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Enzyme Nomenclature
Information on EC 1.3.99.31 - phytoene desaturase (lycopene-forming)
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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
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EC NUMBER 
COMMENTARY 
1.3.99.31
-
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RECOMMENDED NAME
GeneOntology No.
phytoene desaturase (lycopene-forming)
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
15-cis-phytoene + 4 acceptor = all-trans-lycopene + 4 reduced acceptor
overall reaction
-
-
-
15-cis-phytoene + acceptor = all-trans-phytofluene + reduced acceptor
-
-
-
-
all-trans-neurosporene + acceptor = all-trans-lycopene + reduced acceptor
-
-
-
-
all-trans-phytofluene + acceptor = all-trans-zeta-carotene + reduced acceptor
-
-
-
-
all-trans-zeta-carotene + acceptor = all-trans-neurosporene + reduced acceptor
-
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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SYSTEMATIC NAME
IUBMB Comments
15-cis-phytoene:acceptor oxidoreductase (lycopene-forming)
Requires FAD. The enzyme is involved in carotenoid biosynthesis and catalyses up to four desaturation steps (cf. EC 1.3.99.28 [phytoene desaturase (neurosporene-forming)], EC 1.3.99.29 [phytoene desaturase (zeta-carotene-forming)] and EC 1.3.99.30 [phytoene desaturase (3,4-didehydrolycopene-forming)]).
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
bifunctional enzyme, catalyzes both reactions of EC 1.3.99.30 and EC 1.3.99.31
UniProt
bifunctional enzyme, catalyzes both reactions of EC 1.3.99.30 and EC 1.3.99.31
UniProt
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
-
CRTI-type phytoene desaturases prevailing in bacteria and fungi can form lycopene directly from phytoene while plants employ two distinct desaturases and two cis-tans isomerases for the same purpose
malfunction
-
a mutant of Rubrivivax gelatinosus lacking the crtI gene produces only phytoene, indicating that this organism has no other phytoene desaturases. When the crtI deletion mutant is complemented by the three-step phytoene desaturase of Rhodobacter capsulatus, spirilloxanthin and its precursors are not synthesized, although spheroidene and OH-spheroidene are accumulated
metabolism
physiological function
additional information
metabolism
-
CrtI produces lycopene exclusively as an end product, not as an intermediate in spirilloxanthin, carotenoid biosynthesis pathway in Rhodospirillum rubrum, overview
metabolism
the enzyme is involved catalyzing several steps in the beta-carotene biosynthetic pathway via phytoene, zeta-carotene, and lycopene, overview
metabolism
-
CrtI produces lycopene exclusively as an end product, not as an intermediate in spirilloxanthin, carotenoid biosynthesis pathway in Rhodospirillum rubrum, overview
-
physiological function
-
the enzyme simultaneously catalyzes a three- and four-step desaturation of phytoene producing both neurosporene and lycopene. These carotenes are intermediates for the synthesis of spheroidene and spirilloxanthin, respectively
physiological function
-
the enzyme simultaneously catalyzes a three- and four-step desaturation of phytoene producing both neurosporene and lycopene
physiological function
-
in vivo, lycopene is incorporated into the light-harvesting complex 1 as efficiently as the methoxylated carotenoids spirilloxanthin (in the wild-type) and 3,4,3',4'-tetrahydrospirilloxanthin (in a crtD mutant), both under semiaerobic, chemoheterotrophic, and photosynthetic, anaerobic conditions, quantitative growth experiments, overview
physiological function
-
CRTI is a membrane-peripheral oxidoreductase which utilizes FAD as the sole redox-active cofactor. Oxygen, replaceable by quinones in its absence, is needed as the terminal electron acceptor. FAD, besides its catalytic role also displays a structural function by enabling the formation of enzymatically active CRTI membrane associates. Under anaerobic conditions the enzyme can act as a carotene cis-trans isomerase. In silico-docking experiments yielded information on substrate binding sites, potential catalytic residues and is in favor of single half-site recognition of the symmetrical C40 hydrocarbon substrate
physiological function
the expression product of crtI is essential for phytoene conversion to lycopene and 3,4-didehydrolycopene
physiological function
-
in vivo, lycopene is incorporated into the light-harvesting complex 1 as efficiently as the methoxylated carotenoids spirilloxanthin (in the wild-type) and 3,4,3',4'-tetrahydrospirilloxanthin (in a crtD mutant), both under semiaerobic, chemoheterotrophic, and photosynthetic, anaerobic conditions, quantitative growth experiments, overview
-
physiological function
-
the enzyme simultaneously catalyzes a three- and four-step desaturation of phytoene producing both neurosporene and lycopene. These carotenes are intermediates for the synthesis of spheroidene and spirilloxanthin, respectively
-
physiological function
-
the expression product of crtI is essential for phytoene conversion to lycopene and 3,4-didehydrolycopene
-
additional information
Rhodobacter azotoformans contains a carotenogenesis gene cluster with an unusual organization and a phytoene desaturase catalyzing both three- and four-step desaturations. CrtI from Rhodobacter azotoformans CGMCC 6086 can produce three-step desaturated neurosporene and four-step desaturated lycopene as major products, see also EC 1.3.99.28, together with small amounts of five-step desaturated 3,4-didehydrolycopene, EC 1.3.99.30
additional information
-
Rhodobacter azotoformans contains a carotenogenesis gene cluster with an unusual organization and a phytoene desaturase catalyzing both three- and four-step desaturations. CrtI from Rhodobacter azotoformans CGMCC 6086 can produce three-step desaturated neurosporene and four-step desaturated lycopene as major products, see also EC 1.3.99.28, together with small amounts of five-step desaturated 3,4-didehydrolycopene, EC 1.3.99.30
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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
15-cis-phytoene + 4 acceptor
all-trans-lycopene + reduced 4 acceptor
-
-
-
-
?
