Genomes and Genes
deoxyribodipyrimidine photo lyase
Summary: An enzyme that catalyzes the reactivation by light of UV-irradiated DNA. It breaks two carbon-carbon bonds in PYRIMIDINE DIMERS in DNA.
- Kao Y, Saxena C, Wang L, Sancar A, Zhong D. Direct observation of thymine dimer repair in DNA by photolyase. Proc Natl Acad Sci U S A. 2005;102:16128-32 pubmed..These results show that the photocycle of DNA repair by photolyase is through a radical mechanism and completed on subnanosecond time scale at the dynamic active site, with no net change in the redox state of the flavin cofactor. ..
- Selby C, Sancar A. A cryptochrome/photolyase class of enzymes with single-stranded DNA-specific photolyase activity. Proc Natl Acad Sci U S A. 2006;103:17696-700 pubmed..Here, we show that Cry-DASH proteins from bacterial, plant, and animal sources actually are photolyases with high degree of specificity for cyclobutane pyrimidine dimers in ssDNA. ..
- Zhong D. Ultrafast catalytic processes in enzymes. Curr Opin Chem Biol. 2007;11:174-81 pubmed
- Srinivasan V, Schnitzlein W, Tripathy D. Fowlpox virus encodes a novel DNA repair enzyme, CPD-photolyase, that restores infectivity of UV light-damaged virus. J Virol. 2001;75:1681-8 pubmed..Although expression of a homologous protein has been predicted for some chordopoxviruses, this report is the first to demonstrate that a poxvirus can utilize light to repair damage to its genome...
- Ozgur S, Sancar A. Purification and properties of human blue-light photoreceptor cryptochrome 2. Biochemistry. 2003;42:2926-32 pubmed..These findings reveal new properties of this protein already known to function as a circadian photoreceptor and a light-independent negative transcriptional regulator of the clock genes. ..
- Chiganças V, Batista L, Brumatti G, Amarante Mendes G, Yasui A, Menck C. Photorepair of RNA polymerase arrest and apoptosis after ultraviolet irradiation in normal and XPB deficient rodent cells. Cell Death Differ. 2002;9:1099-107 pubmed..These results demonstrate that marsupial photolyase has access to CPDs blocking RNA synthesis in vivo, and this may be affected by the presence of a mutated XPB protein. ..
- Sancar G. Enzymatic photoreactivation: 50 years and counting. Mutat Res. 2000;451:25-37 pubmed..Additionally, genetic and molecular studies of PHR1, the S. cerevisiae gene encoding the apoenzyme of photolyase, have led to the identification of previously unknown damage-responsive transcriptional regulators. ..
- Ng W, Pakrasi H. DNA photolyase homologs are the major UV resistance factors in the cyanobacterium Synechocystis sp. PCC 6803. Mol Gen Genet. 2001;264:924-30 pubmed..Based on these findings, we conclude that enzymatic photoreactivation is the primary process used for repairing UV-induced damage in Synechocystis 6803. ..
- Sancar A. Regulation of the mammalian circadian clock by cryptochrome. J Biol Chem. 2004;279:34079-82 pubmed
- Lin C, Shalitin D. Cryptochrome structure and signal transduction. Annu Rev Plant Biol. 2003;54:469-96 pubmed..Recent studies suggest that cryptochromes undergo a blue light-dependent phosphorylation that affects the conformation, intermolecular interactions, physiological activities, and protein abundance of the photoreceptors. ..
- Berndt A, Kottke T, Breitkreuz H, Dvorsky R, Hennig S, Alexander M, et al. A novel photoreaction mechanism for the circadian blue light photoreceptor Drosophila cryptochrome. J Biol Chem. 2007;282:13011-21 pubmed..radical represents the light-activated state that mediates resetting of the Drosophila circadian clock. ..
- Kao Y, Saxena C, Wang L, Sancar A, Zhong D. Femtochemistry in enzyme catalysis: DNA photolyase. Cell Biochem Biophys. 2007;48:32-44 pubmed..These observed synergistic motions in the active site reveal a perfect correlation of structural integrity and dynamical locality to ensure maximum repair efficiency on the ultrafast time scale. ..
- Worthington E, Kavakli I, Berrocal Tito G, Bondo B, Sancar A. Purification and characterization of three members of the photolyase/cryptochrome family blue-light photoreceptors from Vibrio cholerae. J Biol Chem. 2003;278:39143-54 pubmed publisher..In addition, VcCry1 exhibits RNA binding activity and co-purifies with an RNA of 60-70 nucleotides in length...
