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PDBsum entry 1dnp
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Lyase (carbon-carbon) PDB id
1dnp

 

 

 

 

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Contents
Protein chains
469 a.a. *
Ligands
FAD ×2
MHF ×2
Waters ×373
* Residue conservation analysis
PDB id:
1dnp
Name: Lyase (carbon-carbon)
Title: Structure of deoxyribodipyrimidine photolyase
Structure: DNA photolyase. Chain: a, b. Synonym: DNA cyclobutane dipyrimidine photolyase. Other_details: photoreactivating enzyme
Source: Escherichia coli. Organism_taxid: 562
Resolution:
2.30Å     R-factor:   0.172     R-free:   0.246
Authors: H.-W.Park,A.Sancar,J.Deisenhofer
Key ref: H.W.Park et al. (1995). Crystal structure of DNA photolyase from Escherichia coli. Science, 268, 1866-1872. PubMed id: 7604260 DOI: 10.1126/science.7604260
Date:
03-Jul-95     Release date:   01-Aug-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00914  (PHR_ECOLI) -  Deoxyribodipyrimidine photo-lyase from Escherichia coli (strain K12)
Seq:
Struc: 		472 a.a.
469 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.1.99.3  - deoxyribodipyrimidine photo-lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		EC 4.1.99.3
      Reaction: cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA)
cyclobutadipyrimidine (in DNA)
 = 2 × pyrimidine residues (in DNA)
      Cofactor: 5,10-methenyltetrahydrofolate; FAD
5,10-methenyltetrahydrofolate
FAD
Bound ligand (Het Group name = FAD) corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1126/science.7604260 Science 268:1866-1872 (1995)
PubMed id: 7604260  
 
 
Crystal structure of DNA photolyase from Escherichia coli.
H.W.Park, S.T.Kim, A.Sancar, J.Deisenhofer.
 
  ABSTRACT  
 
Photolyase repairs ultraviolet (UV) damage to DNA by splitting the cyclobutane ring of the major UV photoproduct, the cis, syn-cyclobutane pyrimidine dimer (Pyr <> Pyr). The reaction is initiated by blue light and proceeds through long-range energy transfer, single electron transfer, and enzyme catalysis by a radical mechanism. The three-dimensional crystallographic structure of DNA photolyase from Escherichia coli is presented and the atomic model was refined to an R value of 0.172 at 2.3 A resolution. The polypeptide chain of 471 amino acids is folded into an amino-terminal alpha/beta domain resembling dinucleotide binding domains and a carboxyl-terminal helical domain; a loop of 72 residues connects the domains. The light-harvesting cofactor 5,10-methenyltetrahydrofolylpolyglutamate (MTHF) binds in a cleft between the two domains. Energy transfer from MTHF to the catalytic cofactor flavin adenine dinucleotide (FAD) occurs over a distance of 16.8 A. The FAD adopts a U-shaped conformation between two helix clusters in the center of the helical domain and is accessible through a hole in the surface of this domain. Dimensions and polarity of the hole match those of a Pyr <> Pyr dinucleotide, suggesting that the Pyr <> Pyr "flips out" of the helix to fit into this hole, and that electron transfer between the flavin and the Pyr <> Pyr occurs over van der Waals contact distance.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21469225 A.M.Blanco-Rodríguez, A.J.Di Bilio, C.Shih, A.K.Museth, I.P.Clark, M.Towrie, A.Cannizzo, J.Sudhamsu, B.R.Crane, J.Sýkora, J.R.Winkler, H.B.Gray, S.Záliš, and A.Vlček (2011).
Phototriggering electron flow through Re(I)-modified Pseudomonas aeruginosa azurins.
  Chemistry, 17, 5350-5361.  
21187431 N.Ozturk, C.P.Selby, Y.Annayev, D.Zhong, and A.Sancar (2011).
Reaction mechanism of Drosophila cryptochrome.
  Proc Natl Acad Sci U S A, 108, 516-521.  
20133751 C.W.Chang, L.Guo, Y.T.Kao, J.Li, C.Tan, T.Li, C.Saxena, Z.Liu, L.Wang, A.Sancar, and D.Zhong (2010).
Ultrafast solvation dynamics at binding and active sites of photolyases.
  Proc Natl Acad Sci U S A, 107, 2914-2919.  