all-trans-phytofluene + 3 acceptor
all-trans-lycopene + 3 reduced acceptor
-
-
-
-
?
15-cis-phytoene + 3 acceptor
all-trans-neurosporene + 3 reduced acceptor
-
-
-
-
?
15-cis-phytoene + 3 acceptor
all-trans-neurosporene + 3 reduced acceptor
-
the enzyme simultaneously catalyzes a three- and four-step desaturation of phytoene producing both neurosporene and lycopene. These carotenes are intermediates for the synthesis of spheroidene and spirilloxanthin, respectively
-
-
?
15-cis-phytoene + 3 acceptor
all-trans-neurosporene + 3 reduced acceptor
-
the enzyme simultaneously catalyzes a three- and four-step desaturation of phytoene producing both neurosporene and lycopene. The ratio of lycopene to neurosporene of the wild-type enzyme under assay conditions is 88:12 after complementation of CrtI in pUC8(DH5a/pACCrtEBEU/pUCCrtIRg) and 26:74 after complementation of CrtI in pPEU(DH5a/pACCrtEBEU/pPEUCrtIRg). The affinity for neurosporene conversion is poorer than for phytoene conversion. This explains the formation of two desaturation products
-
-
?
15-cis-phytoene + 4 acceptor
all-trans-lycopene + 4 reduced acceptor
-
overall reaction. all-trans-Lycopene is the principal desaturase product constituting 60% of the total reaction products. The desaturase intermediates all-trans-phytofluene and all-trans-zeta-carotene are also detected and constitute 27 and 12% of the total desaturase products formed
-
-
?
15-cis-phytoene + 4 acceptor
all-trans-lycopene + 4 reduced acceptor
-
-
-
-
?
15-cis-phytoene + 4 acceptor
all-trans-lycopene + 4 reduced acceptor
-
the enzyme simultaneously catalyzes a three- and four-step desaturation of phytoene producing both neurosporene and lycopene. These carotenes are intermediates for the synthesis of spheroidene and spirilloxanthin, respectively
-
-
?
15-cis-phytoene + 4 acceptor
all-trans-lycopene + 4 reduced acceptor
-
the enzyme simultaneously catalyzes a three- and four-step desaturation of phytoene producing both neurosporene and lycopene. The ratio of lycopene to neurosporene of the wild-type enzyme under assay conditions is 88:12 after complementation of CrtI in pUC8(DH5a/pACCrtEBEU/pUCCrtIRg) and 26:74 after complementation of CrtI in pPEU(DH5a/pACCrtEBEU/pPEUCrtIRg). The affinity for neurosporene conversion is poorer than for phytoene conversion. This explains the formation of two desaturation products
-
-
?
15-cis-phytoene + acceptor
all-trans-phytofluene + reduced acceptor
-
-
-
?
15-cis-phytoene + acceptor
all-trans-phytofluene + reduced acceptor
-
-
-
?
15-cis-phytoene + acceptor
all-trans-phytofluene + reduced acceptor
-
-
-
-
?
