Information on EC 5.3.1.14 - L-rhamnose isomerase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
5.3.1.14
-
RECOMMENDED NAME
GeneOntology No.
L-rhamnose isomerase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
L-rhamnopyranose = L-rhamnulose
show the reaction diagram
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-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
intramolecular oxidoreduction
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-
-
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isomerization
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Fructose and mannose metabolism
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L-rhamnose degradation I
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Microbial metabolism in diverse environments
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degradation of hexoses
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SYSTEMATIC NAME
IUBMB Comments
L-rhamnose aldose-ketose-isomerase
Contains two divalent metal ions located at different metal-binding sites within the active site. The enzyme binds the closed ring form of the substrate and catalyses ring opening to generate a form of open-chain conformation that is coordinated to one of the metal sites. Isomerization proceeds via a hydride-shift mechanism. While the enzyme from the bacterium Escherichia coli is specific for L-rhamnose, the enzyme from the bacterium Pseudomonas stutzeri has broad substrate specificity and catalyses the interconversion of L-mannose and L-fructose, L-lyxose and L-xylulose, D-ribose and D-ribulose, and D-allose and D-psicose [2].
CAS REGISTRY NUMBER
COMMENTARY hide
9023-84-1
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
fragment; i.e. Geobacillus pallidus, a facultative thermophilic bacterium, strain Y25, gene L-rhi
SwissProt
Manually annotated by BRENDA team
Arthrobacter pyridinolis
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-
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Manually annotated by BRENDA team
strain K12
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-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
strain LL172
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-
Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
3-Deoxy-L-rhamnose
?
show the reaction diagram
D-Allose
?
show the reaction diagram
D-Allose
D-Psicose
show the reaction diagram
D-allose
D-psicose + D-altrose
show the reaction diagram
-
-
-
-
?
D-allose
D-talose
show the reaction diagram
-
-
-
-
?
D-altrose
?
show the reaction diagram
-
-
-
?
D-altrose
D-psicose + D-altrose
show the reaction diagram
-
-
-
-
r
D-Arabinose
?
show the reaction diagram
D-arabinose
D-ribulose + D-ribose
show the reaction diagram
-
-
-
-
r
D-erythrose
D-erythrulose + D-threose
show the reaction diagram
-
-
-
-
r
D-Galactose
?
show the reaction diagram
-
slight activity
-
-
?
D-galactose
D-tagatose
show the reaction diagram
-
-
-
-
r
D-glucose
?
show the reaction diagram
D-glucose
D-fructose + D-mannose
show the reaction diagram
-
-
-
-
r
D-Gulose
?
show the reaction diagram
-
10% of the activity relative to L-rhamnose
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-
-
D-gulose
D-sorbose
show the reaction diagram
D-Lyxose
?
show the reaction diagram
-
slight activity
-
-
?
D-lyxose
D-xylulose + D-xylose
show the reaction diagram
-
-
-
-
r
D-Mannose
?
show the reaction diagram
D-psicose
D-allose
show the reaction diagram
-
-
the product mixture contains 25% D-allose, 8% D-altrose, and 67% D-psicose
-
?
D-Ribose
?
show the reaction diagram
D-Ribose
D-Ribulose
show the reaction diagram
D-ribose
D-ribulose + D-arabinose
show the reaction diagram
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-
-
-
r
D-talose
?
show the reaction diagram
-
slight activity
-
-
?
D-talose
D-allose
show the reaction diagram
-
slight activity
-
-
?
D-threose
D-erythrulose + D-erythrose
show the reaction diagram
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-
-
-
r
D-Xylose
?
show the reaction diagram
-
-
-
?
D-xylose
D-xylulose + D-lyxose
show the reaction diagram
-
-
-
-
r
L-Arabinose
?
show the reaction diagram
-
slight activity
-
-
?
L-Arabinose
L-Ribulose
show the reaction diagram
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-
-
-
r
L-erythrose
L-erythrulose + L-threose
show the reaction diagram
-
-
-
-
r
L-fructose
L-mannose
show the reaction diagram
L-galactose
?
show the reaction diagram
-
slight activity
-
-
?
L-galactose
L-tagatose + L-talose
show the reaction diagram
-
-
-
-
r
L-glucose
L-fructose + L-mannose
show the reaction diagram
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-
-
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r
L-lyxose
?
show the reaction diagram
L-Lyxose
L-Xylulose
show the reaction diagram
L-lyxose
L-xylulose + L-xylose
show the reaction diagram
-
-
-
-
r
L-mannose
?
show the reaction diagram
L-Mannose
L-Fructose
show the reaction diagram
L-mannose
L-fructose + L-glucose
show the reaction diagram
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-
-
-
r
L-Rhamnose
L-Rhamnulose
show the reaction diagram
L-rhamnulose
L-rhamnulose
show the reaction diagram
-
-
-
-
r
L-ribose
?
show the reaction diagram
-
slight activity
-
-
?
L-ribose
L-ribulose + L-arabinose
show the reaction diagram
-
-
-
-
r
L-tagatose
L-talose
show the reaction diagram
10% conversion at 50°C
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-
r
L-talose
?
show the reaction diagram
L-threose
L-erythrulose + L-erythrose
show the reaction diagram
-
-
-
-
r
L-xylose
?
show the reaction diagram
-
-
-
?
L-xylose
L-xylulose + L-lyxose
show the reaction diagram
-
-
-
-
r
L-xylulose
L-lyxose
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
D-Allose
D-Psicose
show the reaction diagram
-
-
-
-
r
D-psicose
D-allose
show the reaction diagram
-
-
-
-
?
