Any feedback?
Information on EC 4.1.99.13 - (6-4)DNA photolyase and Organism(s) Arabidopsis thaliana and UniProt Accession O48652
for references in articles please use BRENDA:EC4.1.99.13Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
EC Tree
4.1.99.13 (6-4)DNA photolyaseIUBMB Comments
A flavoprotein (FAD). The overall repair reaction consists of two distinct steps, one of which is light-independent and the other one light-dependent. In the initial light-independent step, a 6-iminium ion is thought to be generated via proton transfer induced by two histidines highly conserved among the (6-4) photolyases. This intermediate spontaneously rearranges to form an oxetane intermediate by intramolecular nucleophilic attack. In the subsequent light-driven reaction, one electron is believed to be transferred from the fully reduced FAD cofactor (FADH-) to the oxetane intermediate thus forming a neutral FADH radical and an anionic oxetane radical, which spontaneously fractures. The excess electron is then back-transferred to the flavin radical restoring the fully reduced flavin cofactor and a pair of pyrimidine bases .
Specify your search results
Word Map
- 4.1.99.13
- photoproducts
-
cyclobutane
-
uv-induced
-
cryptochromes
-
photoreactivation
-
light-dependent
-
pyrimidone
-
blue-light
-
photorepair
-
oxetane
-
pyrimidine-pyrimidone
-
photoreduction
-
photolesion
-
dash
- ostreococcus
-
four-membered
- fadox
-
photoreception
- cry-dashs
-
dewar
- cryptochrome-dash
The taxonomic range for the selected organisms is: Arabidopsis thaliana
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
(6-4) photolyase, (6-4) phr, (6-4)photolyase, 6-4 photolyase, nf-10, otcpf1, 6-4ciphr, 6-4pp-photolyase, prokaryotic (6-4) photolyase, h64prh, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
reaction mechanism of repair of (6-4) lesions by (6-4) photolyase, detailed overview. The repair-active redox state of the FAD cofactor is fully reduced FADH- and (6-4) PP-containing substrates are bound in a specific manner
(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
The overall repair reaction consists of two distinct steps, one of which is light-independent and the other one light-dependent. In the initial light-independent step, a 6-iminium ion is thought to be generated via proton transfer induced by two histidines highly conserved among the (6-4) photolyases.This intermediate spontaneously rearranges to form an oxetane intermediate by intramolecular nucleophilic attack. In the subsequent light-driven reaction, one electron is believed to be transferred from the fully reduced FAD cofactor (FADH-) to the oxetane intermediate thus forming a neutral FADH radical and an anionic oxetane radical, which spontaneously fractures. The excess electron is then back-transferred to the flavin radical restoring the fully reduced flavin cofactor and a pair of pyrimidine bases
-
(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
ultrafast spectroscopy is used to show that the key step in the repair photocycle is a cyclic proton transfer between the enzyme and the substrate. By femtosecond synchronization of the enzymatic dynamics with the repair function, direct electron transfer from the excited flavin cofactor to the 6-4 photoproduct is observed in 225 ps but fast back electron transfer in 50 ps without repair. The catalytic proton transfer between a histidine residue in the active site and the 6-4 photoproduct, induced by the initial photoinduced electron transfer from the excited flavin cofactor to 6-4 photoproduct, occurs in 425 ps and leads to 6-4 photoproduct repair in tens of nanoseconds
-
SYSTEMATIC NAME
IUBMB Comments
(6-4) photoproduct pyrimidine-lyase
A flavoprotein (FAD). The overall repair reaction consists of two distinct steps, one of which is light-independent and the other one light-dependent. In the initial light-independent step, a 6-iminium ion is thought to be generated via proton transfer induced by two histidines highly conserved among the (6-4) photolyases. This intermediate spontaneously rearranges to form an oxetane intermediate by intramolecular nucleophilic attack. In the subsequent light-driven reaction, one electron is believed to be transferred from the fully reduced FAD cofactor (FADH-) to the oxetane intermediate thus forming a neutral FADH radical and an anionic oxetane radical, which spontaneously fractures. The excess electron is then back-transferred to the flavin radical restoring the fully reduced flavin cofactor and a pair of pyrimidine bases [2].
CAS REGISTRY NUMBER
COMMENTARY
37290-70-3
not distinguished from DNA photolyase, spore photoproduct lyase
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
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
-
-
-
?
deoxyoligonucleotide containing (6-4) photoproduct + H2O
deoxyoligonucleotide containing 2 pyrimidine residues
-
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
-
-
-
-
?
additional information
?
-
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
-
-
?