  20871655 L.Xu, and G.Zhu (2010).
The Roles of Several Residues of Escherichia coli DNA Photolyase in the Highly Efficient Photo-Repair of Cyclobutane Pyrimidine Dimers.
  J Nucleic Acids, 2010, 0.  
  20981145 R.Morita, S.Nakane, A.Shimada, M.Inoue, H.Iino, T.Wakamatsu, K.Fukui, N.Nakagawa, R.Masui, and S.Kuramitsu (2010).
Molecular mechanisms of the whole DNA repair system: a comparison of bacterial and eukaryotic systems.
  J Nucleic Acids, 2010, 179594.  
20532362 S.Krapf, T.Koslowski, and T.Steinbrecher (2010).
The thermodynamics of charge transfer in DNA photolyase: using thermodynamic integration calculations to analyse the kinetics of electron transfer reactions.
  Phys Chem Chem Phys, 12, 9516-9525.  
19375431 C.Huerta, D.Borek, M.Machius, N.V.Grishin, and H.Zhang (2009).
Structure and mechanism of a eukaryotic FMN adenylyltransferase.
  J Mol Biol, 389, 388-400.
PDB codes: 3fwk 3g59 3g5a 3g6k
19624734 E.Schleicher, R.Bittl, and S.Weber (2009).
New roles of flavoproteins in molecular cell biology: blue-light active flavoproteins studied by electron paramagnetic resonance.
  FEBS J, 276, 4290-4303.  
19228922 J.I.Lucas-Lledó, and M.Lynch (2009).
Evolution of mutation rates: phylogenomic analysis of the photolyase/cryptochrome family.
  Mol Biol Evol, 26, 1143-1153.  
19531478 J.Moldt, R.Pokorny, C.Orth, U.Linne, Y.Geisselbrecht, M.A.Marahiel, L.O.Essen, and A.Batschauer (2009).
Photoreduction of the folate cofactor in members of the photolyase family.
  J Biol Chem, 284, 21670-21683.  
19359474 K.Hitomi, L.DiTacchio, A.S.Arvai, J.Yamamoto, S.T.Kim, T.Todo, J.A.Tainer, S.Iwai, S.Panda, and E.D.Getzoff (2009).
Functional motifs in the (6-4) photolyase crystal structure make a comparative framework for DNA repair photolyases and clock cryptochromes.
  Proc Natl Acad Sci U S A, 106, 6962-6967.
PDB code: 3fy4
19487120 M.Müller, and T.Carell (2009).
Structural biology of DNA photolyases and cryptochromes.
  Curr Opin Struct Biol, 19, 277-285.  
19165842 S.Aoki, Y.Tomiyama, Y.Kageyama, Y.Yamada, M.Shiro, and E.Kimura (2009).
Photolysis of the sulfonamide bond of metal complexes of N-dansyl-1,4,7,10-tetraazacyclododecane in aqueous solution: a mechanistic study and application to the photorepair of cis,syn-cyclobutane thymine photodimer.
  Chem Asian J, 4, 561-573.  
18682397 A.Sancar (2008).
Structure and function of photolyase and in vivo enzymology: 50th anniversary.
  J Biol Chem, 283, 32153-32157.  
18799743 K.B.Henbest, K.Maeda, P.J.Hore, M.Joshi, A.Bacher, R.Bittl, S.Weber, C.R.Timmel, and E.Schleicher (2008).
Magnetic-field effect on the photoactivation reaction of Escherichia coli DNA photolyase.
  Proc Natl Acad Sci U S A, 105, 14395-14399.  
18086248 K.Yang, and R.J.Stanley (2008).
The extent of DNA deformation in DNA photolyase-substrate complexes: a solution state fluorescence study.
  Photochem Photobiol, 84, 741-749.  
18597555 N.Hoang, E.Schleicher, S.Kacprzak, J.P.Bouly, M.Picot, W.Wu, A.Berndt, E.Wolf, R.Bittl, and M.Ahmad (2008).
Human and Drosophila cryptochromes are light activated by flavin photoreduction in living cells.
  PLoS Biol, 6, e160.  
18771290 N.Oztürk, Y.T.Kao, C.P.Selby, I.H.Kavakli, C.L.Partch, D.Zhong, and A.Sancar (2008).
Purification and characterization of a type III photolyase from Caulobacter crescentus.
  Biochemistry, 47, 10255-10261.  
