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4.1.99.3: deoxyribodipyrimidine photo-lyase

This is an abbreviated version!
For detailed information about deoxyribodipyrimidine photo-lyase, go to the full flat file.

Word Map on EC 4.1.99.3

Reaction

cyclobutadipyrimidine (in DNA)
= 2 pyrimidine residues (in DNA)

Synonyms

AMV025, AnPL, AtCry1, AtCry3, AtPL, BcCRY1, BcCRY2, BCIN_05g08060, BCIN_09g01620, BsUvrC, Cc-phr2, CcPL, CDP photolyase, class I CPD photolyase, class I cyclobutane pyrimidine dimer photolyase, class I photolyase, class I PL, class II AtPL, class II CPD photolyase, class II CPD-DNA photolyase, class II CPD-photolyase, class II cyclobutane pyrimidine dimer photolyase, class II DmPL, class II DNA photolyase, class II photolyase, class II PL, class III PL, cold-adapted DNA photolyase, CPD class I photolyase, CPD photolyase, CPD photolyase photolyase, CPD specific photolyase, CPD-class I photolyase, CPD-photolyase, CPD-Phr, CPD-specific DNA photolyase, CPD1, CPD2PHR, CPDI, CPDII, CPDphr, CPH1, CPH1-PHR, CpPL, Cry-DASH, Cry1, Cry2, cry3, CryA, CRYD, cryptochrome 1, cryptochrome 3, CRYPTOCHROME DASH, cryptochrome-3, cryptochrome-DASH, CsPHR, cyclobutane pyrimidine dimer photolyase, cyclobutane pyrimidine dimer PHR, cyclobutane pyrimidine dimer specific photolyase, cyclobutane pyrimidine dimer-class I photolyase, cyclobutane pyrimidine dimer-specific DNA photolyase, cyclobutane pyrimidine dimers photolyase, CYME_CMA044C, cytochrome DASH, DASH cryptochrome, deoxyribodipyrimidine photolyase, deoxyribodipyrimidine photolyase type I enzyme, deoxyribonucleate pyrimidine dimer lyase (photosensitive), deoxyribonucleic cyclobutane dipyrimidine photolyase, deoxyribonucleic photolyase, dipyrimidine photolyase (photosensitive), DmPL, DNA cyclobutane dipyrimidine photolyase, DNA photolyase, DNA photolyase type I enzyme, DNA repair protein photolyase, DNA-photoreactivating enzyme, EcPL, eukaryotic Class II CPD PHR, eukaryotic class II cyclobutane pyrimidine dimer photolyase, lyase, deoxyribonucleate pyrimidine dimer, MmCPDII, MmPL, MM_0852, photolyase, photolyase I, photolyase orthologue, photoreactivating enzyme, PHR, phr A photolyase, PHR1, PHR2, phrA, PhrB, PhrB orthologue, PhrB photolyase, PL, PRE, primase, Saci_1227, ssDNA, ssDNA AtCRY3, ssDNA photolyase, ssDNA PL, SsPL, St-photolyase, tetur12g04440, tetur12g04460, tetur35g00010, tetur35g00030, thymine dimer by photolyase, VcCry1, VcPHR, Ver3Phr, VPA1471, XlCry-DASH

ECTree

     4 Lyases
         4.1 Carbon-carbon lyases
             4.1.99 Other carbon-carbon lyases
                4.1.99.3 deoxyribodipyrimidine photo-lyase