15-cis-phytoene + acceptor
all-trans-phytofluene + reduced acceptor
-
-
-
-
?
all-trans-neurosporene + acceptor
all-trans-lycopene + reduced acceptor
-
-
-
-
?
all-trans-neurosporene + acceptor
all-trans-lycopene + reduced acceptor
-
-
-
?
all-trans-neurosporene + acceptor
all-trans-lycopene + reduced acceptor
-
-
-
?
all-trans-neurosporene + acceptor
all-trans-lycopene + reduced acceptor
-
-
-
-
?
all-trans-neurosporene + acceptor
all-trans-lycopene + reduced acceptor
-
-
-
-
?
all-trans-phytofluene + acceptor
all-trans-zeta-carotene + reduced acceptor
-
-
-
?
all-trans-phytofluene + acceptor
all-trans-zeta-carotene + reduced acceptor
-
-
-
?
all-trans-phytofluene + acceptor
all-trans-zeta-carotene + reduced acceptor
-
-
-
-
?
all-trans-phytofluene + acceptor
all-trans-zeta-carotene + reduced acceptor
-
-
-
-
?
all-trans-zeta-carotene + 2 acceptor
all-trans-lycopene + 2 reduced acceptor
-
-
-
?
all-trans-zeta-carotene + 2 acceptor
all-trans-lycopene + 2 reduced acceptor
-
-
-
-
?
all-trans-zeta-carotene + acceptor
all-trans-neurosporene + reduced acceptor
-
-
-
?
all-trans-zeta-carotene + acceptor
all-trans-neurosporene + reduced acceptor
-
-
-
?
all-trans-zeta-carotene + acceptor
all-trans-neurosporene + reduced acceptor
-
-
-
-
?
all-trans-zeta-carotene + acceptor
all-trans-neurosporene + reduced acceptor
-
-
-
-
?
additional information
?
-
-
enzyme catalyzes lycopene formation in in four steps from phytoeneto phytofluene to zeta-carotene to neurosporene to lycopene, with 100% efficiency of formation of the end product
-
-
-
additional information
?
-
-
enzyme catalyzes lycopene formation in in four steps from phytoeneto phytofluene to zeta-carotene to neurosporene to lycopene, with 100% efficiency of formation of the end product
-
-
-
additional information
?
-
at higher concentrations, phytoene is the preferred substrate for CrtI, and neurosporene is produced as the major desaturation product, EC 1.3.99.28. At lower phytoene concentrations, neurosporene can be further desaturated by CrtI to produce lycopene
-
-
-
additional information
?
-
catalyzes both enzymatic conversion of phytoene to lycopene (fourth step product) and 3,4-didehydrolycopene (fifth step product), reactions of EC 1.3.99.30 and EC 1.3.99.31, respectively
-
-
-
additional information
?
-
catalyzes both enzymatic conversion of phytoene to lycopene (fourth step product) and 3,4-didehydrolycopene (fifth step product), reactions of EC 1.3.99.30 and EC 1.3.99.31, respectively
-
-
-
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NATURAL SUBSTRATES
NATURAL PRODUCTS
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
15-cis-phytoene + 4 acceptor
all-trans-lycopene + reduced 4 acceptor
-
-
-
-
?
all-trans-phytofluene + 3 acceptor
all-trans-lycopene + 3 reduced acceptor
-
-
-
-
?
additional information
?
-
G3FHJ1
at higher concentrations, phytoene is the preferred substrate for CrtI, and neurosporene is produced as the major desaturation product, EC 1.3.99.28. At lower phytoene concentrations, neurosporene can be further desaturated by CrtI to produce lycopene
-
-
-
15-cis-phytoene + 3 acceptor
all-trans-neurosporene + 3 reduced acceptor
-
-
-
-
?
15-cis-phytoene + 3 acceptor
all-trans-neurosporene + 3 reduced acceptor
-
the enzyme simultaneously catalyzes a three- and four-step desaturation of phytoene producing both neurosporene and lycopene. These carotenes are intermediates for the synthesis of spheroidene and spirilloxanthin, respectively
-
-
?
15-cis-phytoene + 4 acceptor
all-trans-lycopene + 4 reduced acceptor
-
overall reaction. all-trans-Lycopene is the principal desaturase product constituting 60% of the total reaction products. The desaturase intermediates all-trans-phytofluene and all-trans-zeta-carotene are also detected and constitute 27 and 12% of the total desaturase products formed
-
-
?
15-cis-phytoene + 4 acceptor
all-trans-lycopene + 4 reduced acceptor
-
-
-
-
?
15-cis-phytoene + 4 acceptor
all-trans-lycopene + 4 reduced acceptor
-
the enzyme simultaneously catalyzes a three- and four-step desaturation of phytoene producing both neurosporene and lycopene. These carotenes are intermediates for the synthesis of spheroidene and spirilloxanthin, respectively
-
-
?
