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Identification of the key residues determining the product specificity of isomerohydrolase

Takahashi, Y.; Moiseyev, G.; Nikolaeva, O.; Ma, J.X.; Biochemistry 51, 4217-4225 (2012)

Data extracted from this reference:

Cloned(Commentary)
EC Number
Commentary
Organism
3.1.1.64
expression of wild-type enzyme and mutants in HEK-293A cells
Danio rerio
3.1.1.64
recombinant expression in HEK-293A cells
Gallus gallus
3.1.1.90
expressed in HEK-293A cells; expression of wild-type enzyme and mutants in HEK-293A cells
Danio rerio
Engineering
EC Number
Amino acid exchange
Commentary
Organism
3.1.1.64
F103L
site-directed mutagenesis, the mutation reverses the enzyme isomerization product specificity from formation of 11-cis-retinol to 13-cis-retinol, product of EC 3.1.1.90. Formation of 95.7% 13-cis-retinol and 4.3% 11-cis-retinol
Danio rerio
3.1.1.64
K222M
site-directed mutagenesis, the mutation reverses the enzyme isomerization product specificity from formation of 11-cis-retinol to 13-cis-retinol, product of EC 3.1.1.90. Formation of 55.1% 13-cis-retinol and 44.9% 11-cis-retinol
Danio rerio
3.1.1.64
L133S
site-directed mutagenesis, the mutation reverses the enzyme isomerization product specificity from formation of 11-cis-retinol to 13-cis-retinol, product of EC 3.1.1.90. Formation of 71-3% 13-cis-retinol and 28.7% 11-cis-retinol
Danio rerio
3.1.1.64
Y58N
site-directed mutagenesis, the mutation completely reverses the enzyme isomerization product specificity from formation of 11-cis-retinol to 13-cis-retinol, product of EC 3.1.1.90. Exclusive formation of 13-cis-retinol
Danio rerio
3.1.1.90
F103L
in terms of isomerization specificity mutant shows a substantially increases level of production of 13-cis retinol
Danio rerio
3.1.1.90
K222M
in terms of isomerization specificity mutant only slightly increases level of production of 13-cis retinol
Danio rerio
3.1.1.90
L103F
in terms of isomerization specificity mutant shows a highly reduced level of 13-cis retinol while increasing the level of 11-cis-retinol (compared to wild-tpye); site-directed mutagenesis, site-directed mutagenesis, the mutation reverses the enzyme isomerization product specificity from formation of 13-cis-retinol to 11-cis-retinol, product of EC 3.1.1.64. Formation of 62.5% 13-cis-retinol and 37.5% 11-cis-retinol
Danio rerio
3.1.1.90
L133S
in terms of isomerization specificity mutant shows a substantially increases level of production of 13-cis retinol
Danio rerio
3.1.1.90
M222K
in terms of isomerization specificity mutant shows no effect and generates exclusively 13-cis-retinol similar to wild-type; site-directed mutagenesis, the mutation does not affect the enzyme isomerization product specificity of the enzyme
Danio rerio
3.1.1.90
N58Y
in terms of isomerization specificity mutant shows a highly reduced level of 13-cis retinol while increasing the level of 11-cis-retinol (compared to wild-tpye); site-directed mutagenesis, the mutation completely reverses the enzyme isomerization product specificity from formation of 13-cis-retinol to 11-cis-retinol, product of EC 3.1.1.64. Formation of 28.7% 13-cis-retinol and 71.3% 11-cis-retinol
Danio rerio
3.1.1.90
N58Y/L103F
N58Y/L103F double mutant shows a product specificity identical to that of wild-type 13cIMH; site-directed mutagenesis, the mutation does not affect the enzyme isomerization product specificity of the enzyme
Danio rerio
3.1.1.90
S133L
in terms of isomerization specificity mutant shows only a slightly reduced level of 13-cis retinol while increasing the level of 11-cis-retinol (compared to wild-tpye); site-directed mutagenesis, site-directed mutagenesis, the mutation reverses the enzyme isomerization product specificity from formation of 13-cis-retinol to 11-cis-retinol, product of EC 3.1.1.64. Formation of 94.4% 13-cis-retinol and 5.6% 11-cis-retinol
Danio rerio
3.1.1.90
Y58N
in terms of isomerization specificity mutant generates exclusively 13-cis retinol
Danio rerio
3.1.1.90
Y58N/F103L
double mutant generates predominantly 11-cis retinol
Danio rerio
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
3.1.1.64
an all-trans-retinyl ester + H2O
Gallus gallus
the enzyme generates predominantly 11-cis-retinol and a minor amount of 13-cis-retinol, from all-trans-retinyl ester
11-cis-retinol + a fatty acid
-
-
?
