Information on EC 4.1.99.3 - deoxyribodipyrimidine photo-lyase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
4.1.99.3
-
RECOMMENDED NAME
GeneOntology No.
deoxyribodipyrimidine photo-lyase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA)
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C-C-bond cleavage
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-
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SYSTEMATIC NAME
IUBMB Comments
deoxyribocyclobutadipyrimidine pyrimidine-lyase
A flavoprotein (FAD), containing a second chromophore group. The enzyme catalyses the reactivation by light of irradiated DNA. A similar reactivation of irradiated RNA is probably due to a separate enzyme.
CAS REGISTRY NUMBER
COMMENTARY hide
37290-70-3
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
gene CL42_09140; UV-resistant strain isolated from high-altitude Andean lakes in Argentinean Puna, gene CL42_09140
UniProt
Manually annotated by BRENDA team
gene CL42_09140; UV-resistant strain isolated from high-altitude Andean lakes in Argentinean Puna, gene CL42_09140
UniProt
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
strain D9/F6-69
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-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
strain CB15
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-
Manually annotated by BRENDA team
fragment of CPD1; strain SCOH1-5
UniProt
Manually annotated by BRENDA team
fragment of CPD1; strain SCOH1-5
UniProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
strain pMS969
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-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
Frog
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-
-
Manually annotated by BRENDA team
-
UniProt
Manually annotated by BRENDA team
-
UniProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
gene phrB or NGO1707
UniProt
Manually annotated by BRENDA team
gene phrB or NGO1707
UniProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
no acitivity in Haemophilus influenzae
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-
-
Manually annotated by BRENDA team
no activity in Ashbya gossypii
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-
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Manually annotated by BRENDA team
no activity in Caenorhabditis briggsae
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-
-
Manually annotated by BRENDA team
no activity in Caenorhabditis elegans
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-
-
Manually annotated by BRENDA team
no activity in Candida albicans
-
-
-
Manually annotated by BRENDA team
no activity in Cryptococcus neoformans
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-
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Manually annotated by BRENDA team
no activity in Dictyostelium discoideum
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-
-
Manually annotated by BRENDA team
no activity in Guillardia theta
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-
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Manually annotated by BRENDA team
no activity in Homo sapiens
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-
-
Manually annotated by BRENDA team
no activity in mammalia
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-
-
Manually annotated by BRENDA team
no activity in Prochlorococcus marinus
strains MIT 9303, MIT 9313 and CCMP1375
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-
Manually annotated by BRENDA team
no activity in Schizosaccharomyces pombe
-
-
-
Manually annotated by BRENDA team
no activity in Yarrowia lipolytica
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-
-
Manually annotated by BRENDA team
strains W0652 and W0698
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-
Manually annotated by BRENDA team
strain C7366
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-
Manually annotated by BRENDA team
strain C7366
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-
Manually annotated by BRENDA team
strains W0596, W1294, W1729, and W2003
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-
Manually annotated by BRENDA team
subsp. japonica, gene phr
SwissProt
Manually annotated by BRENDA team
pinto bean
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-
Manually annotated by BRENDA team
isolate No.115
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-
Manually annotated by BRENDA team
strain MED4
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-
Manually annotated by BRENDA team
strain MED4
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-
Manually annotated by BRENDA team
isolate 1980
UniProt
Manually annotated by BRENDA team
cv. ACME Broomcorn
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-
Manually annotated by BRENDA team
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UniProt
Manually annotated by BRENDA team
-
UniProt
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
metabolism
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
adenosine 5'-(beta,gamma-imido)triphosphate
?
show the reaction diagram
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Cry1
-
-
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cis,syn-cyclobutane pyrimidine dimer
2 pyrimidine residues
show the reaction diagram
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substrate binding and substrate conformation by isothermal titration calorimetry, overview
-
-
?
cis-syn cyclobutadipyrimidine dimer DNA
pyrimidine residues in DNA
show the reaction diagram
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-
-
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?
cyclobutadipyrimidine (in DNA)
2 pyrimidine residues (in DNA)
show the reaction diagram
cyclobutadipyrimidine in calf thymus DNA
2 pyrimidine residues in calf thymus DNA
show the reaction diagram
-
optimal activity at 400 nm wavelength, no activity at 300 nm, 500 nm and in the dark
-
?
cyclobutadipyrimidine in DNA
2 pyrimidine residues in DNA
show the reaction diagram
cyclobutadipyrimidine in DNA
?
show the reaction diagram
cyclobutadipyrimidine in DNA
pyrimidine residues in DNA
show the reaction diagram
cyclobutadipyrimidine in minichromosomes
2 pyrimidine residues in minichromosomes
show the reaction diagram
-
removes cyclobutane pyrimidine dimers predominantly from the ARS1 region
-
?
cyclobutadipyrimidine in nucleosome DNA
2 pyrimidine residues in nucleosome DNA
show the reaction diagram
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folding of DNA in nucleosomes efficiently protects DNA from being repaired
-
?
cyclobutadipyrimidine in oligodeoxythymidylates
pyrimidine residues in oligodeoxythymidylates
show the reaction diagram
-
minimum size is about 9 residues
-
?
cyclobutadipyrimidine in RNA
2 pyrimidine residues in RNA
show the reaction diagram
cyclobutadipyrimidine in salmon sperm DNA
2 pyrimidine residues in salmon sperm DNA
show the reaction diagram
cyclobutadipyrimidine in yeast urea3 gene
2 pyrimidine residues in yeast urea3 gene
show the reaction diagram
thymine
?
show the reaction diagram
-
-
-
-
?
thymine dimers in AnCPDI and Atcry3 complexes
?
