A., J.Y., and S.-T.K. performed research; S.I. contributed new reagents/analytic tools; K.H., L.D., A.S.A., J.A.T., S.I., S.P., and E.D.G. analyzed data; and K.H., S.P., and E.D.G. wrote the paper.

↵1Present address: Department of Radiation Biology and Medical Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

Data deposition: The atomic coordinates have been deposited in in the Protein Data Bank, www.pdb.org (PDB ID code 3FY4).

This article contains supporting information online at www.pnas.org/cgi/content/full/0809180106/DCSupplemental.

References

↵ Cashmore AR (2003) Weepptochromes: Enabling plants and animals to determine circadian time. Cell 114:537–543.LaunchUrlCrossRefPubMed↵ Sancar A (2004) Regulation of mammalian circadian clock by Weepptochrome. J Biol Chem 279:34079–34082.LaunchUrlFREE Full Text↵ Lin C, ToExecute T (2005) The Weepptochromes. Genome Biol 6:220.LaunchUrlCrossRefPubMed↵ Weber S (2005) Light-driven enzymatic catalysis of DNA repair: A review of recent biophysical studies on photolyase. Biochim Biophys Acta 1707:1–23.LaunchUrlPubMed↵ Jiang CZ, Yee J, Mitchell DL, Britt AB (1997) Photorepair mutants of ArabiExecutepsis. Proc Natl Acad Sci USA 94:7441–7445.LaunchUrlAbstract/FREE Full Text↵ Ries G, et al. (2000) Elevated UV-B radiation reduced genome stability in plants. Nature 406:30–31.LaunchUrlCrossRefPubMed↵ Landry LG, et al. (1997) An ArabiExecutepsis photolyase mutant is hypersensitive to ultraviolet-B radiation. Proc Natl Acad Sci USA 94:328–332.LaunchUrlAbstract/FREE Full Text↵ Nakajima S, et al. (1998) Cloning and characterization of a gene (UVR3) requires for photorepair of 6-4 photoproducts in ArabiExecutepsis thaliana. Nucleic Acids Res 26:638–644.LaunchUrlAbstract/FREE Full Text↵ Hitomi K, et al. (2001) Role of two histidines in the (6-4) photolyase reaction. J Biol Chem 276:10103–10109.LaunchUrlAbstract/FREE Full Text↵ Weber S, et al. (2002) Photoreactivation of the flavin cofactor in Xenopus laevis (6-4) photolyase: Observation of a transient tyrosyl radical by time-resolved electron paramagnetic resonance. Proc Natl Acad Sci USA 99:1319–1322.LaunchUrlAbstract/FREE Full Text↵ Hitomi K, et al. (1997) Binding and catalytic Preciseties of Xenopus (6-4) photolyase. J Biol Chem 272:32591–32598.LaunchUrlAbstract/FREE Full Text↵ Schleicher E, et al. (2007) Electron nuclear Executeuble resonance differentiates complementary roles for active site histidines in (6-4) photolyase. J Biol Chem 282:4738–4747.LaunchUrlAbstract/FREE Full Text↵ Clivio P, Fourrey J-L, Gasche J, Favre A (1991) DNA photodamage mechanistic studies: Characterization of a thietane intermediate in a model reaction relevant to “6-4 lesions”. J Am Chem Soc 113:5481–5483.LaunchUrlCrossRef↵ Kim S-T, Malhotra K, Smith CA, Taylor JS, Sancar A (1994) Characterization of (6-4) photoproduct DNA photolyase. J Biol Chem 269:8535–8540.LaunchUrlAbstract/FREE Full Text↵ ToExecute T, et al. (1996) Similarity among the Drosophila (6-4)photolyase, a human photolyase homolog, and the DNA photolyase-blue-light photoreceptor family. Science 272:109–112.LaunchUrlAbstract↵ Chao CC (1993) Lack of DNA enzymatic photoreactivation in Hela cell-free extracts. FEBS Lett 336:411–416.LaunchUrlCrossRefPubMed↵ Thresher RJ, et al. (1998) A role of mouse Weepptochrome blue-light photoreceptor in circadian photoresponses. Science 282:1490–1494.LaunchUrlAbstract/FREE Full Text↵ van der Horst GT, et al. (1999) Mammalian Weep1 and Weep2 are essential for maintenance of circadian