RegulonDB

Gene
Name:	phr
Synonym(s):	ECK0697, EG10736, b0708, phrB
Genome position(nucleotides):	739507 --> 740925 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	53.49
External database links:

ASAP:	ABE-0002417
CGSC:	391
ECHOBASE:	EB0729
OU-MICROARRAY:	b0708
PortEco:	phr
STRING:	511145.b0708
COLOMBOS:	phr

Shine dalgarno
Sequence:	acttgcgccaTTCAGGagttttATG

Transcriptional Regulation
	Display Regulation
Repressed by:	LexA

Reference(s)
[1] Akasaka S., Yamamoto K., 1991, Construction of Escherichia coli K12 phr deletion and insertion mutants by gene replacement., Mutat Res 254(1):27-35
[2] Alcorn JL., Rupert CS., 1990, Regulation of photolyase in Escherichia coli K-12 during adenine deprivation., J Bacteriol 172(12):6885-91
[3] Baer M., Sancar GB., 1989, Photolyases from Saccharomyces cerevisiae and Escherichia coli recognize common binding determinants in DNA containing pyrimidine dimers., Mol Cell Biol 9(11):4777-88
[4] Begley TP., 1991, Mechanistic studies on DNA photolyase, II. Is the blue enzyme isolated from Escherichia coli a mutant?, Mutat Res 264(3):117-8
[5] Byrdin M., Lukacs A., Thiagarajan V., Eker AP., Brettel K., Vos MH., 2010, Quantum yield measurements of short-lived photoactivation intermediates in DNA photolyase: toward a detailed understanding of the triple tryptophan electron transfer chain., J Phys Chem A 114(9):3207-14
[6] Byrdin M., Villette S., Eker AP., Brettel K., 2007, Observation of an intermediate tryptophanyl radical in W306F mutant DNA photolyase from Escherichia coli supports electron hopping along the triple tryptophan chain., Biochemistry 46(35):10072-7
[7] Chanderkar LP., Jorns MS., 1991, Effect of flavin structure and redox state on catalysis by and flavin-pterin energy transfer in Escherichia coli DNA photolyase., Biochemistry 30(3):745-54
[8] Chang CW., Guo L., Kao YT., Li J., Tan C., Li T., Saxena C., Liu Z., Wang L., Sancar A., Zhong D., 2010, Ultrafast solvation dynamics at binding and active sites of photolyases., Proc Natl Acad Sci U S A 107(7):2914-9
[9] Cheung MS., Daizadeh I., Stuchebrukhov AA., Heelis PF., 1999, Pathways of electron transfer in Escherichia coli DNA photolyase: Trp306 to FADH., Biophys J 76(3):1241-9
[10] Christine KS., MacFarlane AW., Yang K., Stanley RJ., 2002, Cyclobutylpyrimidine dimer base flipping by DNA photolyase., J Biol Chem 277(41):38339-44
[11] Hamm-Alvarez S., Sancar A., Rajagopalan KV., 1990, The folate cofactor of Escherichia coli DNA photolyase acts catalytically., J Biol Chem 265(30):18656-62
[12] Hearst JE., 1995, The structure of photolyase: using photon energy for DNA repair., Science 268(5219):1858-9
[13] Heelis PF., Okamura T., Sancar A., 1990, Excited-state properties of Escherichia coli DNA photolyase in the picosecond to millisecond time scale., Biochemistry 29(24):5694-8
[14] Heelis PF., Payne G., Sancar A., 1987, Photochemical properties of Escherichia coli DNA photolyase: selective photodecomposition of the second chromophore., Biochemistry 26(15):4634-40
[15] Heelis PF., Sancar A., 1986, Photochemical properties of Escherichia coli DNA photolyase: a flash photolysis study., Biochemistry 25(25):8163-6
[16] Holub D., Kubar T., Mast T., Elstner M., Gillet N., 2019, What accounts for the different functions in photolyases and cryptochromes: a computational study of proton transfers to FAD., Phys Chem Chem Phys 21(22):11956-11966
[17] Ihara M., Yamamoto K., Ohnishi T., 1987, Induction of phr gene expression by irradiation of ultraviolet light in Escherichia coli., Mol Gen Genet 209(1):200-2
[18] Ihara M., Yamamoto K., Ohnishi T., 1987, Induction of phr gene expression by pyrimidine dimers in Escherichia coli., Photochem Photobiol 46(3):359-61
[19] Jorns MS., Baldwin ET., Sancar GB., Sancar A., 1987, Action mechanism of Escherichia coli DNA photolyase. II. Role of the chromophores in catalysis., J Biol Chem 262(1):486-91
