Crystal structure of cryptochrome 3 from
            <i>Arabidopsis thaliana</i>
            and its implications for photolyase activity

Huang, Yihua; Baxter, Richard H. G.; Smith, Barbara; Partch, Carrie L.; Colbert, Christopher L.; Deisenhofer, Johann

doi:10.1073/pnas.0608554103

Cited by 118 publications

(136 citation statements)

References 33 publications

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“…All of the amino acids that act in binding of FAD in Arabidopsis Cry3 (20,35) or are essential for hydrogen bonding of MTHF are conserved across the five species, suggesting that Phycomyces CryA might bind FAD and MTHF in a manner similar to that of other members in the cry-DASH subfamily (35,36) (SI Appendix, Fig. S2).…”

Section: Resultsmentioning

confidence: 99%

Fungal cryptochrome with DNA repair activity reveals an early stage in cryptochrome evolution

Tagua

Pausch

Eckel

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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DASH (Drosophila, Arabidopsis, Synechocystis, Human)-type cryp- tochromes (cry-DASH) belong to a family of flavoproteins acting as repair enzymes for UV-B–induced DNA lesions (photolyases) or as UV-A/blue light photoreceptors (cryptochromes). They are present in plants, bacteria, various vertebrates, and fungi and were originally considered as sensory photoreceptors because of their incapability to repair cyclobutane pyrimidine dimer (CPD) lesions in duplex DNA. However, cry-DASH can repair CPDs in single-stranded DNA, but their role in DNA repair in vivo remains to be clarified. The genome of the fungus Phycomyces blakesleeanus contains a single gene for a protein of the cryptochrome/photolyase family (CPF) encoding a cry-DASH, cryA, despite its ability to photoreactivate. Here, we show that cryA expression is induced by blue light in a Mad complex-dependent man- ner. Moreover, we demonstrate that CryA is capable of binding flavin (FAD) and methenyltetrahydrofolate (MTHF), fully complements the Escherichia coli photolyase mutant and repairs in vitro CPD lesions in single-stranded and double-stranded DNA with the same efficiency. These results support a role for Phycomyces cry-DASH as a photolyase and suggest a similar role for cry-DASH in mucoromycotina fung

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Section: Resultsmentioning

confidence: 99%

Fungal cryptochrome with DNA repair activity reveals an early stage in cryptochrome evolution

Tagua

Pausch

Eckel

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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“…3, inset b). However, the PhrA crystal structure reveals a unique MTHF binding site different from other CPF structures: in Escco-PL and Arath-Cry3, MTHF is coordinated by amino acids from helices ␣2, ␣5, and ␣14 (20,21,58), and the distance between MTHF-N10 and FAD-N5 is 15-17 Å. In PhrA, MTHF is located on the opposite side relative to the isoalloxazine ring of FAD (Fig.…”

Section: Table 2 Residues Forming the Fad Access Cavitymentioning

confidence: 99%

“…In this way, light capture is increased severalfold over that of FADH Ϫ alone, which has a low extinction coefficient in the visible range. The nature of the antenna chromophore and its position within the protein structure varies between photolyases: flavin mononucleotide (FMN) (17), 8-hydroxy-5-deazaflavin (18), FAD (19), and 6,7-dimethyl-8-ribityllumazine (10,11) bind to a homologous position inside the protein at the C-terminal edge of a ␤-sheet, whereas MTHF binds to a groove at the outside of the protein (20,21). Whether cryptochromes carry an antenna chromophore is still unclear: an action spectrum for degradation of recombinant Arath-Cry2 in living cells has a peak at 380 nm, providing strong evidence for a pterin antenna chromophore in Cry2 (22).…”

mentioning

confidence: 99%

The Class III Cyclobutane Pyrimidine Dimer Photolyase Structure Reveals a New Antenna Chromophore Binding Site and Alternative Photoreduction Pathways

Scheerer

Zhang

Kalms

et al. 2015

Journal of Biological Chemistry

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Background: Photolyases use light energy to repair UV-damaged DNA. Results: The crystal structure of a "class III CPD" photolyase reveals a new binding pocket for an "5,10-methenyltetrahydrofolate" antenna chromophore. Conclusion: Related plant cryptochromes might use the same antenna chromophore binding pocket. Significance: The photolyase crystal structure allows a better understanding of the evolutionary transition of photolyases to plant cryptochromes.

