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Information on EC 1.13.12.18 - dinoflagellate luciferase
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1.13.12.18 dinoflagellate luciferaseIUBMB Comments
A luciferase from dinoflagellates such as Gonyaulax polyedra, Lingulodinium polyedrum, Noctiluca scintillans, and Pyrocystis lunula. It is a single protein with three luciferase domains. The luciferin is strongly bound by a luciferin binding protein above a pH of 7.
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Word Map
- 1.13.12.18
-
bioluminescence
-
emit
-
lingulodinium
- gonyaulax
-
luminescence
- tetrapyrrole
- polyedrum
- luciferases
- alexandrium
-
circadian
-
clap
-
whitting
- fundyense
- spinifera
-
pyrocystis
-
open-chain
-
naked
- flash
-
intramolecularly
-
ph-activity
- lunula
-
interspecific
-
light-emitting
- catenella
-
genus-specific
- biotechnology
The enzyme appears in viruses and cellular organisms
Reaction Schemes
Synonyms
dinoflagellate luciferase, d2-lcf, d3-lcf, 
more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
LCF
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
dinoflagellate luciferin + O2 = oxidized dinoflagellate luciferin + H2O + hnu
-
-
-
-
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PATHWAY SOURCE
PATHWAYS
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-
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SYSTEMATIC NAME
IUBMB Comments
dinoflagellate-luciferin:oxygen 132-oxidoreductase
A luciferase from dinoflagellates such as Gonyaulax polyedra, Lingulodinium polyedrum, Noctiluca scintillans, and Pyrocystis lunula. It is a single protein with three luciferase domains. The luciferin is strongly bound by a luciferin binding protein above a pH of 7.
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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
dinoflagellate luciferin + O2
oxidized dinoflagellate luciferin + H2O + hnu
-
-
-
-
?
additional information
?
-
each of the three domains of Lingulodinium polyedrum luciferase encodes an active luciferase that catalyzes the oxidation of a chlorophyll-derived open tetrapyrrole (dinoflagellate luciferin) to produce blue light
-
-
?
dinoflagellate luciferin + O2
oxidized dinoflagellate luciferin + H2O + hv
-
-
-
-
?
dinoflagellate luciferin + O2
oxidized dinoflagellate luciferin + H2O + hv
-
-
-
-
ir
dinoflagellate luciferin + O2
oxidized dinoflagellate luciferin + H2O + hv
-
-
-
?
dinoflagellate luciferin + O2
oxidized dinoflagellate luciferin + H2O + hv
-
-
-
-
?
dinoflagellate luciferin + O2
oxidized dinoflagellate luciferin + H2O + hv
-
-
-
-
?
dinoflagellate luciferin + O2
oxidized dinoflagellate luciferin + H2O + hv
-
-
-
?
dinoflagellate luciferin + O2
oxidized dinoflagellate luciferin + H2O + hv
-
-
-
-
?
dinoflagellate luciferin + O2
oxidized dinoflagellate luciferin + H2O + hv
-
-
-
-
?
dinoflagellate luciferin + O2
oxidized dinoflagellate luciferin + H2O + hv
-
-
-
-
?
dinoflagellate luciferin + O2
oxidized dinoflagellate luciferin + H2O + hv
-
-
-
-
?
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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
dinoflagellate luciferin + O2
oxidized dinoflagellate luciferin + H2O + hnu
-
-
-
-
?
additional information
?
-
each of the three domains of Lingulodinium polyedrum luciferase encodes an active luciferase that catalyzes the oxidation of a chlorophyll-derived open tetrapyrrole (dinoflagellate luciferin) to produce blue light
-
-
?
dinoflagellate luciferin + O2
oxidized dinoflagellate luciferin + H2O + hv
-
-
-
-
?
dinoflagellate luciferin + O2
oxidized dinoflagellate luciferin + H2O + hv
-
-
-
?
dinoflagellate luciferin + O2
oxidized dinoflagellate luciferin + H2O + hv
-
-
-
-
?
