4.1.99.13: (6-4)DNA photolyase
This is an abbreviated version!
For detailed information about (6-4)DNA photolyase, go to the full flat file.
Word Map on EC 4.1.99.13
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4.1.99.13
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photoproducts
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cyclobutane
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uv-induced
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cryptochromes
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photoreactivation
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light-dependent
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pyrimidone
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blue-light
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photorepair
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oxetane
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pyrimidine-pyrimidone
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photoreduction
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photolesion
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dash
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ostreococcus
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four-membered
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fadox
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photoreception
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cry-dashs
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dewar
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cryptochrome-dash
- 4.1.99.13
- photoproducts
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cyclobutane
-
uv-induced
-
cryptochromes
-
photoreactivation
-
light-dependent
-
pyrimidone
-
blue-light
-
photorepair
-
oxetane
-
pyrimidine-pyrimidone
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photoreduction
-
photolesion
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dash
- ostreococcus
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four-membered
- fadox
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photoreception
- cry-dashs
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dewar
- cryptochrome-dash
Reaction
Synonyms
(6-4) DNA photolyase, (6-4) photolyase, (6-4) PHR, (6-4) PL, (6-4) PP-specific PL, (6-4)-Phr, (6-4)photolyase, 6-4 DNA photolyase, 6-4 photolyase, 6-4CiPhr, 6-4PP-photolyase, animal (6-4) photolyase, At64, At64PHR, bacterial (6-4) photolyase, CmPHR1, Cry1, CryB, deoxyribodipyrimidine photolyase-related protein, Dm64, DNA photolyase, Ds64PHR, H64PRH, human (6-4) photolyase homologous protein, NF-10, OtCPF1, phr (6-4), PhrB, PL-(6-4), prokaryotic (6-4) photolyase, RSP_3077, TRIREDRAFT_77473, XELAEV_18035355mg, Xl64phr
ECTree
4.1.99.13 (6-4)DNA photolyaseAdvanced search results
results (
results (Substrates Products
Substrates Products on EC 4.1.99.13 - (6-4)DNA photolyase
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SUBSTRATE 
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
cyclobutadipyrimidine in DNA
2 pyrimidine residues in DNA
-
-
?
cyclobutadipyrimidine in herring sperm DNA
2 pyrimidine residues in herring sperm DNA
-
-
?
deoxyoligonucleotide containing (6-4) photoproduct + H2O
deoxyoligonucleotide containing 2 pyrimidine residues
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-
-
?
Dewar photoproduct
?
-
although the affinity of the enzyme for the Dewar photoproduct-containing duplex is similar to that for the (6-4) photoproduct containing substrate a repair rate could not be shown. These results indicate that the (6-4) photolyase binds the DNA containing the Dewar photoproduct and induces a structural change in DNA to some extent, suggesting a difference in the binding mode compared to the (6-4) photoproduct
-
-
?
T(6-4)C photoproduct (in DNA)
2 thymidine + cytosine (in DNA)
-
-
-
-
?
T(6-4)C photoproduct (in DNA)
T-C (in DNA)
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A T(6-4)C photoproduct is synthesized. Differences from T(6-4)T is formation of cytosine hydrates by UV irradiation, and acylation of the amino function with the capping reagent. The capping step is omitted to improve the yield of the desired oligonucleotides. (6-4) photolyase restores the pyrimidines in T(6-4)C to their original structures
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-
?