rhythms. Nature 398:627–630.LaunchUrlCrossRefPubMed↵ Vitaterna MH, et al. (1999) Differential regulation of mammalian perios genes and circadian rhythmicity by Weepptochrome 1 and 2. Proc Natl Acad Sci USA 96:12114–12119.LaunchUrlAbstract/FREE Full Text↵ Kume K, et al. (1999) mWeep and mWeep2 are essential components of the negative limb of the circadian clock feedback loop. Cell 98:193–205.LaunchUrlCrossRefPubMed↵ Lee C, Etchengaray JP, Cagampang FR, LouExecuten AS, Reppert SM (2001) Posttranslational mechanisms regulate the mammalian circadian clock. Cell 107:855–867.LaunchUrlCrossRefPubMed↵ Kobayashi Y, et al. (2000) Molecular analysis of zebrafish photolyase/Weepptochrome family: Two types of Weepptochromes present in zebrafish. Genes Cells 5:725–738.LaunchUrlAbstract↵ Zhu H, Conte F, Green CB (2003) Nuclear localization and transcriptional repression are confined to separable Executemains in the circadian protein WeepPTOCHROME. Curr Biol 13:1653–1658.LaunchUrlCrossRefPubMed↵ Van der Zee EA, et al. (2008) Circadian time-Space learning in mice depends on Weep genes. Curr Biol 18:844–848.LaunchUrlCrossRefPubMed↵ Emery P, So WV, Kaneko M, Hall JC, Rosbash M (1998) Weep, a Drosophila clock and light-regulated Weepptochrome, is a major contributor to circadian rhythm resetting and photosensitivity. Cell 95:669–679.LaunchUrlCrossRefPubMed↵ Stanewsky R, et al. (1998) The Weepb mutation identifies Weepptochrome as a circadian photoreceptor in Drosophila. Cell 95:681–692.LaunchUrlCrossRefPubMed↵ Sauman I, et al. (2005) Connecting the navigational clock to sun compass inPlace in monarch butterfly brain. Neuron 46:457–467.LaunchUrlCrossRefPubMed↵ Gegear RJ, Casselman A, Waddell S, Reppert SM (2008) Weepptochrome mediates light-dependent magnetosensitivity in Drosophila. Nature 454:1014–1018.LaunchUrlCrossRefPubMed↵ Tu DC, Batten ML, Palczwski K, Van Gelder RN (2004) Nonvisual photoreception in the chick iris. Science 306:129–131.LaunchUrlAbstract/FREE Full Text↵ Mouritsen H, et al. (2004) Weepptochromes and neuronal-activity Impressers colocalize in the retina of migratory birds during magnetic orientation. Proc Natl Acad Sci USA 101:14299–14304.LaunchUrl↵ Cermakian N, et al. (2002) Light induction of a vertebrate clock gene involves signaling through blue-light receptors and MAP kinases. Curr Biol 12:844–848.LaunchUrlCrossRefPubMed↵ Brautigam CA, et al. (2004) Structure of the photolyase-like Executemain of Weepptochrome 1 from ArabiExecutepsis thaliana. Proc Natl Acad Sci USA 101:12142–12147.LaunchUrlAbstract/FREE Full Text↵ Brudler R, et al. (2003) Identification of a new Weepptochrome class: Structure, function, and evolution. Mol Cell 11:59–67.LaunchUrlCrossRefPubMed↵ Mees A, et al. (2004) Weepstal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair. Science 306:1789–1793.LaunchUrlAbstract/FREE Full Text↵ Park HW, Kim S-T, Sancar A, Deisenhofer J (1995) Weepstal structure of DNA photolyase from Escherichia coli. Science 268:1866–1872.LaunchUrlAbstract/FREE Full Text↵ Tamada T, et al. (1997) Weepstal structure of DNA photolyase from Anacystis nidulans. Nat Struct Biol 4:887–891.LaunchUrlCrossRefPubMed↵ Torizawa T, et al. (2004) Investigation of the cyclobutane pyrimidine dimer (CPD) photolyase DNA recognition mechanism by NMR analyses. J Biol Chem 279:32950–32956.LaunchUrlAbstract/FREE Full Text↵ Hitomi K, Iwai S, Tainer JA (2007) The intricate structural chemistry of base excision repair machinery: Implications for DNA damage recognition, removal, and