3.1.1.64
an all-trans-retinyl ester + H2O
Danio rerio
the enzyme generates predominantly 11-cis-retinol and a minor amount of 13-cis-retinol, from all-trans-retinyl ester
11-cis-retinol + a fatty acid
-
-
?
3.1.1.90
an all-trans-retinyl ester + H2O
Danio rerio
the enzyme generates exclusively 13-cis-retinol
13-cis-retinol + a fatty acid
-
-
?
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
3.1.1.64
Danio rerio
-
homologue RPE65c
-
3.1.1.64
Gallus gallus
-
homologue RPE65
-
3.1.1.90
Danio rerio
-
-
-
Source Tissue
EC Number
Source Tissue
Commentary
Organism
Textmining
3.1.1.64
epithelium
-
Danio rerio
-
3.1.1.64
epithelium
-
Gallus gallus
-
3.1.1.64
additional information
enzyme homologue RPE65c is expressed in retinal Müller cells, not in the retinal pigment epithelium. Zebrafish is a cone-dominant species with 79% cones and 21% rods
Danio rerio
-
3.1.1.64
Mueller cell
-
Danio rerio
-
3.1.1.64
retina
inner
Danio rerio
-
3.1.1.64
retina
-
Gallus gallus
-
3.1.1.64
retinal pigment epithelium
-
Gallus gallus
-
3.1.1.90
brain
-
Danio rerio
-
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
3.1.1.64
an all-trans-retinyl ester + H2O
the enzyme generates predominantly 11-cis-retinol and a minor amount of 13-cis-retinol, from all-trans-retinyl ester
729213
Gallus gallus
11-cis-retinol + a fatty acid
-
-
-
?
3.1.1.64
an all-trans-retinyl ester + H2O
the enzyme generates predominantly 11-cis-retinol and a minor amount of 13-cis-retinol, from all-trans-retinyl ester
729213
Danio rerio
11-cis-retinol + a fatty acid
-
-
-
?
3.1.1.64
an all-trans-retinyl ester + H2O
the enzyme generates predominantly 11-cis-retinol (72.2%) and a minor amount of 13-cis-retinol (27.8%), from all-trans-retinyl ester
729213
Danio rerio
11-cis-retinol + a fatty acid
-
-
-
?
3.1.1.64
an all-trans-retinyl ester + H2O
the enzyme generates predominantly 11-cis-retinol (87.3%) and a minor amount of 13-cis-retinol (12.7%), from all-trans-retinyl ester
729213
Gallus gallus
11-cis-retinol + a fatty acid
-
-
-
?
3.1.1.90
all-trans retinyl ester + H2O
13cIMH generates exclusively 13-cis retinol
729213
Danio rerio
13-cis retinol + ?
-
-
-
-
3.1.1.90
all-trans retinyl ester + H2O
RPE65c generates predominatly 11-cis retinol and only little 13-cis retinol
729213
Danio rerio
11-cis retinol + ?
-
-
-
-
3.1.1.90
an all-trans-retinyl ester + H2O
the enzyme generates exclusively 13-cis-retinol
729213
Danio rerio
13-cis-retinol + a fatty acid
-
-
-
?