- van Oers M, Abma Henkens M, Herniou E, de Groot J, Peters S, Vlak J. Genome sequence of Chrysodeixis chalcites nucleopolyhedrovirus, a baculovirus with two DNA photolyase genes. J Gen Virol. 2005;86:2069-80 pubmed..Twenty-two additional unique baculovirus genes were identified, including a gene encoding a novel putative RING finger protein with a possible homologue in poxviruses. ..
- Chang C, Guo L, Kao Y, Li J, Tan C, Li T, et al. Ultrafast solvation dynamics at binding and active sites of photolyases. Proc Natl Acad Sci U S A. 2010;107:2914-9 pubmed publisher..Such unusual solvation and synergetic dynamics should be general in function sites of proteins. ..
- Zhao X, Liu J, Hsu D, Zhao S, Taylor J, Sancar A. Reaction mechanism of (6-4) photolyase. J Biol Chem. 1997;272:32580-90 pubmed..Taken together, the data are consistent with photoinduced electron transfer from reduced FAD to substrate, in a manner analogous to the cyclobutane pyrimidine dimer photolyase. ..
- Yamamoto J, Tanaka Y, Iwai S. Spectroscopic analysis of the pyrimidine(6-4)pyrimidone photoproduct: insights into the (6-4) photolyase reaction. Org Biomol Chem. 2009;7:161-6 pubmed publisher..The results of this study have implications not only for the recognition and reaction mechanisms of (6-4) photolyase, but also for the chemical nature of the (6-4) photoproduct. ..
- Schleicher E, Hitomi K, Kay C, Getzoff E, Todo T, Weber S. Electron nuclear double resonance differentiates complementary roles for active site histidines in (6-4) photolyase. J Biol Chem. 2007;282:4738-47 pubmed..5, where the enzymatic repair activity is highest, His(358) is deprotonated, whereas His(354) is protonated. Hence, the latter is likely the proton donor that initiates oxetane formation from the (6-4) photoproduct. ..
- Yamamoto J, Hitomi K, Hayashi R, Getzoff E, Iwai S. Role of the carbonyl group of the (6-4) photoproduct in the (6-4) photolyase reaction. Biochemistry. 2009;48:9306-12 pubmed publisher..These results indicate that the carbonyl group of the 3' pyrimidone ring plays an important role in the (6-4) photolyase reaction. On the basis of these results, we discuss the repair mechanism. ..
- Todo T, Kim S, Hitomi K, Otoshi E, Inui T, Morioka H, et al. Flavin adenine dinucleotide as a chromophore of the Xenopus (6-4)photolyase. Nucleic Acids Res. 1997;25:764-8 pubmed..Here we report isolation of a Xenopus laevis(6-4)photolyase gene and show that the (6-4)photolyase binds non- covalently to stoichiometric amounts of FAD. This is the first indication of FAD as the chromophore of (6-4)photolyase. ..
- Kao Y, Tan C, Song S, Ozturk N, Li J, Wang L, et al. Ultrafast dynamics and anionic active states of the flavin cofactor in cryptochrome and photolyase. J Am Chem Soc. 2008;130:7695-701 pubmed publisher..These unique properties of anionic flavins suggest a universal mechanism of electron transfer for the initial functional steps of the photolyase/cryptochrome blue-light photoreceptor family. ..
- Domratcheva T, Schlichting I. Electronic structure of (6-4) DNA photoproduct repair involving a non-oxetane pathway. J Am Chem Soc. 2009;131:17793-9 pubmed publisher..This repair mechanism is in line with the recent structural data on the (6-4) photolyase from D. melanogaster . ..
- Li J, Uchida T, Ohta T, Todo T, Kitagawa T. Characteristic structure and environment in FAD cofactor of (6-4) photolyase along function revealed by resonance Raman spectroscopy. J Phys Chem B. 2006;110:16724-32 pubmed
- Yasui A, Eker A, Yasuhira S, Yajima H, Kobayashi T, Takao M, et al. A new class of DNA photolyases present in various organisms including aplacental mammals. EMBO J. 1994;13:6143-51 pubmed..Our results suggest a divergence of photolyase genes in early evolution...
- Kobayashi Y, Ishikawa T, Hirayama J, Daiyasu H, Kanai S, Toh H, et al. Molecular analysis of zebrafish photolyase/cryptochrome family: two types of cryptochromes present in zebrafish. Genes Cells. 2000;5:725-38 pubmed..The expressions of these cry genes oscillate in a circadian manner, but their patterns differ. These findings suggest that functionally diverse cry genes are present in zebrafish and each gene has different role in the molecular clock. ..