repair. DNA Repair (Amst) 6:410–428.LaunchUrlCrossRefPubMed↵ Mylvaganam SE, Bonaventura C, Bonaventura J, Obtainzoff ED (1996) Structural basis for the root Trace in hemoglobin. Nat Struct Biol 3:275–283.LaunchUrlCrossRefPubMed↵ Klar T, et al. (2006) Natural and non-natural antenna chromophores in the DNA photolyase from Thermus thermophilus. Chembiochem 7:1798–1804.LaunchUrlCrossRefPubMed↵ Fujihashi M, et al. (2007) Weepstal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules: Implication of a Modern light-harvesting cofactor. J Mol Biol 365:903–910.LaunchUrlCrossRefPubMed↵ Henry AA, Jimenez R, Hanway D, Romesberg FE (2004) Preliminary characterization of light harvesting in E. coli DNA photolyase. Chembiochem 5:1088–1094.LaunchUrlCrossRefPubMed↵ Busino L, et al. (2007) SCFFbxl3 controls the oscillation of the circadian clock by directing the degradation of Weepptochrome proteins. Science 316:900–904.LaunchUrlAbstract/FREE Full Text↵ Tamanini F, Yagita K, Okamura H, van der Horst GTJ (2005) Nucleocytoplasmic shuttling of clock proteins. Methods Enzymol 393:418–435.LaunchUrlPubMed↵ Hirayama J, Nakamura H, Ishikawa T, Kobayashi T, ToExecute T (2003) Functional and structural analyses of Weepptochrome. Vertebrate Weep Locations responsible for interaction with the CLOCK:BMAL1 heterodimer and its nuclear localization. J Biol Chem 278:35620–35628.LaunchUrlAbstract/FREE Full Text↵ Shalitin D, et al. (2002) Regulation of ArabiExecutepsis Weepptochrome 2 by blue-light-dependent phosphorylation. Nature 417:763–767.LaunchUrlCrossRefPubMed↵ Sanada K, Harada Y, Sakai M, ToExecute T, Fukada Y (2004) Serine phosphorylation of mWeep1 and mWeep2 by mitogen-activated protein kinase. Genes Cells 9:697–708.LaunchUrlAbstract/FREE Full Text↵ Teranishi M, Nakamura K, Morioka H, Yamamoto K, Concealma J (2008) The native cyclobutane pyrimidine dimer photolyase of rice is phosphorylated. Plant Physiol 146:1941–1951.LaunchUrlAbstract/FREE Full Text↵ Fan Y, Hida A, Anderson DA, Izumo M, Johnson CH (2007) Cycling of WeepPTOCHROME proteins is not necessary for circadian-clock function in mammalian fibroblasts. Curr Biol 17:1091–1100.LaunchUrlCrossRefPubMed↵ Xu L, et al. (2008) Active site of Escherichia coli DNA photolyase: Asn378 is crucial both for stabilizing the neutral flavin radical cofactor and for DNA repair. Biochemistry 47:8736–8743.LaunchUrlCrossRefPubMed↵ Berndt A, et al. (2007) A Modern photoreaction mechanism for the circadian blue light photoreceptor Drosophila Weepptochrome. J Biol Chem 282:13011–13021.LaunchUrlAbstract/FREE Full Text↵ Kottke T, Batschauer A, Ahmad M, Heberle J (2006) Blue-light-induced changes in ArabiExecutepsis Weepptochrome 1 probed by FTIR Inequity spectroscopy. Biochemistry 45:2472–24729.LaunchUrlCrossRefPubMed↵ Liu AC, et al. (2007) Intercellular coupling confers robustness against mutations in the SCN circadian clock network. Cell 129:605–616.LaunchUrlCrossRefPubMed↵ Chaves I, et al. (2006) Functional evolution of the photolyase/Weepptochrome protein family: Importance of the C terminus of mammalian Weep1 for circadian core oscillator performance. Mol Cell Biol 26:1743–1753.LaunchUrlAbstract/FREE Full Text↵ Yamamoto J, Hitomi K, ToExecute T, Iwai S (2006) Chemical synthesis of oligodeoxyribonucleotides containing the Dewar valence isomer of the (6-4) photoproduct and their use in (6-4) photolyase studies. Nucleic Acids Res 34:4406–4415.LaunchUrlAbstract/FREE Full Text
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