3.1.1.90
an all-trans-retinyl ester + H2O
the enzyme generates exclusively 13-cis-retinol, no formation of 11-cis-retinol
729213
Danio rerio
13-cis-retinol + a fatty acid
-
-
-
?
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
3.1.1.64
expression of wild-type enzyme and mutants in HEK-293A cells
Danio rerio
3.1.1.64
recombinant expression in HEK-293A cells
Gallus gallus
3.1.1.90
expressed in HEK-293A cells; expression of wild-type enzyme and mutants in HEK-293A cells
Danio rerio
Engineering (protein specific)
EC Number
Amino acid exchange
Commentary
Organism
3.1.1.64
F103L
site-directed mutagenesis, the mutation reverses the enzyme isomerization product specificity from formation of 11-cis-retinol to 13-cis-retinol, product of EC 3.1.1.90. Formation of 95.7% 13-cis-retinol and 4.3% 11-cis-retinol
Danio rerio
3.1.1.64
K222M
site-directed mutagenesis, the mutation reverses the enzyme isomerization product specificity from formation of 11-cis-retinol to 13-cis-retinol, product of EC 3.1.1.90. Formation of 55.1% 13-cis-retinol and 44.9% 11-cis-retinol
Danio rerio
3.1.1.64
L133S
site-directed mutagenesis, the mutation reverses the enzyme isomerization product specificity from formation of 11-cis-retinol to 13-cis-retinol, product of EC 3.1.1.90. Formation of 71-3% 13-cis-retinol and 28.7% 11-cis-retinol
Danio rerio
3.1.1.64
Y58N
site-directed mutagenesis, the mutation completely reverses the enzyme isomerization product specificity from formation of 11-cis-retinol to 13-cis-retinol, product of EC 3.1.1.90. Exclusive formation of 13-cis-retinol
Danio rerio
3.1.1.90
F103L
in terms of isomerization specificity mutant shows a substantially increases level of production of 13-cis retinol
Danio rerio
3.1.1.90
K222M
in terms of isomerization specificity mutant only slightly increases level of production of 13-cis retinol
Danio rerio
3.1.1.90
L103F
in terms of isomerization specificity mutant shows a highly reduced level of 13-cis retinol while increasing the level of 11-cis-retinol (compared to wild-tpye); site-directed mutagenesis, site-directed mutagenesis, the mutation reverses the enzyme isomerization product specificity from formation of 13-cis-retinol to 11-cis-retinol, product of EC 3.1.1.64. Formation of 62.5% 13-cis-retinol and 37.5% 11-cis-retinol
Danio rerio
3.1.1.90
L133S
in terms of isomerization specificity mutant shows a substantially increases level of production of 13-cis retinol
Danio rerio
3.1.1.90
M222K
in terms of isomerization specificity mutant shows no effect and generates exclusively 13-cis-retinol similar to wild-type; site-directed mutagenesis, the mutation does not affect the enzyme isomerization product specificity of the enzyme
Danio rerio
3.1.1.90
N58Y
in terms of isomerization specificity mutant shows a highly reduced level of 13-cis retinol while increasing the level of 11-cis-retinol (compared to wild-tpye); site-directed mutagenesis, the mutation completely reverses the enzyme isomerization product specificity from formation of 13-cis-retinol to 11-cis-retinol, product of EC 3.1.1.64. Formation of 28.7% 13-cis-retinol and 71.3% 11-cis-retinol
Danio rerio
3.1.1.90
N58Y/L103F
N58Y/L103F double mutant shows a product specificity identical to that of wild-type 13cIMH; site-directed mutagenesis, the mutation does not affect the enzyme isomerization product specificity of the enzyme
Danio rerio
3.1.1.90
S133L
in terms of isomerization specificity mutant shows only a slightly reduced level of 13-cis retinol while increasing the level of 11-cis-retinol (compared to wild-tpye); site-directed mutagenesis, site-directed mutagenesis, the mutation reverses the enzyme isomerization product specificity from formation of 13-cis-retinol to 11-cis-retinol, product of EC 3.1.1.64. Formation of 94.4% 13-cis-retinol and 5.6% 11-cis-retinol
Danio rerio
3.1.1.90
Y58N
in terms of isomerization specificity mutant generates exclusively 13-cis retinol
Danio rerio
3.1.1.90
Y58N/F103L
double mutant generates predominantly 11-cis retinol
Danio rerio
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
3.1.1.64
an all-trans-retinyl ester + H2O
Gallus gallus
the enzyme generates predominantly 11-cis-retinol and a minor amount of 13-cis-retinol, from all-trans-retinyl ester
11-cis-retinol + a fatty acid
-
-
?