- Schul W, Jans J, Rijksen Y, Klemann K, Eker A, de Wit J, et al. Enhanced repair of cyclobutane pyrimidine dimers and improved UV resistance in photolyase transgenic mice. EMBO J. 2002;21:4719-29 pubmed..Thus, providing mice with CPD photolyase significantly improves repair and uncovers the biological effects of CPD lesions. ..
- Christine K, MacFarlane A, Yang K, Stanley R. Cyclobutylpyrimidine dimer base flipping by DNA photolyase. J Biol Chem. 2002;277:38339-44 pubmed..This is consistent with base flipping of the lesion into the protein binding cavity with concomitant destacking of the opposing complementary 2-Ap nucleotide. ..
- You Y, Lee D, Yoon J, Nakajima S, Yasui A, Pfeifer G. Cyclobutane pyrimidine dimers are responsible for the vast majority of mutations induced by UVB irradiation in mammalian cells. J Biol Chem. 2001;276:44688-94 pubmed..We conclude that CPDs are responsible for at least 80% of the UVB-induced mutations in this mammalian cell model. ..
- Okano S, Kanno S, Takao M, Eker A, Isono K, Tsukahara Y, et al. A putative blue-light receptor from Drosophila melanogaster. Photochem Photobiol. 1999;69:108-13 pubmed..The mammalian photolyase homologs are more closely related to Drosophila 6-4 photolyase than to the Drosophila photolyase homolog, suggesting different roles of the photolyase homologs. ..
- Fujihashi M, Numoto N, Kobayashi Y, Mizushima A, Tsujimura M, Nakamura A, et al. Crystal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules: implication of a novel light-harvesting cofactor. J Mol Biol. 2007;365:903-10 pubmed publisher..In addition, two of the four CPD recognition residues in the crystal structure of An-photolyase are not found in St-photolyase, which might utilize a different mechanism to recognize the CPD from that of An-photolyase...
- Todo T. Functional diversity of the DNA photolyase/blue light receptor family. Mutat Res. 1999;434:89-97 pubmed
- Hsu D, Zhao X, Zhao S, Kazantsev A, Wang R, Todo T, et al. Putative human blue-light photoreceptors hCRY1 and hCRY2 are flavoproteins. Biochemistry. 1996;35:13871-7 pubmed..We conclude that these newly discovered members of the photolyase/photoreceptor family are not photolyases and instead may function as blue-light photoreceptors in humans. ..
- Prytkova T, Beratan D, Skourtis S. Photoselected electron transfer pathways in DNA photolyase. Proc Natl Acad Sci U S A. 2007;104:802-7 pubmed..Therefore, in photolyase, the photo-excitation itself enhances the electron transfer rate by moving the electron towards the dimer. ..
- Yu Z, Chen J, Ford B, Brackley M, Glickman B. Human DNA repair systems: an overview. Environ Mol Mutagen. 1999;33:3-20 pubmed..While some associations are already well understood, it is clear that additional diseases will be found which are linked to DNA repair defects or deficiencies. ..
- Bucceri A, Kapitza K, Thoma F. Rapid accessibility of nucleosomal DNA in yeast on a second time scale. EMBO J. 2006;25:3123-32 pubmed..The data impact our view on the repressive and dynamic nature of chromatin and illustrate how proteins like photolyase can access DNA in structurally and functionally diverse chromatin regions. ..
- Gaillard H, Fitzgerald D, Smith C, Peterson C, Richmond T, Thoma F. Chromatin remodeling activities act on UV-damaged nucleosomes and modulate DNA damage accessibility to photolyase. J Biol Chem. 2003;278:17655-63 pubmed..Similar activities might relieve the inhibitory effect of nucleosomes on DNA repair processes in living cells. ..
- Niedner H, Christen R, Lin X, Kondo A, Howell S. Identification of genes that mediate sensitivity to cisplatin. Mol Pharmacol. 2001;60:1153-60 pubmed..Elucidation of the molecular mechanisms that mediate cDDP resistance holds promise for the design of pharmacological strategies for preventing, overcoming, or reversing this form of drug resistance. ..
- Kartalou M, Essigmann J. Recognition of cisplatin adducts by cellular proteins. Mutat Res. 2001;478:1-21 pubmed..Here we describe the structural information available for cisplatin and related platinum adducts, the interactions of the adducts with cellular proteins and the implications of these interactions for cell survival. ..
- Sancar A. No "End of History" for photolyases. Science. 1996;272:48-9 pubmed
- Yasui A, Takao M, Oikawa A, Kiener A, Walsh C, Eker A. Cloning and characterization of a photolyase gene from the cyanobacterium Anacystis nidulans. Nucleic Acids Res. 1988;16:4447-63 pubmed..A 40.7% similarity was found between the deduced amino acid sequences of Anacystis and E. coli photolyases, notwithstanding the difference in chromophore structure. ..