dinoflagellate luciferin + O2
oxidized dinoflagellate luciferin + H2O + hv
-
-
-
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ca2+
Mg2+
Mn2+
additional information
-
luciferase is not a Mn2+, Mg2+ , or Ca2+ metalloprotein
Ca2+
-
increases the flash height and the total light emitted by dinoflagellate luciferase
Ca2+
-
increases the flash height and the total light emitted by dinoflagellate luciferase
Ca2+
-
increases the flash height and the total light emitted by dinoflagellate luciferase
Mg2+
-
increases the flash height and the total light emitted by dinoflagellate luciferase
Mg2+
-
increases the flash height and the total light emitted by dinoflagellate luciferase
Mg2+
-
increases the flash height and the total light emitted by dinoflagellate luciferase
Mn2+
-
increases the flash height and the total light emitted by dinoflagellate luciferase
Mn2+
-
increases the flash height and the total light emitted by dinoflagellate luciferase
Mn2+
-
increases the flash height and the total light emitted by dinoflagellate luciferase
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
-
after a 15 min incubation at pH 8.0 and 20°C with subtilisin, trypsin, chymotrypsin, pepsin, carboxypeptidase, and leucine aminopeptidase, the flash height measured in the presence of saturating luciferin is 50% lowered and, after 1 h, the flash height is 10% of the control. Moreover, proteolysis of the extracts completely inactivates the luciferase
-
additional information
-
after a 15 min incubation at pH 8.0 and 20°C with subtilisin, trypsin, chymotrypsin, pepsin, carboxypeptidase, and leucine aminopeptidase, the flash height measured in the presence of saturating luciferin is 50% lowered and, after 1 h, the flash height is 10% of the control. Moreover, proteolysis of the extracts completely inactivates the luciferase
-
additional information
-
after a 15 min incubation at pH 8.0 and 20°C with subtilisin, trypsin, chymotrypsin, pepsin, carboxypeptidase, and leucine aminopeptidase, the flash height measured in the presence of saturating luciferin is 50% lowered and, after 1 h, the flash height is 10% of the control. Moreover, proteolysis of the extracts completely inactivates the luciferase
-
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0025
dinoflagellate luciferin
-
in 0.2 M sodium phosphate, 0.25 mM EDTA, 0.1 mg/ml of bovine serum albumin at pH 6.3, temperature not specified in the publication
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
-
the crude extract has a specific activity of 0.000000258 at pH 8.0 and 20°C and the purified enzyme shows a specific activity of 0.00000348 quanta/min/mg at pH 8.0 and 20°C
additional information
-
the crude extract has a specific activity of 0.000000258 at pH 8.0 and 20°C and the purified enzyme shows a specific activity of 0.00000348 quanta/min/mg at pH 8.0 and 20°C
additional information
-
the crude extract has a specific activity of 0.000000258 at pH 8.0 and 20°C and the purified enzyme shows a specific activity of 0.00000348 quanta/min/mg at pH 8.0 and 20°C
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6.3
additional information
6
-
the optimum pH of Lingulodinium polyedrum luciferase and for each of its domains is approximately 6.0
6
constant pH accelerated molecular dynamics (CpHaMD) is applied to investigate the conformational changes associated with the activation of the enzyme (LCF) upon acidification. The protonation of several residues, including the previously identifies intramolecularly conserved histidines and the H1064/H1065 dyad, correlates with a large scale conformational change in which the N-terminal domain reorganizes to allow the substrate access to the active site
additional information
the oxidation of luciferin by Dinoflagellates luciferase only takes place at low pH. Computational tools are used to predict the open structure of the luciferase in Lingulodinium polyedra and to decipher the nature of the opening mechanism. Through accelerated molecular dynamics simulations, it is demonstrated that the closed-open conformational change likely takes place via a tilt of the pH-regulatory helix-loop-helix domain. It is proposed that the molecular basis for the transition is electrostatic repulsion between histidine-cation pairs, which destabilizes the closed conformation at low pH
additional information
-
