Any feedback?
Please rate this page
(enzyme.php)
(0/150)

BRENDA support

BRENDA Home
show all | hide all No of entries

Information on EC 4.1.99.3 - deoxyribodipyrimidine photo-lyase and Organism(s) Thermus thermophilus and UniProt Accession P61497

for references in articles please use BRENDA:EC4.1.99.3
Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
EC Tree
     4 Lyases
         4.1 Carbon-carbon lyases
             4.1.99 Other carbon-carbon lyases
                4.1.99.3 deoxyribodipyrimidine photo-lyase
IUBMB Comments
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.
Specify your search results
Select one or more organisms in this record: ?
This record set is specific for:
Thermus thermophilus
UNIPROT: P61497
Show additional data
Do not include text mining results
Include (text mining) results
Include results (AMENDA + additional results, but less precise)
Word Map
hide
The taxonomic range for the selected organisms is: Thermus thermophilus
The enzyme appears in selected viruses and cellular organisms
Synonyms
ssdna, primase, photolyase, dna photolyase, cryptochrome 1, cpd photolyase, cry-dash, cpd-photolyase, cryptochrome dash, cyclobutane pyrimidine dimer photolyase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
cyclobutane pyrimidine dimer photolyase
-
CPD-photolyase
-
-
deoxyribodipyrimidine photolyase
-
-
-
-
deoxyribonucleate pyrimidine dimer lyase (photosensitive)
-
-
-
-
deoxyribonucleic cyclobutane dipyrimidine photolyase
-
-
-
-
deoxyribonucleic photolyase
-
-
-
-
dipyrimidine photolyase (photosensitive)
-
-
-
-
DNA cyclobutane dipyrimidine photolyase
-
-
-
-
DNA photolyase
-
-
-
-
DNA-photoreactivating enzyme
-
-
-
-
lyase, deoxyribonucleate pyrimidine dimer
-
-
-
-
photolyase
-
-
-
-
photoreactivating enzyme
-
-
-
-
phr A photolyase
-
-
-
-
PhrB photolyase
-
-
-
-
PRE
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA)
show the reaction diagram
mechanism
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C-C-bond cleavage
-
-
-
-
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
-
SUBSTRATE
PRODUCT                       
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
pyrimidine residues in DNA
show the reaction diagram
NMR study of repair mechanism of DNA photolyase by FAD-induced paramagnetic relaxation enhancement
-
-
?
thymine
?
show the reaction diagram
-
-
-
?
cyclobutadipyrimidine in DNA
pyrimidine residues in DNA
show the reaction diagram
additional information
?
-
enzyme in complex with CPD moiety, molecular docking study
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
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
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
7,8-didemethyl-8-hydroxy-5-deazariboflavin
chromophore binding site of Thermus photolyase is reconstited also with 7,8-didemethyl-8-hydroxy-5-deazariboflavin (8-HDF). However, in the genome sequence of Thermus thermophilus it is found that the genes essential for the biosynthesis of 8-HDF are missing
8-hydroxy-5-deazariboflavin
photolyase can bind next to the natural cofactor 8-hydroxy-5-deazariboflavin also FMN
8-iodo-8-demethylriboflavin
-
8-iodoflavin
chromophore binding site of Thermus photolyase is reconstited also with a novel synthetic flavin, 8-iodoflavin
flavin
flavin-mononucleotide (FMN), crystal strucutre analysis reveals the binding of flavin mononucleotide as an antenna chromophore
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
enzyme structure comparisons and molecular modeling, overview. The enzyme from Thermus thermophilus is thermophile. There is a significant adenine-mediated superexchange contribution to the electron transfer repair reaction when CPD is complexed with the photolyases in Anacystis nidulans (mesophile) and in the two extremophiles (Thermus thermophilus and Solfolobus tokodaii) at their physiological temperatures. In contrast, the predominant electron transfer mechanism in the Escherichia coli photolyase at its physiological temperature (37°C) is direct electron transfer, with only about 3% of the strongest electron transfer pathways mediated by adenine. Role of adenine in the CPD repair, adenine flipping