- Gurudas U, Schelvis J. Resonance Raman spectroscopy of the neutral radical Trp306 in DNA photolyase. J Am Chem Soc. 2004;126:12788-9 pubmed..This important new result demonstrates the potential of time-resolved resonance Raman spectroscopy as a powerful tool to investigate these radicals in protein electron-transfer processes and in enzymatic reactions in real time. ..
- Nishigaki R, Mitani H, Shima A. Evasion of UVC-induced apoptosis by photorepair of cyclobutane pyrimidine dimers. Exp Cell Res. 1998;244:43-53 pubmed..Among the various kinds of damage induced by UVC irradiation, the presence of pyrimidine dimers is proposed to be the major trigger for UVC-induced apoptosis. ..
- Krapf S, Koslowski T, Steinbrecher T. The thermodynamics of charge transfer in DNA photolyase: using thermodynamic integration calculations to analyse the kinetics of electron transfer reactions. Phys Chem Chem Phys. 2010;12:9516-25 pubmed publisher..As applied here to a biomolecular system of considerable scientific interest, we believe the method to be easily adaptable to the study of charge-transfer phenomena in biochemistry and other fields. ..
- Iwata T, Zhang Y, Hitomi K, Getzoff E, Kandori H. Key dynamics of conserved asparagine in a cryptochrome/photolyase family protein by fourier transform infrared spectroscopy. Biochemistry. 2010;49:8882-91 pubmed publisher..We discuss potential roles for this conserved asparagine position and functional diversity in the Cry/Phr frame. ..
- Berrocal Tito G, Esquivel Naranjo E, Horwitz B, Herrera Estrella A. Trichoderma atroviride PHR1, a fungal photolyase responsible for DNA repair, autoregulates its own photoinduction. Eukaryot Cell. 2007;6:1682-92 pubmed..This is the first evidence for a regulatory role of photolyase, a role usually attributed to cryptochromes. ..
- Garinis G, Mitchell J, Moorhouse M, Hanada K, de Waard H, Vandeputte D, et al. Transcriptome analysis reveals cyclobutane pyrimidine dimers as a major source of UV-induced DNA breaks. EMBO J. 2005;24:3952-62 pubmed..Thus, conversion of unrepaired CPD lesions into DNA breaks during DNA replication may comprise one of the principal instigators of UV-mediated cytotoxicity. ..
- Hirouchi T, Nakajima S, Najrana T, Tanaka M, Matsunaga T, Hidema J, et al. A gene for a Class II DNA photolyase from Oryza sativa: cloning of the cDNA by dilution-amplification. Mol Genet Genomics. 2003;269:508-16 pubmed..One of the mRNAs encodes an ORF for 506 amino acid residues, while the other is predicted to code for 364 amino acid residues. The two RNAs occur in about equal amounts in O. sativa cells. ..
- Cardon G, Hohmann S, Klein J, Nettesheim K, Saedler H, Huijser P. Molecular characterisation of the Arabidopsis SBP-box genes. Gene. 1999;237:91-104 pubmed..In addition to the Arabidopsis SPL genes, we isolated and determined the sequences of three SBP-box genes from Antirrhinum majus and seven from Zea mays. ..
- Saxena C, Wang H, Kavakli I, Sancar A, Zhong D. Ultrafast dynamics of resonance energy transfer in cryptochrome. J Am Chem Soc. 2005;127:7984-5 pubmed..The results for the first time show energy transfer in cryptochrome suggesting some mechanistic similarities between photolyase that repairs damaged DNA and cryptochrome that mediates blue-light signaling. ..
- Nakayama T, Todo T, Notsu S, Nakazono M, Zaitsu K. Assay method for Escherichia coli photolyase activity using single-strand cis-syn cyclobutane pyrimidine dimer DNA as substrate. Anal Biochem. 2004;329:263-8 pubmed..998. The limit of detection (S/N = 3) was 26 nU/assay tube. The photolyase activity was increased 1.6-fold in the presence of 5,10-methenyltetrahydrofolic acid in the enzyme reaction mixture. ..
- Flick J, Thorner J. An essential function of a phosphoinositide-specific phospholipase C is relieved by inhibition of a cyclin-dependent protein kinase in the yeast Saccharomyces cerevisiae. Genetics. 1998;148:33-47 pubmed..Unlike single mutants, plc1delta pho81delta and plc1delta spl2delta double mutants were unable to grow on synthetic complete medium, but were able to grow on rich medium. ..