T(6-4)T photoproduct (in DNA)
2 thymidine resdiues (in DNA)
-
-
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
-
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
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(6-4)TT
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-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
Agrobacterium fabrum C58 / ATCC 33970
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-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
PhrB is active with ssDNA and dsDNA TT (6-4) photoproducts
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
substrates are single stranded or double stranded DNA probe comprising the AGGT(6-4)TGGC or GCGGT(6-4)TGGCG paired with TCGCCAACCGCT. PhrB is active with ssDNA and dsDNA TT (6-4) photoproducts, substrate binding structure, detailed overview. Arg183 is part of the loop region connecting alpha7 and alpha8
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
Agrobacterium tumefaciens C58 / ATCC 33970
PhrB is active with ssDNA and dsDNA TT (6-4) photoproducts
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
Agrobacterium tumefaciens C58 / ATCC 33970
substrates are single stranded or double stranded DNA probe comprising the AGGT(6-4)TGGC or GCGGT(6-4)TGGCG paired with TCGCCAACCGCT. PhrB is active with ssDNA and dsDNA TT (6-4) photoproducts, substrate binding structure, detailed overview. Arg183 is part of the loop region connecting alpha7 and alpha8
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-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
-
-
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
-
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
-
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
Cereibacter sphaeroides ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158
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-
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
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-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
(6-4) photolyases repair (6-4) pyrimidine-pyrimidone photoproducts. CmPHR1 exhibits a repair activity of both (6-4)-ssDNA and (6-4)-dsDNA. Cryptochromes CmPHR2 and CmPHR5 show CPD repair activity only on ssDNA, and have no repair activity when CPD-damaged dsDNA is used as a substrate
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-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
substrate is radio-labeled 48-bp DNA substrates that contains CPD or (6-4) damages within MseI restriction sites (TTAA), pyrimidine(6-4)pyrimidone photoptoducts
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-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
(6-4) photolyases repair (6-4) pyrimidine-pyrimidone photoproducts. CmPHR1 exhibits a repair activity of both (6-4)-ssDNA and (6-4)-dsDNA. Cryptochromes CmPHR2 and CmPHR5 show CPD repair activity only on ssDNA, and have no repair activity when CPD-damaged dsDNA is used as a substrate
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-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
substrate is radio-labeled 48-bp DNA substrates that contains CPD or (6-4) damages within MseI restriction sites (TTAA), pyrimidine(6-4)pyrimidone photoptoducts
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-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
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-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
-
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
-
-
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
-
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
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substrate is a 10-mer oligonucleotide d(HHHHT(6-4)TTHHH), i.e. DHT (6-4)PP 10-mer, where H represents non-absorbing dihydrothymine
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-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
i.e. (6-4) PP
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-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
Xiphophorus maculatus Jp 163 B
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-
-
-
?
T(6-4)T photoproduct (in DNA)
2 thymidine residues (in DNA)
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-
-
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?
additional information
?
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analysis of the repair of a T(6-4)T lesion by the (6-4) PL of Arabidopsis thaliana (At64) by ultrafast fluorescence and transient absorption spectroscopy between 315 and 800 nm. About 90% of the FADH- radicals formed by this primary electron transfer are re-reduced very quickly
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-
?
additional information
?
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the repair function requires to transfer a functional group (OH in the case T(6-4)T) from the 5' to the 3' base, in addition to intradimer bond cleavage
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-
?
additional information
?
-
-
the repair function requires to transfer a functional group (OH in the case T(6-4)T) from the 5' to the 3' base, in addition to intradimer bond cleavage
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-
?
additional information
?
-
the repair function requires to transfer a functional group (OH in the case T(6-4)T) from the 5' to the 3' base, in addition to intradimer bond cleavage
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-
?
additional information
?
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binding and catalytic properties of the enzyme are investigated using natural substrates, T[6-4]T and T[6-4]C, and the Dewar isomer of (6-4) photoproduct and substrate analogs s5T[6-4]T/thietane, mes5T[6-4]T, and the N-methyl-3T thietane analog of the oxetane intermediate. The enzyme binds to the natural substrates and to mes5T[6-4]T with high affinity and produces a DNase I footprint of about 20 base pairs around the photolesion. Of the four substrates that bind with high affinity to the enzyme, T[6-4]T and T[6-4]C are repaired with relatively high quantum yields compared with the Dewar isomer and the mes5T[6-4]T which are repaired with 300-400-fold lower quantum yield
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-
?
additional information
?
-
-
enzyme catalyzes the light-dependent repair of (6-4) photoproducts in Drosophilia melanogaster
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-
?
additional information
?
-
-
can not repair T(Dew)T lesion, direct electron injection into the lesion may be the first step of the repair reaction performed by (6-4) DNA photolyase
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-
?
additional information
?
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by electrophoretic mobility shift assay it is demonstrated that NF-10 binds to UV-irradiated double-stranded DNA but not to unirradiated DNA
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-
?
additional information
?