17981903 O.Efimova, and P.J.Hore (2008).
Role of exchange and dipolar interactions in the radical pair model of the avian magnetic compass.
  Biophys J, 94, 1565-1574.  
19074258 R.Pokorny, T.Klar, U.Hennecke, T.Carell, A.Batschauer, and L.O.Essen (2008).
Recognition and repair of UV lesions in loop structures of duplex DNA by DASH-type cryptochrome.
  Proc Natl Acad Sci U S A, 105, 21023-21027.
PDB code: 2vtb
18767842 Y.T.Kao, C.Saxena, T.F.He, L.Guo, L.Wang, A.Sancar, and D.Zhong (2008).
Ultrafast dynamics of flavins in five redox states.
  J Am Chem Soc, 130, 13132-13139.  
18500802 Y.T.Kao, C.Tan, S.H.Song, N.Oztürk, J.Li, L.Wang, A.Sancar, and D.Zhong (2008).
Ultrafast dynamics and anionic active states of the flavin cofactor in cryptochrome and photolyase.
  J Am Chem Soc, 130, 7695-7701.  
17895582 A.Yamamoto, T.Hirouchi, T.Mori, M.Teranishi, J.Hidema, H.Morioka, T.Kumagai, and K.Yamamoto (2007).
Biochemical and biological properties of DNA photolyases derived from utraviolet-sensitive rice cultivars.
  Genes Genet Syst, 82, 311-319.  
17971869 M.Liedvogel, K.Maeda, K.Henbest, E.Schleicher, T.Simon, C.R.Timmel, P.J.Hore, and H.Mouritsen (2007).
Chemical magnetoreception: bird cryptochrome 1a is excited by blue light and forms long-lived radical-pairs.
  PLoS ONE, 2, e1106.  
18419269 N.Oztürk, S.H.Song, S.Ozgür, C.P.Selby, L.Morrison, C.Partch, D.Zhong, and A.Sancar (2007).
Structure and function of animal cryptochromes.
  Cold Spring Harb Symp Quant Biol, 72, 119-131.  
17209014 T.R.Prytkova, D.N.Beratan, and S.S.Skourtis (2007).
Photoselected electron transfer pathways in DNA photolyase.
  Proc Natl Acad Sci U S A, 104, 802-807.  
17438275 X.Yu, D.Shalitin, X.Liu, M.Maymon, J.Klejnot, H.Yang, J.Lopez, X.Zhao, K.T.Bendehakkalu, and C.Lin (2007).
Derepression of the NC80 motif is critical for the photoactivation of Arabidopsis CRY2.
  Proc Natl Acad Sci U S A, 104, 7289-7294.  
17703066 Y.T.Kao, C.Saxena, L.Wang, A.Sancar, and D.Zhong (2007).
Femtochemistry in enzyme catalysis: DNA photolyase.
  Cell Biochem Biophys, 48, 32-44.  
17062752 C.P.Selby, and A.Sancar (2006).
A cryptochrome/photolyase class of enzymes with single-stranded DNA-specific photolyase activity.
  Proc Natl Acad Sci U S A, 103, 17696-17700.  
16391771 Q.H.Song, H.B.Wang, W.J.Tang, Q.X.Guo, and S.Q.Yu (2006).
Model studies of the (6-4) photoproduct photoreactivation: efficient photosensitized splitting of thymine oxetane units by covalently linked tryptophan in high polarity solvents.
  Org Biomol Chem, 4, 291-298.  
17051659 T.Klar, G.Kaiser, U.Hennecke, T.Carell, A.Batschauer, and L.O.Essen (2006).
Natural and non-natural antenna chromophores in the DNA photolyase from Thermus thermophilus.
  Chembiochem, 7, 1798-1806.
PDB codes: 2j07 2j08 2j09
17101984 Y.Huang, R.Baxter, B.S.Smith, C.L.Partch, C.L.Colbert, and J.Deisenhofer (2006).
Crystal structure of cryptochrome 3 from Arabidopsis thaliana and its implications for photolyase activity.
  Proc Natl Acad Sci U S A, 103, 17701-17706.
PDB code: 2ijg
16944231 Y.Yamada, and S.Aoki (2006).
Efficient cycloreversion of cis,syn-thymine photodimer by a Zn2+ -1,4,7,10-tetraazacyclododecane complex bearing a lumiflavin and tryptophan by chemical reduction and photoreduction of a lumiflavin unit.