the oxidation of luciferin by Dinoflagellates luciferase only takes place at low pH. Computational tools are used to predict the open structure of the luciferase in Lingulodinium polyedra and to decipher the nature of the opening mechanism. Through accelerated molecular dynamics simulations, it is demonstrated that the closed-open conformational change likely takes place via a tilt of the pH-regulatory helix-loop-helix domain. It is proposed that the molecular basis for the transition is electrostatic repulsion between histidine-cation pairs, which destabilizes the closed conformation at low pH
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
20
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5.7
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
bioluminescent dinoflagellates isolated from the Patagonian Shelf region surface water
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-
brenda
formerly Gonyaulax polyedra
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-
brenda
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
cytoplasmic dense bodies with a finely vermiculate texture
brenda
-
cytoplasmic dense bodies with a finely vermiculate texture
-
brenda
-
the space between the crystalline shaft and the sheaths of mature trichocysts
brenda
-
the space between the crystalline shaft and the sheaths of mature trichocysts
-
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
-
in Lingulodinium polyedrum, three components are involved in luminescence: the enzyme luciferase, the substrate luciferin, and a luciferin-binding protein which protects luciferin from autoxidation
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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). LUCIF_LINPO
1241
0
136889
Swiss-Prot
other Location (Reliability: 1)
A0A6M5KB06_NOCSC
664
0
74161
TrEMBL
other Location (Reliability: 1)
A0A1V0D946_PYRLU
102
0
11141
TrEMBL
other Location (Reliability: 3)
A0A6M5K9T0_NOCSC
664
0
74043
TrEMBL
other Location (Reliability: 1)
A0A6M5K9P1_NOCSC
664
0
74096
TrEMBL
other Location (Reliability: 1)
A0A1V0D947_PYRLU
102
0
11245
TrEMBL
other Location (Reliability: 2)
A0A1V0D945_PYRLU
102
0
11259
TrEMBL
other Location (Reliability: 2)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
130000
137000
40000
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homotrimer
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
domains D2-LCF and D3-LCF, sitting drop vapor diffusion method, using 13% (w/v) PEG 10000, 0.075 M bicine pH 7.7, 25% (v/v) glycerol for domain D2-LCF and 18-20% methyl ether PEG 2000, 100 mM EPPS buffer pH 7.8-8.4 for domain D3-LCF
-
Lingulodinium polyedrum luciferase domain 3, vapor diffusion method, using 18-20% (w/v) polyethylene glycol 2000 methyl ether and 100 mM (2-hydroxyethyl)piperazine-N-(3-propanesulfonic acid) (pH 8.0)
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
-
deletion mutants for N-terminal region of domain 3 of the luciferase show above 20% of wild type activity, the activities of C-terminal deleted mutants decrease drastically to below 1% of wild type
additional information
-
for each luciferase domain (D1, D2, D3) the removal of approximately 50 N-terminal amino acids results in an increase in the ratio of luciferase activity at pH 8.0 relative to that at pH 6.3. At pH 8.0, peptides D1167-486, D2535-897, and D3927-1241, lacking the first 55, 47, and 62 amino acids of their N-termini retain about 40%, 50%, and 70% of the pH 6.3 luciferase activity, respectively
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6.7 - 8
8
-
the activity of the full-length native enzyme drops to near zero at pH 8.0, the activity of domain fragments also peaks at pH 6.3 but remains high at 8.0
711192
6.7 - 8
-
the crude enzyme extracts are more stable at pH 8.0 and 5°C in HEPES buffer than at pH 6.7 and 5°C
710987
6.7 - 8
-
the crude enzyme extracts are more stable at pH 8.0 and 5°C in HEPES buffer than at pH 6.7 and 5°C
710987
6.7 - 8
-
the crude enzyme extracts are more stable at pH 8.0 and 5°C in HEPES buffer than at pH 6.7 and 5°C
710987
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
20 - 40
20 - 40
-
at 20°C the luciferase is progressively inactivated after a 4 h incubation time at each pH, about 50% residual activity is observed at 30°C, the enzyme appears completely inactive at 40°C and pH 7.9 and shows about 10% residual activity at 40°C and pH 6.7
20 - 40
-