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cyclobutane pyrimidine dimer-photolyase (EC 4.1.99.3) or 6-4PP-photolyase are able to prevent UV-induced apoptosis in cells deficient for nucleotide excision repair to a similar extent, while in nucleotide excision repair-proficient cells UV-induced apoptosis is prevented only by cyclobutane pyrimidine dimer-photolyase, with no effects observed when pyrimidine-(6-4)-pyrimidone photoproducts are removed by the specific photolyase. Both cyclobutane pyrimidine dimers and pyrimidine-(6-4)-pyrimidone photoproducts contribute to UV-induced apoptosis in nucleotide excision repair-deficient cells, while in nucleotide excision repair-proficient cells, cyclobutane pyrimidine dimers are the only lesions responsible for UV-killing, probably due to the rapid repair of pyrimidine-(6-4)-pyrimidone photoproducts by nucleotide excision repair
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-
?
additional information
?
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Cry1, heterologously expressed and purified from Escherichia coli, is capable of binding to undamaged and 6-4PP damaged DNA. Cry1 repairs 6-4PP, but not CPD and Dewar DNA lesions
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-
?
additional information
?
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Cry1, heterologously expressed and purified from Escherichia coli, is capable of binding to undamaged and 6-4PP damaged DNA. Cry1 repairs 6-4PP, but not CPD and Dewar DNA lesions
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?
additional information
?
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(6-4) photolyase is examined by optical spectroscopy, electron paramagnetic resonance, and pulsed electron nuclear double resonance spectroscopy. It is suggested that His354 and His358 catalyze the formation of the oxetane intermediate that precedes light-initiated DNA repair. At pH 9.5 where the enzyme repair activity is highest His358 is deprotonated, whereas His354 is protonated, acting as the proton donor that initiates oxetane formation from the (6-4) photoproduct
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-
?
additional information
?
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-
2-thio analog of the the (6-4) photoproduct, in which the carbonyl group at the C2 of the 3'pyrimidone is replaced with a thiocarbonyl group, is not repaired by the (6-4) photolyase. Cationic imine analogue of the (6-4) photoproduct, in which the carbonyl group at the C2 of the 3'pyrimidone is replaced with an imine (T(6-4)TNH2), is not repaired by the (6-4) photolyase, even in the presence of a 10 molar excess of the enzyme. 3'carbonyl group of the (6-4) photoproduct is involved in the recognition and reaction of the (6-4) photolyse
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-
?
additional information
?
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imine analogue of the (6-4) photoproduct (T(6-4)TNH2), in which the carbonyl group is replaced with an iminium cation, is not repaired by the (6-4) photolyase, even in the presence of a 10fold molar excess of the enzyme, although the enzyme binds to the oligonucleotide with considerable affinity. Carbonyl group of the 3' pyrimidone ring plays an important role in the (6-4) photolyase reaction
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?
additional information
?
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inability of (6-4) PL to repair the Dewar photoproduct T(Dew) T lesion (formed via an electrocyclic reaction of the 3' pyrimidone ring in (6-4) PPs upon photoexcitation in the 325-nm band of the (6-4) PP), which cannot be attributed to poor substrate binding, as a high affinity for T(Dew)T-containing substrates has been demonstrated. Rather, reversion of the T(Dew)T to the T(6-4)T lesion appears to be inhibited, either by an unfavorable electron transfer from photoexcited FADH- to T(Dew)T. QM/MM calculations of the absorption spectra of different potential reaction intermediates
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?
additional information
?
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polarizable molecular dynamics simulations and constrained density functional theory calculations reveal the energetics of charge migration along the tryptophan tetrad. Migration toward the fourth tryptophan is thermodynamically favorable. Electron transfer mechanisms occur either through an incoherent hopping mechanism or through a multiple sites tunneling process. The Jortner-Bixon formulation of electron transfer (ET) theory is employed to characterize the hopping mechanism, interplay between electron transfer and relaxation of protein and solvent, overview. Electron transfer in (6-4) photolyase proceeds out of equilibrium. Multiple site tunneling is modeled with the recently proposed flickering resonance mechanism
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?
additional information
?
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polarizable molecular dynamics simulations and constrained density functional theory calculations reveal the energetics of charge migration along the tryptophan tetrad. Migration toward the fourth tryptophan is thermodynamically favorable. Electron transfer mechanisms occur either through an incoherent hopping mechanism or through a multiple sites tunneling process. The Jortner-Bixon formulation of electron transfer (ET) theory is employed to characterize the hopping mechanism, interplay between electron transfer and relaxation of protein and solvent, overview. Electron transfer in (6-4) photolyase proceeds out of equilibrium. Multiple site tunneling is modeled with the recently proposed flickering resonance mechanism
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?