3.1.1.64
an all-trans-retinyl ester + H2O
Danio rerio
the enzyme generates predominantly 11-cis-retinol and a minor amount of 13-cis-retinol, from all-trans-retinyl ester
11-cis-retinol + a fatty acid
-
-
?
3.1.1.90
an all-trans-retinyl ester + H2O
Danio rerio
the enzyme generates exclusively 13-cis-retinol
13-cis-retinol + a fatty acid
-
-
?
Source Tissue (protein specific)
EC Number
Source Tissue
Commentary
Organism
Textmining
3.1.1.64
epithelium
-
Danio rerio
-
3.1.1.64
epithelium
-
Gallus gallus
-
3.1.1.64
additional information
enzyme homologue RPE65c is expressed in retinal Müller cells, not in the retinal pigment epithelium. Zebrafish is a cone-dominant species with 79% cones and 21% rods
Danio rerio
-
3.1.1.64
Mueller cell
-
Danio rerio
-
3.1.1.64
retina
inner
Danio rerio
-
3.1.1.64
retina
-
Gallus gallus
-
3.1.1.64
retinal pigment epithelium
-
Gallus gallus
-
3.1.1.90
brain
-
Danio rerio
-
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
3.1.1.64
an all-trans-retinyl ester + H2O
the enzyme generates predominantly 11-cis-retinol and a minor amount of 13-cis-retinol, from all-trans-retinyl ester
729213
Gallus gallus
11-cis-retinol + a fatty acid
-
-
-
?
3.1.1.64
an all-trans-retinyl ester + H2O
the enzyme generates predominantly 11-cis-retinol and a minor amount of 13-cis-retinol, from all-trans-retinyl ester
729213
Danio rerio
11-cis-retinol + a fatty acid
-
-
-
?
3.1.1.64
an all-trans-retinyl ester + H2O
the enzyme generates predominantly 11-cis-retinol (72.2%) and a minor amount of 13-cis-retinol (27.8%), from all-trans-retinyl ester
729213
Danio rerio
11-cis-retinol + a fatty acid
-
-
-
?
3.1.1.64
an all-trans-retinyl ester + H2O
the enzyme generates predominantly 11-cis-retinol (87.3%) and a minor amount of 13-cis-retinol (12.7%), from all-trans-retinyl ester
729213
Gallus gallus
11-cis-retinol + a fatty acid
-
-
-
?
3.1.1.90
all-trans retinyl ester + H2O
13cIMH generates exclusively 13-cis retinol
729213
Danio rerio
13-cis retinol + ?
-
-
-
-
3.1.1.90
all-trans retinyl ester + H2O
RPE65c generates predominatly 11-cis retinol and only little 13-cis retinol
729213
Danio rerio
11-cis retinol + ?
-
-
-
-
3.1.1.90
an all-trans-retinyl ester + H2O
the enzyme generates exclusively 13-cis-retinol
729213
Danio rerio
13-cis-retinol + a fatty acid
-
-
-
?
3.1.1.90
an all-trans-retinyl ester + H2O
the enzyme generates exclusively 13-cis-retinol, no formation of 11-cis-retinol
729213
Danio rerio
13-cis-retinol + a fatty acid
-
-
-
?