NATURAL SUBSTRATE
NATURAL 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
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
FAD
in the structure of (6-4) photolyase, there is a phosphate anion bound to Glu-243 and Trp-238, close to FAD
FAD
-
Resonance Raman spectra of (6-4) photolyase having neutral semiquinoid and oxidized forms of FAD. Density functional theory (DFT) calculations are carried out on the neutral semiquinone. The marker band of a neutral semiquinone at 1606 cm-1 in H2O, splits into two comparable bands at 1594 and 1608 cm-1 in D2O, and similarly, that at 1522 cm-1 in H2O does into three bands at 1456, 1508, and 1536 cm-1 in D2O. This D2O effect is recognized only after being oxidized once and photoreduced to form a semiquinone again, but not by simple H/D exchange of solvent. Some Raman bands of the oxidized form are observed at significantly low frequencies (1621, 1576 cm-1) and with band splittings (1508/1493, 1346/1320 cm-1). These Raman spectral characteristics indicate strong H-bonding interactions (at N5-H, N1), a fairly hydrophobic environment, and an electron-lacking feature in benzene ring of the FAD cofactor, which seems to specifically control the reactivity of (6-4) photolyase
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
repair is triggered by non-saturating 100-ps laser flashes
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
additional information
-
it is found that the 6-4 photoreactivating activity is constitutively expressed prior to as well as during the period of repair
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
exposure of DNA to ultraviolet (UV) light from the sun or from other sources causes the formation of harmful and carcinogenic crosslinks between adjacent pyrimidine nucleobases, namely cyclobutane pyrimidine dimers and pyrimidine(6-4)pyrimidone photoproducts. Unique flavoenzymes, called DNA photolyases, utilize blue light, that is photons of lower energy than those of the damaging light, to repair these lesions. The chemically challenging repair of the (6-4) photoproducts by (6-4) photolyase and reaction mechanisms, overview
malfunction
-
in contrast to transgenic mice expressing Potorous tridactylus CPD-photolyase transgenic mice expressing Arabidopsis thaliana (6-4) photolyase do not show any altered circadian behaviour
additional information
two His residues are important in catalysis of enzyme (6-4) PL
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). UVR3_ARATH
556
0
63790
Swiss-Prot
Mitochondrion (Reliability: 4)
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
H364A
-
compared to wild-type mutant similar electron transfer dynamics in the range of 70-260 ps but decay to zero without any long plateaus, H364 is irreplaceable: Steady-state quantum yield measurements reveal a total lack of repair with the mutant
H364D
-
compared to wild-type mutant similar electron transfer dynamics in the range of 70-260 ps but decay to zero without any long plateaus, H364 is irreplaceable: Steady-state quantum yield measurements reveal a total lack of repair with the mutant
H364K
-
compared to wild-type mutant similar electron transfer dynamics in the range of 70-260 ps but decay to zero without any long plateaus, H364 is irreplaceable: Steady-state quantum yield measurements reveal a total lack of repair with the mutant
H364M
-
compared to wild-type mutant similar electron transfer dynamics in the range of 70-260 ps but decay to zero without any long plateaus, H364 is irreplaceable: Steady-state quantum yield measurements reveal a total lack of repair with the mutant
H364N
-
compared to wild-type mutant similar electron transfer dynamics in the range of 70-260 ps but decay to zero without any long plateaus, H364 is irreplaceable: Steady-state quantum yield measurements reveal a total lack of repair with the mutant
H364Y
-
compared to wild-type mutant similar electron transfer dynamics in the range of 70-260 ps but decay to zero without any long plateaus, H364 is irreplaceable: Steady-state quantum yield measurements reveal a total lack of repair with the mutant
additional information
-
light-dependent repair of UV-induced (6-4) photoproducts is investigated in an excision repair-deficient Arabidopsis mutant. It is demonstrated that (6-4) photoproducts are efficiently eliminated in a light-dependent manner which occurs in the presence of blue light (435 nm) but not upon exposure to light of longer wavelengths
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Li, J.; Uchida, T.; Ohta, T.; Todo, T.; Kitagawa, T.
Characteristic structure and environment in FAD cofactor of (6-4) photolyase along function revealed by resonance Raman spectroscopy
J. Phys. Chem. B
110
16724-16732
2006
Arabidopsis thaliana
Chen, J.J.; Mitchell, D.L.; Britt, A.B.
A light-dependent pathway for the elimination of UV-induced pyrimidine (6-4) pyrimidinone photoproducts in Arabidopsis
Plant Cell
6
1311-1317
1994
Arabidopsis thaliana
Hitomi, K.; DiTacchio, L.; Arvai, A.S.; Yamamoto, J.; Kim, S.T.; Todo, T.; Tainer, J.A.; Iwai, S.; Panda, S.; Getzoff, E.D.
Functional motifs in the (6-4) photolyase crystal structure make a comparative framework for DNA repair photolyases and clock cryptochromes
Proc. Natl. Acad. Sci. USA
106
6962-6967
2009
Arabidopsis thaliana (O48652), Arabidopsis thaliana
Mueller, M.; Carell, T.
Structural biology of DNA photolyases and cryptochromes
Curr. Opin. Struct. Biol.
19
277-285
2009
Arabidopsis thaliana (O48652), Drosophila melanogaster
Li, J.; Liu, Z.; Tan, C.; Guo, X.; Wang, L.; Sancar, A.; Zhong, D.
Dynamics and mechanism of repair of ultraviolet-induced (6-4) photoproduct by photolyase
Nature
466
887-890
2010
Arabidopsis thaliana
Chaves, I.; Nijman, R.M.; Biernat, M.A.; Bajek, M.I.; Brand, K.; da Silva, A.C.; Saito, S.; Yagita, K.; Eker, A.P.; van der Horst, G.T.
The potorous CPD photolyase rescues a cryptochrome-deficient mammalian circadian clock
PLoS ONE
6
e23447
2011
Arabidopsis thaliana
EXTERNAL LINKS (specific for EC-Number 4.1.99.13)
Use of this online version of BRENDA is free under the CC BY 4.0 license. See terms of use for full details.
Release 2023.1 (January 2023)
Legal
Curated at
Member of