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“…Crystal structures of several photolyases are available and are quite similar (Huang et al 2006;Fujihashi et al 2007). In contrast, only the PHR domain of AtCRY1 has been crystallized (Brautigam et al 2004).…”

Section: Structures Of Photolyase and Cryptochromementioning

confidence: 99%

Structure and Function of Animal Cryptochromes

Öztürk

Song²,

Özgür³

et al. 2007

Cold Spring Harbor Symposia on Quantitative Biology

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Cryptochrome (CRY) is a photolyase-like flavoprotein with no DNA-repair activity but with known or presumed blue-light receptor function. Animal CRYs have DNA-binding and autokinase activities, and their flavin cofactor is reduced by photoinduced electron transfer. In Drosophila, CRY is a major circadian photoreceptor, and in mammals, the two CRY proteins are core components of the molecular clock and potential circadian photoreceptors. In mammals, CRYs participate in cell cycle regulation and the cellular response to DNA damage by controlling the expression of some cell cycle genes and by directly interacting with checkpoint proteins. in response to blue light (Koornneef et al. 1980), was isolated and sequenced, it revealed high sequence homology with Escherichia coli photolyase, and hence, it was in retrospect, correctly speculated that HY4 encoded a blue light photoreceptor and not a signal transducer involved in blue light response (Ahmad and Cashmore 1993). Later, this protein was named cryptochrome 1 (Lin et al. 1995, and a second Arabidopsis protein that has high homology with CRY1 identified by genomics was named CRY2 . The role of CRY in Arabidopsis growth (CRY1) and differentiation (CRY2) was well established by 1995 (see Guo et al. 1998). However, as late as 1997, it was thought that CRY had no role in circadian photoreception in plants (Millar and Kay 1997).The first report implicating CRY in the circadian clock of any organism, plant or animal, came about from the study of DNA repair, in particular, the repair of UV damage in humans by photolyase. This issue had been controversial for nearly 25 years when Li et al. (1993) conducted an exhaustive study with a highly specific and sensitive assay, concluding that humans, like all placental mammals, lacked photolyase (Li et al. 1993). However, a 1995 release of a human expressed sequence tag (EST) list contained a "photolyase ortholog" entry (Adams et al. 1995). In light of this finding and the discovery of a photolyase in Drosophila and rattlesnake (Todo et al. 1993Kim et al. 1996) that repairs the minor UV-induced lesion, the (6-4) photoproduct, in contrast to the classic photolyase that repairs cyclobutane pyrimidine dimers (CPDs), the earlier conclusion regarding the lack of photolyase in humans needed reevaluation. This was done by Hsu et al. (1996) who, in addition to the "photolyase ortholog" in public databases, discovered a second human photolyase gene. Human cells expressing both genes and recombinant proteins encoded by both genes were tested for CPD and (6-4) photolyase activities and were found to lack both. Moreover, the proteins encoded by these genes, like most photolyases (Johnson et al. 1988) and Arabidopsis CRY (Lin et al. 1995; Malhorta et al. 1995), contained FAD (flavin-adenine dinucleotide) and a pterin cofactor. Therefore, it was concluded that these proteins were not repair enzymes but that, like Arabidopsis CRYs, they performed non-repair-related blue light functions and were named human CRY1 and 2 (Hsu et al. 1996). In humans ...

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Crystal structure of cryptochrome 3 from Arabidopsis thaliana and its implications for photolyase activity

Cited by 118 publications

References 33 publications

Fungal cryptochrome with DNA repair activity reveals an early stage in cryptochrome evolution

Fungal cryptochrome with DNA repair activity reveals an early stage in cryptochrome evolution

The Class III Cyclobutane Pyrimidine Dimer Photolyase Structure Reveals a New Antenna Chromophore Binding Site and Alternative Photoreduction Pathways

Structure and Function of Animal Cryptochromes

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