at 20°C the luciferase is progressively inactivated after a 4 h incubation time at each pH, about 50% residual activity is observed at 30°C, the enzyme appears completely inactive at 40°C and pH 7.9 and shows about 10% residual activity at 40°C and pH 6.7
20 - 40
-
at 20°C the luciferase is progressively inactivated after a 4 h incubation time at each pH, about 50% residual activity is observed at 30°C, the enzyme appears completely inactive at 40°C and pH 7.9 and shows about 10% residual activity at 40°C and pH 6.7
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ORGANIC SOLVENT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
guanidine-HCl
urea
guanidine-HCl
-
at 18 and 5°C guanidine-HCl in the concentration range from 2-6 M, denatures irreversibly the luciferase. Luciferin does not protect the luciferase against denaturation by this agent
guanidine-HCl
-
at 18°C and 5°C guanidine-HCl in the concentration range from 2-6 M, denatures irreversibly the luciferase. Luciferin does not protect the luciferase against denaturation by this agent
guanidine-HCl
-
at 18 and 5°C guanidine-HCl in the concentration range from 2-6 M, denatures irreversibly the luciferase. Luciferin does not protect the luciferase against denaturation by this agent
urea
-
at 18 and 5°C urea in the concentration range from 2-8 M, denatures irreversibly the luciferase. Luciferin does not protect the luciferase against denaturation by this agent
urea
-
at 18°C and 5°C urea in the concentration range from 2-8 M, denatures irreversibly the luciferase. Luciferin does not protect the luciferase against denaturation by this agent
urea
-
at 18 and 5°C urea in the concentration range from 2-8 M, denatures irreversibly the luciferase. Luciferin does not protect the luciferase against denaturation by this agent
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
ammonium sulfate precipitation and DEAE-Bio-Gel A column chromatography
-
ammonium sulfate precipitation, Chelex column chromatography, hydroxylapatite column chromatography, and Ultrogel gel filtration
ammonium sulfate precipitation, Chelex column chromatography, hydroxylapatite column chromatography, and Ultrogel gel filtration
-
ammonium sulfate precipitation, Chelex column chromatography, hydroxylapatite column chromatography, and Ultrogel gel filtration
-
ammonium sulfate precipitation, Chelex column chromatography, hydroxylapatite column chromatography, and Ultrogel gel filtration
-
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
deletion mutants for N- or C-terminal regions of domain 3 of the luciferase are expressed in Escherichia coli BL21(DE3) cells
-
DNA and amino acid sequence determination and analysis of diverse samples
-
histidine-tagged Lingulodinium polyedrum luciferase domain 3 is expressed in Escherichia coli BL21(DE3) cells
the three intramolecularly homologous domains are separately cloned and expressed in Escherichia coli JM109 cells as fusion proteins
-
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
dinoflagellate luciferase activity is highest during the early night phase
luciferase activity in cell-free extracts of Gonyaulax polyedm undergoes a cyclic daily change such that activities of extracts made in the middle of the night phase may be 10 times greater than in extracts of day phase cells. The circadian rhythm of luciferase activity is a result of biological clock-controlled synthesis and/or degradation of the luciferase polypeptide
dinoflagellate luciferase activity is highest during the early night phase
dinoflagellate luciferase activity is highest during the early night phase
-
-
luciferase activity in cell-free extracts of Gonyaulax polyedm undergoes a cyclic daily change such that activities of extracts made in the middle of the night phase may be 10 times greater than in extracts of day phase cells. The circadian rhythm of luciferase activity is a result of biological clock-controlled synthesis and/or degradation of the luciferase polypeptide
-
luciferase activity in cell-free extracts of Gonyaulax polyedm undergoes a cyclic daily change such that activities of extracts made in the middle of the night phase may be 10 times greater than in extracts of day phase cells. The circadian rhythm of luciferase activity is a result of biological clock-controlled synthesis and/or degradation of the luciferase polypeptide
-
-
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APPLICATION
ORGANISM