  J Biol Inorg Chem, 11, 1007-1023.  
16614917 Y.Yi, C.Yi, L.Qian, L.Min, C.Long, B.Linhan, Y.Zhirong, and Q.Dairong (2006).
Cloning and sequence analysis of the gene encoding (6-4)photolyase from Dunaliella salina.
  Biotechnol Lett, 28, 309-314.  
16164372 C.L.Partch, and A.Sancar (2005).
Photochemistry and photobiology of cryptochrome blue-light photopigments: the search for a photocycle.
  Photochem Photobiol, 81, 1291-1304.  
15892880 C.Lin, and T.Todo (2005).
The cryptochromes.
  Genome Biol, 6, 220.  
16235198 C.W.Kay, E.Schleicher, K.Hitomi, T.Todo, R.Bittl, and S.Weber (2005).
Determination of the g-matrix orientation in flavin radicals by high-field/high-frequency electron-nuclear double resonance.
  Magn Reson Chem, 43, S96-102.  
15819881 E.Schleicher, B.Hessling, V.Illarionova, A.Bacher, S.Weber, G.Richter, and K.Gerwert (2005).
Light-induced reactions of Escherichia coli DNA photolyase monitored by Fourier transform infrared spectroscopy.
  FEBS J, 272, 1855-1866.  
16302973 H.Tanida, E.Tahara, M.Mochizuki, Y.Yamane, and M.Ryoji (2005).
Purification, cDNA cloning, and expression profiles of the cyclobutane pyrimidine dimer photolyase of Xenopus laevis.
  FEBS J, 272, 6098-6108.  
16043698 M.C.DeRosa, A.Sancar, and J.K.Barton (2005).
Electrically monitoring DNA repair by photolyase.
  Proc Natl Acad Sci U S A, 102, 10788-10792.  
15889177 M.G.Friedel, M.K.Cichon, and T.Carell (2005).
Model compounds for (6-4) photolyases: a comparative flavin induced cleavage study of oxetanes and thietanes.
  Org Biomol Chem, 3, 1937-1941.  
16169906 Y.T.Kao, C.Saxena, L.Wang, A.Sancar, and D.Zhong (2005).
Direct observation of thymine dimer repair in DNA by photolyase.
  Proc Natl Acad Sci U S A, 102, 16128-16132.  
15300832 A.A.Henry, R.Jimenez, D.Hanway, and F.E.Romesberg (2004).
Preliminary characterization of light harvesting in E. coli DNA photolyase.
  Chembiochem, 5, 1088-1094.  
15299148 C.A.Brautigam, B.S.Smith, Z.Ma, M.Palnitkar, D.R.Tomchick, M.Machius, and J.Deisenhofer (2004).
Structure of the photolyase-like domain of cryptochrome 1 from Arabidopsis thaliana.
  Proc Natl Acad Sci U S A, 101, 12142-12147.
PDB codes: 1u3c 1u3d
15268493 F.Volcov, and C.Goldman (2004).
The efficiency of photolyase and indole complexes to repair DNA containing dimers of pyrimidine: a theoretical analysis of the electron transfer reactions.
  J Chem Phys, 120, 3381-3386.  
15147276 H.Daiyasu, T.Ishikawa, K.Kuma, S.Iwai, T.Todo, and H.Toh (2004).
Identification of cryptochrome DASH from vertebrates.
  Genes Cells, 9, 479-495.  
15121904 J.H.Lee, C.J.Park, J.S.Shin, T.Ikegami, H.Akutsu, and B.S.Choi (2004).
NMR structure of the DNA decamer duplex containing double T*G mismatches of cis-syn cyclobutane pyrimidine dimer: implications for DNA damage recognition by the XPC-hHR23B complex.
  Nucleic Acids Res, 32, 2474-2481.
PDB codes: 1pib 1snh
15298678 K.Sanada, Y.Harada, M.Sakai, T.Todo, and Y.Fukada (2004).
Serine phosphorylation of mCRY1 and mCRY2 by mitogen-activated protein kinase.
  Genes Cells, 9, 697-708.  
15472947 L.M.Kundu, U.Linne, M.Marahiel, and T.Carell (2004).
RNA is more UV resistant than DNA: the formation of UV-induced DNA lesions is strongly sequence and conformation dependent.
  Chemistry, 10, 5697-5705.  