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
cyclobutadipyrimidine (in DNA)
2 pyrimidine residues (in DNA)
show the reaction diagram
cyclobutadipyrimidine in DNA
2 pyrimidine residues in DNA
show the reaction diagram
cyclobutadipyrimidine in DNA
?
show the reaction diagram
cyclobutadipyrimidine in DNA
pyrimidine residues in DNA
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5,10-methenyltetrahydrofolate
5,10-methenyltetrahydropterolypolyglutamate
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5,10-methylenetetrahydrofolate
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antenna pigment in Escherichia coli absorbs blue/near UV light and transfers the excitation energy fast and efficiently to FADH-
5-deazaflavin
7,8-didemethyl-8-hydroxy-5-deazaflavin
7,8-didemethyl-8-hydroxy-5-deazariboflavin
8-hydroxy-5-deazaflavin
8-hydroxy-5-deazariboflavin
8-hydroxy-7,8-didemethyl-5-deazariboflavin
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antenna pigment in Anacystis nidulans absorbs blue/near UV light and transfers the excitation energy fast and efficiently to FADH-
8-iodo-8-demethylriboflavin
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8-iodoflavin
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chromophore binding site of Thermus photolyase is reconstited also with a novel synthetic flavin, 8-iodoflavin
ATP
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stimulates, utilization of ATP for the photorepair process of the pyrimidine dimer containing DNA, not only an allosteric effector
deazaflavin
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antenna cofactor
flavin
folate
methenyltetrahydrofolate
pterin
additional information
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light-driven blue light flavophotoreceptors all operate from the excited state, whether singlet oxidized (e.g., BLUF and LOV domains) or doublet semiquinone
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Fe
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conserved Fe-S domain at the C-terminus of PriL
additional information
-
no requirement for divalent cations
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
azelastine
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clomifene
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desloratidine
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fenofibrate
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ferricyanide
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blue light irradiation converts fully oxidized FAD to the semiquinone state, but in the presence of ferricyanide as electron acceptor further photoreduction to the fully reduced catalytically active form FADH- is inhibited
lornoxicam
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N-bromosuccinimide
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Prednisone
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RNA polymerase II
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RNA polymerase III
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transcription by RNAPII and RNAPIII slows down the repair by photolyase on the transcribed strands
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rupatadine
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transcription
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transcription inhibits access of enzyme to its substrate
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Triamcinolone
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yeast DNA
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inhibition due to inferences in the binding of photolyase with UV-irradiated DNA by yeast RNA
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additional information
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
4a,5-reduced flavin
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chromophore, enzyme I
5,10-methenyltetrahydrofolate
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binds to the enzyme and acts as a light-harvesting pigment
5,10-methenyltetrahydrofolic acid
5,10-methenyltetrahydrofolylpolyglutamate
-
light-harvesting cofactor
blue-light regulator 2
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the blue-light regulator 2 gene is involved in near-ultraviolet radiation-enhanced PHR1 gene expression
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FADH2
additional information
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0001
cis-syn cyclobutadipyrimidine dimer DNA
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-
additional information
additional information
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.073 - 0.23
cyclobutadipyrimidine in DNA
0.04
pyrimidine dimer in DNA
Escherichia coli
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-
additional information
additional information
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
additional information
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drug ligand binding follows pseudo-first-order kinetics, equivalent and independent for all binding sites, theoretical docking and dissociation constants, overview
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 8.6
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pH 6.0: 45% of maximal activity, pH 8.6: about 35% of maximal activity
6.8 - 8.1
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pH 6.8: 49% of maximal activity, pH 8.1: about 29% of maximal activity
7 - 10
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about 50% activity at pH 7, about 75% activity at pH 10
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
20
-
assay at
30
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assay at
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
15 - 37
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decrease in photoreactivation capacity with increasing temperature
additional information
-
temperature dependence of the binding enthalpy for dsDNA and damaged DNA, overview
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
-
Manually annotated by BRENDA team
low expression
Manually annotated by BRENDA team
the enzyme is expressed in the infectious spore stage
Manually annotated by BRENDA team
additional information
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
-
non-fused PHR1-EGFP is distributed homogeneously over the cytoplasm and the nucleus at all time points analysed, as shown for 96 h post-transfection. PHR2-EGFP fusion protein is distributed over the cytoplasm and nucleus but, over time, it becomes localized predominantly in the nucleus
Manually annotated by BRENDA team
additional information