Crystallization

Crystallization on EC 4.1.99.3 - deoxyribodipyrimidine photo-lyase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
cry3 cocrystallized with a thymine dimer-comprising oligonucleotide containing a synthetic CPD-like lesion. When cocrystals are exposed to UV-A at 180 K, a decrease in absorption at 380 nm together with the accumulation of semiquinoid and probably also fully reduced FAD is observed. Initial strong fluorescence emission of 5,10-methenyltetrahydrofolate at 440-460 nm seen for cry3 in solution is decreased in the crystal
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crystallized in 85 mM Na-citrate, pH 4.6, 170 mM NH4- acetate, 21.5% (w/v) PEG 4000, and 15% (v/v) glycerol
photolyase-like domain of Cry1
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crystal structure analysis, structure comparisons, overview
crystal structure of DNA photolyase from Escherichia coli is representative for the entire family. Enzyme is composed of two domains: an N-terminal alpha/beta domain (residues 1-131) and a C-terminal alpha-helical domain (residues 204-471). The two domains are connected by a long and structured interdomain loop. The photoantenna chromophore (MTHF) is located in a shallow groove between the two domains, while the FADH cofactor is deeply buried within the alpha-helical domain and is tightly bound by hydrogen bonds and ionic interactions with at least 14 amino acids. Distance between the photoantenna and the catalytic chromophore is 16.8 A center to center. A surface potential representation of the enzyme reveals the presence of a positively charged groove running nearly two-thirds of the length of the molecule and, lying in the approximate center of the groove, a hole leading to the flavin cofactor.
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crystal structure of Escherichia coli photolyase, overview
crystal structure of photolyase shows that a positively charged groove on the surface of the protein which might interact with the DNA backbone and a hydrophobic cavity locates at the center. The cavity has the right dimension to hold a cis,syn cyclobutane pyrimidine dimer, and Trp277 forms one side wall of it. Photolyase binds DNA chain containing a cyclobutane pyrimidine dimer, flips it out into the cavity, and Trp277 stacks with the 5' side of the cyclobutane pyrimidine dimer by pi-pi interaction
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shows an N-terminal alpha/beta domain and a C-terminal alpha-helical domain
hanging drop vapour diffusion method, crystal structure of the enzyme alone and in complex with cyclobutane pyrimidine dimer lesion-containing duplex DNA
purified enzyme with or without bound cyclobutadipyrimidine-DNA, hanging drop vapour diffusion method, 7.7 mg/ml protein with 0.5 M lithium sulfate and 7.5% w/v PEG 8000, 3-5 days, 4°C, X-ray diffraction structure determination and analysis at 1.5-2.2 A resolution
purified recombinant detagged enzyme, hanging drop vapor diffusion method, protein in 50 mM Tris-HCl (pH 8.0), 50 mM NaCl, 1 mM DTT, and 5% glycerol is mixed with 100 mM sodium cacodylate, pH 6.5, 200 mM ammonium sulfate, and 30% w/v PEG 8000 for crystal form I, and with 32% w/v PEG 4000, 5% urea, 100 mM imidazole/malate, pH 7.4 for crystal form II, 4°C, X-ray diffraction structure determination and analysis at 1.7 A resolution
crystal structure of the protein is determined at 2.8 A resolution with the molecular replacement method. Crystal structure of the St-photolyase is superimposed very well on the three known photolyases from Escherichia coli, Anacystis nidulans and Thermus thermophilus including the catalytic cofactor FAD. Surprisingly, another FAD molecule is found at the position of the light-harvesting cofactor. This second FAD molecule is well accommodated in the crystal structure, suggesting that FAD works as a novel light-harvesting cofactor of photolyase. In addition, two of the four CPD recognition residues in the crystal structure of Anacystis nidulans are not found in St-photolyase, indicating that St-photolyase might recognize cyclobutane pyrimidine dimer with a geometry different from that of Anphotolyase. RCSB PDB accession code: 2E0I
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crystal structure of a DNA photolyase bound to duplex DNA that is bend by 50° and comprises a synthetic cyclobutane pyrimidine dimer lesion. The synthetic cyclobutane pyrimidine dimer lesion is flipped into the active site and split there into two thymines by synchrotron radiation at -173°C. This structure mimics a structural substrate during light-driven DNA repair in which back-flipping of the thymines into duplex DNA has not yet taken place
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hanging-drop vapour-diffusion method. The crystals belong to the tetragonal space group P4(3)2(1)2, with unit-cell parameters a = b = 90.01, c = 134.78 A
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shows an N-terminal alpha/beta domain and a C-terminal alpha-helical domain. In complex with a DNA-duplex containing a synthetic cyclobutane-pyrimidine-dimers lesion analog, which shows that the protein fold changes only marginally upon DNA binding. CPD-photolyase proteins fully open the DNA-duplex structure at the damaged site and flip the dinucleotide lesion out of the duplex into the active site. Lesion comes in close contact (3 A) with the active FADH-cofactor
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structure at 1.8 A resolution
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hexagonal crystals are obtained by the hangingdrop vapor-diffusion method after four days. Coordinates and structure factors of the photolyase-chromophore complexes are deposited in the RCSB protein databank under the accession codes 2J07, 2J08, and 2J09
vapor diffusion method, native enzyme and complexed with thymine