15213381 R.Kort, H.Komori, S.Adachi, K.Miki, and A.Eker (2004).
DNA apophotolyase from Anacystis nidulans: 1.8 A structure, 8-HDF reconstitution and X-ray-induced FAD reduction.
  Acta Crystallogr D Biol Crystallogr, 60, 1205-1213.
PDB codes: 1owl 1owm 1own 1owo 1owp
12730688 B.Giovani, M.Byrdin, M.Ahmad, and K.Brettel (2003).
Light-induced electron transfer in a cryptochrome blue-light photoreceptor.
  Nat Struct Biol, 10, 489-490.  
14596623 B.K.Muralidhara, and P.Wittung-Stafshede (2003).
Can cofactor-binding sites in proteins be flexible? Desulfovibrio desulfuricans flavodoxin binds FMN dimer.
  Biochemistry, 42, 13074-13080.  
14503000 C.Lin, and D.Shalitin (2003).
Cryptochrome structure and signal transduction.
  Annu Rev Plant Biol, 54, 469-496.  
12846824 J.P.Bouly, B.Giovani, A.Djamei, M.Mueller, A.Zeugner, E.A.Dudkin, A.Batschauer, and M.Ahmad (2003).
Novel ATP-binding and autophosphorylation activity associated with Arabidopsis and human cryptochrome-1.
  Eur J Biochem, 270, 2921-2928.  
12835419 M.Byrdin, A.P.Eker, M.H.Vos, and K.Brettel (2003).
Dissection of the triple tryptophan electron transfer chain in Escherichia coli DNA photolyase: Trp382 is the primary donor in photoactivation.
  Proc Natl Acad Sci U S A, 100, 8676-8681.  
12456887 H.Park, K.Zhang, Y.Ren, S.Nadji, N.Sinha, J.S.Taylor, and C.Kang (2002).
Crystal structure of a DNA decamer containing a cis-syn thymine dimer.
  Proc Natl Acad Sci U S A, 99, 15965-15970.
PDB codes: 1mv7 1n4e 1sm5 1t4i
12194212 J.C.Sutherland (2002).
Biological effects of polychromatic light.
  Photochem Photobiol, 76, 164-170.  
11818067 O.Froy, D.C.Chang, and S.M.Reppert (2002).
Redox potential: differential roles in dCRY and mCRY1 functions.
  Curr Biol, 12, 147-152.  
11805294 S.Weber, C.W.Kay, H.Mögling, K.Möbius, K.Hitomi, and T.Todo (2002).
Photoactivation 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 U S A, 99, 1319-1322.  
11707580 H.Komori, R.Masui, S.Kuramitsu, S.Yokoyama, T.Shibata, Y.Inoue, and K.Miki (2001).
Crystal structure of thermostable DNA photolyase: pyrimidine-dimer recognition mechanism.
  Proc Natl Acad Sci U S A, 98, 13560-13565.
PDB codes: 1iqr 1iqu
11747820 H.Zhu, and C.B.Green (2001).
A putative flavin electron transport pathway is differentially utilized in Xenopus CRY1 and CRY2.
  Curr Biol, 11, 1945-1949.  
11260499 J.L.Weller, G.Perrotta, M.E.Schreuder, A.van Tuinen, M.Koornneef, G.Giuliano, and R.E.Kendrick (2001).
Genetic dissection of blue-light sensing in tomato using mutants deficient in cryptochrome 1 and phytochromes A, B1 and B2.
  Plant J, 25, 427-440.  
11514662 O.Dym, and D.Eisenberg (2001).
Sequence-structure analysis of FAD-containing proteins.
  Protein Sci, 10, 1712-1728.  
11761332 R.J.Stanley (2001).
Advances in flavin and flavoprotein optical spectroscopy.
  Antioxid Redox Signal, 3, 847-866.  
11463661 S.Weber, G.Richter, E.Schleicher, A.Bacher, K.Möbius, and C.W.Kay (2001).
Substrate binding to DNA photolyase studied by electron paramagnetic resonance spectroscopy.
  Biophys J, 81, 1195-1204.  
11578921 T.Carell, L.T.Burgdorf, L.M.Kundu, and M.Cichon (2001).
The mechanism of action of DNA photolyases.
  Curr Opin Chem Biol, 5, 491-498.  
10966452 A.Sancar (2000).
Cryptochrome: the second photoactive pigment in the eye and its role in circadian photoreception.