General Information
EC Number
General Information
Commentary
Organism
3.1.1.64
evolution
it is likely that the two novel homologues of RPE65 (13cIMH and RPE65c, EC 3.1.1.90 and EC 3.1.1.64, respectively) are generated through gene duplication after the separation of fish RPE65 from the ancestral RPE65, because they exhibit an extremely high level of sequence identity (97%) and are located in the same chromosome, but on a different chromosome from RPE65
Danio rerio
3.1.1.64
additional information
key residues determining the isomerization product specificity of the enzyme are Tyr58, Phe103, and Leu133
Danio rerio
3.1.1.64
physiological function
the efficient recycling of the chromophore of visual pigments, 11-cis-retinal, through the retinoid visual cycle is an essential process for maintaining normal vision. RPE65 is the isomerohydrolase in retinal pigment epithelium and generates predominantly 11-cis-retinol and a minor amount of 13-cis-retinol, from all-trans-retinyl ester. Enzyme homologue RPE65c expressed in the inner retina may serve as an alternative isomerohydrolase in the inner retinal visual cycle to meet the high demand for recycling of the chromophore in the cone-dominant retina
Danio rerio
3.1.1.64
physiological function
the efficient recycling of the chromophore of visual pigments, 11-cis-retinal, through the retinoid visual cycle is an essential process for maintaining normal vision. RPE65 is the isomerohydrolase in retinal pigment epithelium and generates predominantly 11-cis-retinol and a minor amount of 13-cis-retinol, from all-trans-retinyl ester
Gallus gallus
3.1.1.90
evolution
it is likely that the two novel homologues of RPE65 (13cIMH and RPE65c, EC 3.1.1.90 and EC 3.1.1.64, respectively) are generated through gene duplication after the separation of fish RPE65 from the ancestral RPE65, because they exhibit an extremely high level of sequence identity (97%) and are located in the same chromosome, but on a different chromosome from RPE65
Danio rerio
3.1.1.90
additional information
key residues determining the isomerization product specificity of the enzyme are Tyr58, Phe103, and Leu133
Danio rerio
General Information (protein specific)
EC Number
General Information
Commentary
Organism
3.1.1.64
evolution
it is likely that the two novel homologues of RPE65 (13cIMH and RPE65c, EC 3.1.1.90 and EC 3.1.1.64, respectively) are generated through gene duplication after the separation of fish RPE65 from the ancestral RPE65, because they exhibit an extremely high level of sequence identity (97%) and are located in the same chromosome, but on a different chromosome from RPE65
Danio rerio
3.1.1.64
additional information
key residues determining the isomerization product specificity of the enzyme are Tyr58, Phe103, and Leu133
Danio rerio
3.1.1.64
physiological function
the efficient recycling of the chromophore of visual pigments, 11-cis-retinal, through the retinoid visual cycle is an essential process for maintaining normal vision. RPE65 is the isomerohydrolase in retinal pigment epithelium and generates predominantly 11-cis-retinol and a minor amount of 13-cis-retinol, from all-trans-retinyl ester. Enzyme homologue RPE65c expressed in the inner retina may serve as an alternative isomerohydrolase in the inner retinal visual cycle to meet the high demand for recycling of the chromophore in the cone-dominant retina
Danio rerio
3.1.1.64
physiological function
the efficient recycling of the chromophore of visual pigments, 11-cis-retinal, through the retinoid visual cycle is an essential process for maintaining normal vision. RPE65 is the isomerohydrolase in retinal pigment epithelium and generates predominantly 11-cis-retinol and a minor amount of 13-cis-retinol, from all-trans-retinyl ester
Gallus gallus
3.1.1.90
evolution
it is likely that the two novel homologues of RPE65 (13cIMH and RPE65c, EC 3.1.1.90 and EC 3.1.1.64, respectively) are generated through gene duplication after the separation of fish RPE65 from the ancestral RPE65, because they exhibit an extremely high level of sequence identity (97%) and are located in the same chromosome, but on a different chromosome from RPE65
Danio rerio
3.1.1.90
additional information
key residues determining the isomerization product specificity of the enzyme are Tyr58, Phe103, and Leu133
Danio rerio