[20] Jorns MS., Sancar GB., Sancar A., 1984, Identification of a neutral flavin radical and characterization of a second chromophore in Escherichia coli DNA photolyase., Biochemistry 23(12):2673-9
[21] Jorns MS., Wang B., Jordan SP., 1987, DNA repair catalyzed by Escherichia coli DNA photolyase containing only reduced flavin: elimination of the enzyme's second chromophore by reduction with sodium borohydride., Biochemistry 26(21):6810-6
[22] Jorns MS., Wang BY., Jordan SP., Chanderkar LP., 1990, Chromophore function and interaction in Escherichia coli DNA photolyase: reconstitution of the apoenzyme with pterin and/or flavin derivatives., Biochemistry 29(2):552-61
[23] Kao YT., Saxena C., Wang L., Sancar A., Zhong D., 2005, Direct observation of thymine dimer repair in DNA by photolyase., Proc Natl Acad Sci U S A 102(45):16128-32
[24] Kao YT., Saxena C., Wang L., Sancar A., Zhong D., 2007, Femtochemistry in enzyme catalysis: DNA photolyase., Cell Biochem Biophys 48(1):32-44
[25] Kavakli IH., Sancar A., 2004, Analysis of the role of intraprotein electron transfer in photoreactivation by DNA photolyase in vivo., Biochemistry 43(48):15103-10
[26] Kay CW., Feicht R., Schulz K., Sadewater P., Sancar A., Bacher A., Mobius K., Richter G., Weber S., 1999, EPR, ENDOR, and TRIPLE resonance spectroscopy on the neutral flavin radical in Escherichia coli DNA photolyase., Biochemistry 38(51):16740-8
[27] Kim ST., Heelis PF., Okamura T., Hirata Y., Mataga N., Sancar A., 1991, Determination of rates and yields of interchromophore (folate----flavin) energy transfer and intermolecular (flavin----DNA) electron transfer in Escherichia coli photolyase by time-resolved fluorescence and absorption spectroscopy., Biochemistry 30(47):11262-70
[28] Kim ST., Malhotra K., Smith CA., Taylor JS., Sancar A., 1993, DNA photolyase repairs the trans-syn cyclobutane thymine dimer., Biochemistry 32(28):7065-8
[29] Kim ST., Sancar A., 1991, Effect of base, pentose, and phosphodiester backbone structures on binding and repair of pyrimidine dimers by Escherichia coli DNA photolyase., Biochemistry 30(35):8623-30
[30] Kim ST., Sancar A., 1995, Photorepair of nonadjacent pyrimidine dimers by DNA photolyase., Photochem Photobiol 61(2):171-4
[31] Knips A., Zacharias M., 2017, Both DNA global deformation and repair enzyme contacts mediate flipping of thymine dimer damage., Sci Rep 7:41324
[32] Kodali G., Siddiqui SU., Stanley RJ., 2009, Charge redistribution in oxidized and semiquinone E. coli DNA photolyase upon photoexcitation: stark spectroscopy reveals a rationale for the position of Trp382., J Am Chem Soc 131(13):4795-807
[33] Li J., Uchida T., Todo T., Kitagawa T., 2006, Similarities and differences between cyclobutane pyrimidine dimer photolyase and (6-4) photolyase as revealed by resonance Raman spectroscopy: Electron transfer from the FAD cofactor to ultraviolet-damaged DNA., J Biol Chem 281(35):25551-9
[34] Li YF., Heelis PF., Sancar A., 1991, Active site of DNA photolyase: tryptophan-306 is the intrinsic hydrogen atom donor essential for flavin radical photoreduction and DNA repair in vitro., Biochemistry 30(25):6322-9
[35] Li YF., Sancar A., 1990, Active site of Escherichia coli DNA photolyase: mutations at Trp277 alter the selectivity of the enzyme without affecting the quantum yield of photorepair., Biochemistry 29(24):5698-706
[36] Lipman RS., Bailey SW., Jarrett JT., Matthews RG., Jorns MS., 1995, Stereospecificity of folate binding to DNA photolyase from Escherichia coli., Biochemistry 34(35):11217-20
[37] Lipman RS., Jorns MS., 1992, Direct evidence for singlet-singlet energy transfer in Escherichia coli DNA photolyase., Biochemistry 31(3):786-91
[38] Lipman RS., Jorns MS., 1996, An unnatural folate stereoisomer is catalytically competent in DNA photolyase., Biochemistry 35(24):7968-73
[39] Liu Z., Guo X., Tan C., Li J., Kao YT., Wang L., Sancar A., Zhong D., 2012, Electron tunneling pathways and role of adenine in repair of cyclobutane pyrimidine dimer by DNA photolyase., J Am Chem Soc 134(19):8104-14