  Annu Rev Biochem, 69, 31-67.  
10871367 K.Hitomi, K.Okamoto, H.Daiyasu, H.Miyashita, S.Iwai, H.Toh, M.Ishiura, and T.Todo (2000).
Bacterial cryptochrome and photolyase: characterization of two photolyase-like genes of Synechocystis sp. PCC6803.
  Nucleic Acids Res, 28, 2353-2362.  
10923805 M.Hada, K.Hino, G.Buchholz, J.Goss, E.Wellmann, and M.Shin (2000).
Assay of DNA photolyase activity in spinach leaves in relation to cell compartmentation-evidence for lack of DNA photolyase in chloroplasts.
  Biosci Biotechnol Biochem, 64, 1288-1291.  
10318899 C.Aubert, P.Mathis, A.P.Eker, and K.Brettel (1999).
Intraprotein electron transfer between tyrosine and tryptophan in DNA photolyase from Anacystis nidulans.
  Proc Natl Acad Sci U S A, 96, 5423-5427.  
10410797 C.D.Mol, S.S.Parikh, C.D.Putnam, T.P.Lo, and J.A.Tainer (1999).
DNA repair mechanisms for the recognition and removal of damaged DNA bases.
  Annu Rev Biophys Biomol Struct, 28, 101-128.  
10581233 F.Thoma (1999).
Light and dark in chromatin repair: repair of UV-induced DNA lesions by photolyase and nucleotide excision repair.
  EMBO J, 18, 6585-6598.  
10216152 M.H.Vos, and J.L.Martin (1999).
Femtosecond processes in proteins.
  Biochim Biophys Acta, 1411, 1.  
10049308 M.S.Cheung, I.Daizadeh, A.A.Stuchebrukhov, and P.F.Heelis (1999).
Pathways of electron transfer in Escherichia coli DNA photolyase: Trp306 to FADH.
  Biophys J, 76, 1241-1249.  
10447684 O.Kleiner, J.Butenandt, T.Carell, and A.Batschauer (1999).
Class II DNA photolyase from Arabidopsis thaliana contains FAD as a cofactor.
  Eur J Biochem, 264, 161-167.  
9461471 B.Holz, S.Klimasauskas, S.Serva, and E.Weinhold (1998).
2-Aminopurine as a fluorescent probe for DNA base flipping by methyltransferases.
  Nucleic Acids Res, 26, 1076-1083.  
9482948 C.Lin, H.Yang, H.Guo, T.Mockler, J.Chen, and A.R.Cashmore (1998).
Enhancement of blue-light sensitivity of Arabidopsis seedlings by a blue light receptor cryptochrome 2.
  Proc Natl Acad Sci U S A, 95, 2686-2690.  
9789012 D.Ramaiah, Y.Kan, T.Koch, H.Orum, and G.B.Schuster (1998).
Enzymatic reaction with unnatural substrates: DNA photolyase (Escherichia coli) recognizes and reverses thymine [2+2] dimers in the DNA strand of a DNA/PNA hybrid duplex.
  Proc Natl Acad Sci U S A, 95, 12902-12905.  
9788986 J.Jortner, M.Bixon, T.Langenbacher, and M.E.Michel-Beyerle (1998).
Charge transfer and transport in DNA.
  Proc Natl Acad Sci U S A, 95, 12759-12765.  
9845369 P.Emery, W.V.So, M.Kaneko, J.C.Hall, and M.Rosbash (1998).
CRY, a Drosophila clock and light-regulated cryptochrome, is a major contributor to circadian rhythm resetting and photosensitivity.
  Cell, 95, 669-679.  
9759487 R.J.Roberts, and X.Cheng (1998).
Base flipping.
  Annu Rev Biochem, 67, 181-198.  
9845370 R.Stanewsky, M.Kaneko, P.Emery, B.Beretta, K.Wager-Smith, S.A.Kay, M.Rosbash, and J.C.Hall (1998).
The cryb mutation identifies cryptochrome as a circadian photoreceptor in Drosophila.
  Cell, 95, 681-692.  
9635738 S.J.van Noort, K.O.van der Werf, A.P.Eker, C.Wyman, B.G.de Grooth, N.F.van Hulst, and J.Greve (1998).
Direct visualization of dynamic protein-DNA interactions with a dedicated atomic force microscope.
  Biophys J, 74, 2840-2849.  