15-cis-phytoene + acceptor
all-trans-phytofluene + reduced acceptor
P21685
-
-
-
?
15-cis-phytoene + acceptor
all-trans-phytofluene + reduced acceptor
G3FHJ1
-
-
-
?
15-cis-phytoene + acceptor
all-trans-phytofluene + reduced acceptor
-
-
-
-
?
15-cis-phytoene + acceptor
all-trans-phytofluene + reduced acceptor
-
-
-
-
?
all-trans-neurosporene + acceptor
all-trans-lycopene + reduced acceptor
-
-
-
-
?
all-trans-neurosporene + acceptor
all-trans-lycopene + reduced acceptor
P21685
-
-
-
?
all-trans-neurosporene + acceptor
all-trans-lycopene + reduced acceptor
G3FHJ1
-
-
-
?
all-trans-neurosporene + acceptor
all-trans-lycopene + reduced acceptor
-
-
-
-
?
all-trans-neurosporene + acceptor
all-trans-lycopene + reduced acceptor
-
-
-
-
?
all-trans-phytofluene + acceptor
all-trans-zeta-carotene + reduced acceptor
P21685
-
-
-
?
all-trans-phytofluene + acceptor
all-trans-zeta-carotene + reduced acceptor
G3FHJ1
-
-
-
?
all-trans-phytofluene + acceptor
all-trans-zeta-carotene + reduced acceptor
-
-
-
-
?
all-trans-phytofluene + acceptor
all-trans-zeta-carotene + reduced acceptor
-
-
-
-
?
all-trans-zeta-carotene + 2 acceptor
all-trans-lycopene + 2 reduced acceptor
P21685
-
-
-
?
all-trans-zeta-carotene + 2 acceptor
all-trans-lycopene + 2 reduced acceptor
-
-
-
-
?
all-trans-zeta-carotene + acceptor
all-trans-neurosporene + reduced acceptor
P21685
-
-
-
?
all-trans-zeta-carotene + acceptor
all-trans-neurosporene + reduced acceptor
G3FHJ1
-
-
-
?
all-trans-zeta-carotene + acceptor
all-trans-neurosporene + reduced acceptor
-
-
-
-
?
all-trans-zeta-carotene + acceptor
all-trans-neurosporene + reduced acceptor
-
-
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
FAD
-
involved in desaturation. FAD is a dissociable moiety and not covalently bound to the enzyme
FAD
-
CRTI utilizes FAD as the sole redox-active cofactor, binding kinetics and structure analysis, molecular docking, overview. Oxygen, replaceable by quinones in its absence, is needed as the terminal electron acceptor. FAD, besides its catalytic role also displays a structural function by enabling the formation of enzymatically active CRTI membrane associates
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Diphenylamine
-
at an illumination of 1200 lx, cells grow slowly at diphenylamine concentrations not exceeding 53 microM, while at illumination of 500 lx they can grow at 71 microM diphenylamine. Independent of illumination level, the inhibitor impairs the functioning of phytoene synthetase and of phytoene desaturase, which results in formation of neurosporene hydroxy derivatives and zeta-carotene
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0176
15-cis-phytoene
-
recombinant His6-tagged enzyme, pH and temperature not specified in the publication
4.8
15-cis-phytoene
-
pH 8, 28°C, mutant enzyme L208F (complementation of CrtI in pPEU (DH5a/pACCrtEBEU/pPEUCrtIRg))
17.1
15-cis-phytoene
-
pH 8, 28°C, mutant enzyme L208P (complementation of CrtI in pUC8 (DH5a/pACCrtEBEU/pUCCrtIRg))
41.7
all-trans-neurosporene
-
pH 8, 28°C, mutant enzyme (complementation of CrtI in pUC8 (DH5a/pACCrtEBEU/pUCCrtIRg))
65.8
all-trans-neurosporene
-
pH 8, 28°C, mutant enzyme L208F (complementation of CrtI in pPEU (DH5a/pACCrtEBEU/pPEUCrtIRg))
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
membrane-peripheral enzyme, phosphatidyl-choline liposome membranes
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
recombinant His6-tagged enzyme from Escherichia coli by nickel affinity cromatography and gel filtration
-
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
expression in Escherichia coli. Synthesis of the enzyme by different vectors with high and lower copy numbers or strong and weak promoters results in variable ratios of lycopene and neurosporene formation. The highest amount of enzyme is produced with pUC vectors with high copy number and a strong promoter. This transformant synthesizes the highest lycopene amount. The lowest enzyme concentrations is found with pPEU carrying a weak promoter. In this transformant lycopene formation is minor. With increased enzyme concentration, a proportion of lycopene higher than in Rubrivivax gelatinosus cells can be obtained
-
gene crtI, cloning of the crt gene cluster crtCDEF, expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