[40] Liu Z., Tan C., Guo X., Kao YT., Li J., Wang L., Sancar A., Zhong D., 2011, Dynamics and mechanism of cyclobutane pyrimidine dimer repair by DNA photolyase., Proc Natl Acad Sci U S A 108(36):14831-6
[41] Liu Z., Tan C., Guo X., Li J., Wang L., Sancar A., Zhong D., 2013, Determining complete electron flow in the cofactor photoreduction of oxidized photolyase., Proc Natl Acad Sci U S A 110(32):12966-71
[42] Liu Z., Tan C., Guo X., Li J., Wang L., Zhong D., 2014, Dynamic Determination of Active-Site Reactivity in Semiquinone Photolyase by the Cofactor Photoreduction., J Phys Chem Lett 5(5):820-825
[43] Liu Z., Zhang M., Guo X., Tan C., Li J., Wang L., Sancar A., Zhong D., 2013, Dynamic determination of the functional state in photolyase and the implication for cryptochrome., Proc Natl Acad Sci U S A 110(32):12972-7
[44] Lorence MC., Maika SD., Rupert CS., 1990, Physical analysis of phr gene transcription in Escherichia coli K-12., J Bacteriol 172(11):6551-6
[45] Lukacs A., Eker AP., Byrdin M., Villette S., Pan J., Brettel K., Vos MH., 2006, Role of the middle residue in the triple tryptophan electron transfer chain of DNA photolyase: ultrafast spectroscopy of a Trp-->Phe mutant., J Phys Chem B 110(32):15654-8
[46] Mahaputra Wijaya IM., Iwata T., Yamamoto J., Hitomi K., Iwai S., Getzoff ED., Kandori H., 2015, FTIR study of CPD photolyase with substrate in single strand DNA., Biophysics (Nagoya-shi) 11:39-45
[47] Muller P., Brettel K., Grama L., Nyitrai M., Lukacs A., 2016, Photochemistry of Wild-Type and N378D Mutant E. coli DNA Photolyase with Oxidized FAD Cofactor Studied by Transient Absorption Spectroscopy., Chemphyschem 17(9):1329-40
[48] Murphy AK., Tammaro M., Cortazar F., Gindt YM., Schelvis JP., 2008, Effect of the cyclobutane cytidine dimer on the properties of Escherichia coli DNA photolyase., J Phys Chem B 112(47):15217-26
[49] Myles GM., Van Houten B., Sancar A., 1987, Utilization of DNA photolyase, pyrimidine dimer endonucleases, and alkali hydrolysis in the analysis of aberrant ABC excinuclease incisions adjacent to UV-induced DNA photoproducts., Nucleic Acids Res 15(3):1227-43
[50] Ozer Z., Reardon JT., Hsu DS., Malhotra K., Sancar A., 1995, The other function of DNA photolyase: stimulation of excision repair of chemical damage to DNA., Biochemistry 34(49):15886-9
[51] Park HW., Kim ST., Sancar A., Deisenhofer J., 1995, Crystal structure of DNA photolyase from Escherichia coli., Science 268(5219):1866-72
[52] Park HW., Sancar A., Deisenhofer J., 1993, Crystallization and preliminary crystallographic analysis of Escherichia coli DNA photolyase., J Mol Biol 231(4):1122-5
[53] Payne G., Heelis PF., Rohrs BR., Sancar A., 1987, The active form of Escherichia coli DNA photolyase contains a fully reduced flavin and not a flavin radical, both in vivo and in vitro., Biochemistry 26(22):7121-7
[54] Payne G., Wills M., Walsh C., Sancar A., 1990, Reconstitution of Escherichia coli photolyase with flavins and flavin analogues., Biochemistry 29(24):5706-11
[55] Payne NS., Sancar A., 1989, The LexA protein does not bind specifically to the two SOS box-like sequences immediately 5' to the phr gene., Mutat Res 218(3):207-10
[56] Raibekas AA., Jorns MS., 1994, Affinity probing of flavin binding sites. 2. Identification of a reactive cysteine in the flavin domain of Escherichia coli DNA photolyase., Biochemistry 33(42):12656-64
[57] Ramsey AJ., Alderfer JL., Jorns MS., 1992, Energy transduction during catalysis by Escherichia coli DNA photolyase., Biochemistry 31(31):7134-42
[58] Ramsey AJ., Jorns MS., 1992, Effect of 5-deazaflavin on energy transduction during catalysis by Escherichia coli DNA photolyase., Biochemistry 31(36):8437-41
[59] Sancar A., 2016, Mechanisms of DNA Repair by Photolyase and Excision Nuclease (Nobel Lecture)., Angew Chem Int Ed Engl 55(30):8502-27