9685504 Y.Jing, J.F.Kao, and J.S.Taylor (1998).
Thermodynamic and base-pairing studies of matched and mismatched DNA dodecamer duplexes containing cis-syn, (6-4) and Dewar photoproducts of TT.
  Nucleic Acids Res, 26, 3845-3853.  
9188741 A.V.Efimov (1997).
Structural trees for protein superfamilies.
  Proteins, 28, 241-260.  
9032058 D.G.Vassylyev, and K.Morikawa (1997).
DNA-repair enzymes.
  Curr Opin Struct Biol, 7, 103-109.  
9301042 H.S.Black, F.R.deGruijl, P.D.Forbes, J.E.Cleaver, H.N.Ananthaswamy, E.C.deFabo, S.E.Ullrich, and R.M.Tyrrell (1997).
Photocarcinogenesis: an overview.
  J Photochem Photobiol B, 40, 29-47.  
  9371633 J.Sekiguchi, and S.Shuman (1997).
Nick sensing by vaccinia virus DNA ligase requires a 5' phosphate at the nick and occupancy of the adenylate binding site on the enzyme.
  J Virol, 71, 9679-9684.  
  9172339 M.G.Weinbauer, S.W.Wilhelm, C.A.Suttle, and D.R.Garza (1997).
Photoreactivation compensates for UV damage and restores infectivity to natural marine virus communities.
  Appl Environ Microbiol, 63, 2200-2205.  
9045609 P.J.Dandliker, R.E.Holmlin, and J.K.Barton (1997).
Oxidative thymine dimer repair in the DNA helix.
  Science, 275, 1465-1468.  
  9335302 R.Kato, K.Hasegawa, Y.Hidaka, S.Kuramitsu, and T.Hoshino (1997).
Characterization of a thermostable DNA photolyase from an extremely thermophilic bacterium, Thermus thermophilus HB27.
  J Bacteriol, 179, 6499-6503.  
9354758 R.S.Lloyd, and X.Cheng (1997).
Mechanistic link between DNA methyltransferases and DNA repair enzymes by base flipping.
  Biopolymers, 44, 139-151.  
9360600 T.Tamada, K.Kitadokoro, Y.Higuchi, K.Inaka, A.Yasui, P.E.de Ruiter, A.P.Eker, and K.Miki (1997).
Crystal structure of DNA photolyase from Anacystis nidulans.
  Nat Struct Biol, 4, 887-891.
PDB code: 1qnf
8994964 D.G.Vassylyev, and K.Morikawa (1996).
Precluding uracil from DNA.
  Structure, 4, 1381-1385.  
8992511 D.L.Terrian, C.N.Kuhl, I.Tessman, and H.Morrison (1996).
On the roles of urocanic acid in photoimmunosuppression: attempted photorepair of urocanic acid-DNA cyclobutane adducts with DNA photolyase.
  Photochem Photobiol, 63, 898-900.  
8650230 F.C.Christians, and L.A.Loeb (1996).
Novel human DNA alkyltransferases obtained by random substitution and genetic selection in bacteria.
  Proc Natl Acad Sci U S A, 93, 6124-6128.  
8653795 H.S.Subramanya, A.J.Doherty, S.R.Ashford, and D.B.Wigley (1996).
Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7.
  Cell, 85, 607-615.
PDB code: 1a0i
8639745 M.Ahmad, and A.R.Cashmore (1996).
Seeing blue: the discovery of cryptochrome.
  Plant Mol Biol, 30, 851-861.  
8931373 M.P.Scannell, S.R.Yeh, and D.E.Falvey (1996).
Model studies of DNA photorepair: enthalpy of cleavage of a pyrimidine dimer measured by photothermal beam deflection calorimetry.
  Photochem Photobiol, 64, 764-768.  
8672500 R.S.Lipman, and M.S.Jorns (1996).
An unnatural folate stereoisomer is catalytically competent in DNA photolyase.
  Biochemistry, 35, 7968-7973.  
8521494 D.G.Vassylyev, T.Kashiwagi, Y.Mikami, M.Ariyoshi, S.Iwai, E.Ohtsuka, and K.Morikawa (1995).
Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition.
  Cell, 83, 773-782.
PDB code: 1vas
8533156 L.H.Pearl, and R.Savva (1995).
DNA repair in three dimensions.
  Trends Biochem Sci, 20, 421-426.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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