gene crtI, recombinant coexpression of genes crtE, crtB, and crtI from Erwinia uredovora and of crtL from Ficus carica in Pichia pastoris X-33 strains for large-scale biosynthesis of carotenoids, subcloning of crtI in Escherichhia coli strain TOP10
gene crtI, recombinant expression of His6-tagged enzyme in Escherichia coli
-
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
L153P/L278P
-
increased formation of neurosporene compared to wild-type enzyme. The ratio of lycopene to neurosporene of the wild-type enzyme under assay conditions is 88:12 after complementation of CrtI in pUC8(DH5a/pACCrtEBEU/pUCCrtIRg), the ratio of the mutant enzyme is 12:88
L208F
-
increased formation of lycopene compared to wild-type enzyme. The ratio of lycopene to neurosporene of the wild-type enzyme under assay conditions is 26:74 after complementation of CrtI in pPEU(DH5a/pACCrtEBEU/pPEUCrtIRg), the ratio of the mutant enzyme is 89:11
L208P
-
increased formation of neurosporene compared to wild-type enzyme. The ratio of lycopene to neurosporene of the wild-type enzyme under assay conditions is 88:12 after complementation of CrtI in pUC8(DH5a/pACCrtEBEU/pUCCrtIRg), the ratio of the mutant enzyme is 3:97
T256M/D355GL424P
-
increased formation of neurosporene compared to wild-type enzyme. The ratio of lycopene to neurosporene of the wild-type enzyme under assay conditions is 88:12 after complementation of CrtI in pUC8(DH5a/pACCrtEBEU/pUCCrtIRg), the ratio of the mutant enzyme is 0:100
Y44C/D53G/P134L/V395A
-
increased formation of neurosporene compared to wild-type enzyme. The ratio of lycopene to neurosporene of the wild-type enzyme under assay conditions is 88:12 after complementation of CrtI in pUC8(DH5a/pACCrtEBEU/pUCCrtIRg), the ratio of the mutant enzyme is 3:97
additional information
additional information
enzyme modification by site-directed mutagenesis, overview
additional information
-
construction of the lycopene-producing mutant, SLYC18, and analysis of mutant strains SLYC18 and ST4, mutated in crtC and crt D or crtC genes, respectively, and quantitative analysis of their carotenoid spectrum as well as light harvesting LH1 complex, functional complementation, overview. The crtC crtD deletion mutant produces lycopene exclusively as a final product
additional information
-
construction of the lycopene-producing mutant, SLYC18, and analysis of mutant strains SLYC18 and ST4, mutated in crtC and crt D or crtC genes, respectively, and quantitative analysis of their carotenoid spectrum as well as light harvesting LH1 complex, functional complementation, overview. The crtC crtD deletion mutant produces lycopene exclusively as a final product
-
additional information
-
two different mutation libraries for the crtI gene are constructed to screen for modified enzymes which synthesize almost exclusively either neurosporene or lycopene. The resulting mutants carry between one and four amino acid exchanges and at least one of them affects the secondary protein structure by shortening or extending one of the helices. A prominent amino acid which is exchanged in the neurosporene or lycopene-forming desaturase is leucine 208. Enzyme kinetic studies are carried out with the L208 modified desaturase and the specificities for phytoene and neurosporene as substrates determined. Higher and lower values correlate well with the higher or lower potential for the synthesis of lycopene from neurosporene. TopPred analysis of the mutations of L208 indicate that the location is in a highly hydrophobic membrane-integrated region which is a good candidate for the substrate-binding site of the desaturase
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
synthesis
-
swapping the native three-step CrtI in Rhodobacter sphaeroides, EC 1.3.99.28, for the four-step Pantoea agglomerans enzyme reroutes carotenoid biosynthesis and culminates in the production of 2,2'-diketo-spirilloxanthin under semi-aerobic conditions. Premature termination of this pathway by inactivating crtC or crtD produces strains with lycopene or rhodopin as major carotenoids. All of the spirilloxanthin series carotenoids are accepted by the assembly pathways for light-harvesting 2 complex and reaction centre-light-harvesting 1-PufX complexes
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LINKS TO OTHER DATABASES (specific for EC-Number 1.3.99.31)
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