[60] Sancar A., Franklin KA., Sancar GB., 1984, Escherichia coli DNA photolyase stimulates uvrABC excision nuclease in vitro., Proc Natl Acad Sci U S A 81(23):7397-401
[61] Sancar A., Rupert CS., 1978, Cloning of the phr gene and amplification of photolyase in Escherichia coli., Gene 4(4):295-308
[62] Sancar GB., Jorns MS., Payne G., Fluke DJ., Rupert CS., Sancar A., 1987, Action mechanism of Escherichia coli DNA photolyase. III. Photolysis of the enzyme-substrate complex and the absolute action spectrum., J Biol Chem 262(1):492-8
[63] Sancar GB., Smith FW., 1989, Interactions between yeast photolyase and nucleotide excision repair proteins in Saccharomyces cerevisiae and Escherichia coli., Mol Cell Biol 9(11):4767-76
[64] Sancar GB., Smith FW., Sancar A., 1985, Binding of Escherichia coli DNA photolyase to UV-irradiated DNA., Biochemistry 24(8):1849-55
[65] Schelvis JP., Zhu X., Gindt YM., 2015, Enzyme-Substrate Binding Kinetics Indicate That Photolyase Recognizes an Extrahelical Cyclobutane Thymidine Dimer., Biochemistry 54(40):6176-85
[66] Schleicher E., Hessling B., Illarionova V., Bacher A., Weber S., Richter G., Gerwert K., 2005, Light-induced reactions of Escherichia coli DNA photolyase monitored by Fourier transform infrared spectroscopy., FEBS J 272(8):1855-66
[67] Svoboda DL., Smith CA., Taylor JS., Sancar A., 1993, Effect of sequence, adduct type, and opposing lesions on the binding and repair of ultraviolet photodamage by DNA photolyase and (A)BC excinuclease., J Biol Chem 268(14):10694-700
[68] Tan C., Guo L., Ai Y., Li J., Wang L., Sancar A., Luo Y., Zhong D., 2014, Direct determination of resonance energy transfer in photolyase: structural alignment for the functional state., J Phys Chem A 118(45):10522-30
[69] Tan C., Liu Z., Li J., Guo X., Wang L., Sancar A., Zhong D., 2015, The molecular origin of high DNA-repair efficiency by photolyase., Nat Commun 6:7302
[70] Wang BY., Jordan SP., Jorns MS., 1988, Identification of a pterin derivative in Escherichia coli DNA photolyase., Biochemistry 27(12):4222-6
[71] Weber S., Mobius K., Richter G., Kay CW., 2001, The electronic structure of the flavin cofactor in DNA photolyase., J Am Chem Soc 123(16):3790-8
[72] Weber S., Richter G., Schleicher E., Bacher A., Mobius K., Kay CW., 2001, Substrate binding to DNA photolyase studied by electron paramagnetic resonance spectroscopy., Biophys J 81(2):1195-204
[73] Wijaya IM., Iwata T., Yamamoto J., Hitomi K., Iwai S., Getzoff ED., Kennis JT., Mathes T., Kandori H., 2014, Flavin adenine dinucleotide chromophore charge controls the conformation of cyclobutane pyrimidine dimer photolyase α-helices., Biochemistry 53(37):5864-75
[74] Wijaya IM., Zhang Y., Iwata T., Yamamoto J., Hitomi K., Iwai S., Getzoff ED., Kandori H., 2013, Detection of distinct α-helical rearrangements of cyclobutane pyrimidine dimer photolyase upon substrate binding by Fourier transform infrared spectroscopy., Biochemistry 52(6):1019-27
[75] Xu L., Mu W., Ding Y., Luo Z., Han Q., Bi F., Wang Y., Song Q., 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(33):8736-43
[76] Xu L., Tian C., Lu X., Ling L., Lv J., Wu M., Zhu G., 2015, Photoreactivation of Escherichia coli is impaired at high growth temperatures., J Photochem Photobiol B 147:37-46
[77] Yamamoto K., 1992, Dissection of functional domains in Escherichia coli DNA photolyase by linker-insertion mutagenesis., Mol Gen Genet 232(1):1-6
[78] Yang K., Matsika S., Stanley RJ., 2007, 6MAP, a fluorescent adenine analogue, is a probe of base flipping by DNA photolyase., J Phys Chem B 111(35):10615-25
[79] Yang K., Stanley RJ., 2006, Differential distortion of substrate occurs when it binds to DNA photolyase: a 2-aminopurine study., Biochemistry 45(37):11239-45
[80] Yang K., Stanley RJ., null, The extent of DNA deformation in DNA photolyase-substrate complexes: a solution state fluorescence study., Photochem Photobiol 84(3):741-9