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
R46E
R46E mutant which lacks a conserved arginine in the binding site for the antenna chromophore shows no flavin-mononucleotide and discloses an eightfold lower activity at 450 nm (blue light) wheras at 370 nm (UV-A light) its activity is only three times lower than wildtype enzyme
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
cells are disrupted by an emulsifier, followed by heat treatment for 15 min at 65°C and centrifugation. Supernatant is purified by using a Blue Sepharose CL-6B affinity column. Recombinant photolyase elutes at a concentration of 1 M KCl in an increasing salt gradient. Fraction containing the protein are combined and concentrated by ultrafiltration. Gel filtration chromatography with Sephacryl S200-HR as a final step give an overal yield of 35 mg of purified CPD-photolyase per liter cell culture
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
cloned in Escherichia coli
expression in Escherichia coli
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
biotechnology
it should be possible to perform wavelength tuning of the Thermus photolyase by using artificial flavin chromophores and photolyase variants whose antenna chromophore-binding sites are reengineered by molecular modeling and mutagenesis
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Kato, R.; Hasegawa, K.; Hidaka, Y.; Kuramitsu, S.; Hoshino, T.
Characterization of a thermostable DNA photolyase from an extremely thermophilic bacterium, Thermus thermophilus HB27
J. Bacteriol.
179
6499-6503
1997
Thermus thermophilus, Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039
Manually annotated by BRENDA team
Komori, H.; Masui, R.; Kuramitsu, S.; Yokoyama, S.; Shibata, T.; Inoue, Y.; Miki, K.
Crystal structure of thermostable DNA photolyase: pyrimidine-dimer recognition mechanism
Proc. Natl. Acad. Sci. USA
98
13560-13565
2001
Thermus thermophilus (P61497), Thermus thermophilus
Manually annotated by BRENDA team
Ueda, T.; Kato, A.; Ogawa, Y.; Torizawa, T.; Kuramitsu, S.; Iwai, S.; Terasawa, H.; Shimada, I.
NMR study of repair mechanism of DNA photolyase by FAD-induced paramagnetic relaxation enhancement
J. Biol. Chem.
279
52574-52579
2004
Thermus thermophilus (P61497), Thermus thermophilus
Manually annotated by BRENDA team
Ueda, T.; Kato, A.; Kuramitsu, S.; Terasawa, H.; Shimada, I.
Identification and characterization of a second chromophore of DNA photolyase from Thermus thermophilus HB27
J. Biol. Chem.
280
36237-36243
2005
Thermus thermophilus (P61497), Thermus thermophilus, Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039 (P61497)
Manually annotated by BRENDA team
Klar, T.; Kaiser, G.; Hennecke, U.; Carell, T.; Batschauer, A.; Essen, L.O.
Natural and non-natural antenna chromophores in the DNA photolyase from Thermus thermophilus
Chembiochem
7
1798-1806
2006
Thermus thermophilus (P61497), Thermus thermophilus
Manually annotated by BRENDA team
Goosen, N.; Moolenaar, G.F.
Repair of UV damage in bacteria
DNA Repair
7
353-379
2008
Synechococcus elongatus PCC 7942 = FACHB-805, Escherichia coli, Thermus thermophilus, no activity in Prochlorococcus marinus
Manually annotated by BRENDA team
Mueller, M.; Carell, T.
Structural biology of DNA photolyases and cryptochromes
Curr. Opin. Struct. Biol.
19
277-285
2009
Synechococcus elongatus PCC 7942 = FACHB-805, Arabidopsis thaliana, Homo sapiens, Sulfurisphaera tokodaii, Escherichia coli (P00914), Thermus thermophilus (P61497)
Manually annotated by BRENDA team
Rousseau, B.J.G.; Shafei, S.; Migliore, A.; Stanley, R.J.; Beratan, D.N.
Determinants of photolyases DNA repair mechanism in Mesophiles and Extremophiles
J. Am. Chem. Soc.
140
2853-2861
2018
Sulfurisphaera tokodaii (F9VNB1), Escherichia coli (P00914), Synechococcus elongatus PCC 7942 = FACHB-805 (P05327), Thermus thermophilus (P61497), Synechococcus elongatus PCC 7942 = FACHB-805 ATCC 27144 / PCC 6301 / SAUG 1402/1 (P05327), Thermus thermophilus HB8 / ATCC 27634 / DSM 579 (P61497), Sulfurisphaera tokodaii DSM 16993 / JCM 10545 / NBRC 100140 / 7 (F9VNB1)
Manually annotated by BRENDA team