L-Rhamnose
L-Rhamnulose
show the reaction diagram
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Al3+
-
1 mM, activates to 104% of control
Ca2+
the enzyme shows 1% activity in the presence of 1 mM Ca2+ as compared to 1 mM Co2+
Fe2+
-
weak activation
Li+
-
1 mM, activates to 106% of control
Na+
the enzyme shows 19% activity in the presence of 1 mM Na+ as compared to 1 mM Co2+
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Ag+
-
1 mM, complete inhibition
Ba2+
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1 mM, 97% inhibition
Co2+
-
1 mM, 79% inhibition
Fe2+
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1 mM, complete inhibition
Mg2+
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1 mM, 45% inhibition
Na+
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1 mM, 12% inhibition
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
sulfhydryl reagents
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activate
thioglycolate
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best activator among sulfhydryl reagents
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.7 - 121
D-Allose
71
D-Altrose
127 - 127.4
D-arabinose
564
D-glucose
3 - 85.1
D-ribose
250
D-xylose
73.2 - 123
L-Fructose
3.65 - 771
L-Lyxose
2 - 119
L-Mannose
0.7 - 528
L-rhamnose
1.7 - 11
L-rhamnulose
5.25
L-talose
-
in 50 mM glycine-NaOH, pH 9.0, 1 mM MnCl2, at 60°C
202 - 203
L-Xylose
63 - 111
L-xylulose
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.3 - 2500
D-Allose
0.05
D-Altrose
Pseudomonas stutzeri
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-
0.17
D-arabinose
Pseudomonas stutzeri
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-
0.024
D-glucose
Pseudomonas stutzeri
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-
0.1 - 3150
D-ribose
33
D-xylose
Pseudomonas stutzeri
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-
116 - 274
L-Fructose
73.8 - 900
L-Lyxose
10 - 1000
L-Mannose
5.1 - 374
L-rhamnose
1717
L-rhamnulose
Pseudomonas stutzeri
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-
7
L-talose
Mesorhizobium loti
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in 50 mM glycine-NaOH, pH 9.0, 1 mM MnCl2, at 60°C
0.017
L-Xylose
Pseudomonas stutzeri
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-
130 - 281
L-xylulose
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.071 - 6.2
D-Allose
945
0.0027 - 3.54
D-ribose
292
1.6 - 2.23
L-Fructose
5168
3.1 - 50.8
L-Lyxose
1647
0.4 - 21.6
L-Mannose
2102
0.283 - 410
L-rhamnose
703
1.3
L-talose
Mesorhizobium loti
-
in 50 mM glycine-NaOH, pH 9.0, 1 mM MnCl2, at 60°C
6883
2.1 - 2.55
L-xylulose
1238
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.5
-
using D-gulose as substrate, purified enzyme, at 85°C for 10 min in 50 mM EPPS buffer (pH 8.0)
1.1
-
using D-psicose as substrate, purified enzyme, at 85°C for 10 min in 50 mM EPPS buffer (pH 8.0)
2.58
purified recombinant His-tagged enzyme, substrate D-allose
2.8
-
using D-ribose as substrate, purified enzyme, at 85°C for 10 min in 50 mM EPPS buffer (pH 8.0)
4.52
purified recombinant His-tagged enzyme, substrate L-mannose
5.1
-
using L-fructose as substrate, purified enzyme, at 85°C for 10 min in 50 mM EPPS buffer (pH 8.0)
5.3
-
using D-gulose as substrate, purified enzyme, at 85°C for 10 min in 50 mM EPPS buffer (pH 8.0)
6.33
purified recombinant His-tagged enzyme, substrate D-ribose
6.7
-
using D-allose as substrate, purified enzyme, at 85°C for 10 min in 50 mM EPPS buffer (pH 8.0)
6.8
-
using D-ribulose as substrate, purified enzyme, at 85°C for 10 min in 50 mM EPPS buffer (pH 8.0)
8.6
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using L-xylulose as substrate, purified enzyme, at 85°C for 10 min in 50 mM EPPS buffer (pH 8.0)
14.8
crude extract, in 50 mM potassium phosphate buffer (pH 7.0) and 1 mM Co2+, at 90°C
15
-
using L-mannose as substrate, purified enzyme, at 85°C for 10 min in 50 mM EPPS buffer (pH 8.0)
19.3
purified recombinant His-tagged enzyme, substrate L-lyxose
20
-
using L-lyxose as substrate, purified enzyme, at 85°C for 10 min in 50 mM EPPS buffer (pH 8.0)
55
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using L-rhamnose as substrate, purified enzyme, at 85°C for 10 min in 50 mM EPPS buffer (pH 8.0)
65.6
crude extract, at 65°C in 50 mM potassium phosphate buffer and 1 mM Co2+ at pH 7.0
77.2
purified recombinant His-tagged enzyme, substrate L-rhamnose
197
after 3fold purification, at 65°C in 50 mM potassium phosphate buffer and 1 mM Co2+ at pH 7.0
379
after 25.6fold purification, in 50 mM potassium phosphate buffer (pH 7.0) and 1 mM Co2+, at 90°C
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 11
-
immobilized enzyme
8
maximum activities of both the free and immobilized enzymes for L-rhamnose isomerization
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 11
-
pH-range of optimal activity, immobilized enzyme
6 - 10
7 - 11
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pH 7: about 50% of maximal activity, pH 11: about 40% of maximal activity, free enzyme
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30
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free enzyme
65
recombinant enzyme
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.5
-
isoelectric focusing
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
45527
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4 * 45527, calculated from amino acid sequence
46000
-
4 * 46000, SDS-PAGE
46695
4 * 46695, calculated from amino acid sequence
46946
-
x * 46946, calculated from amino acid sequence
47636
x * 47636, sequence calculation, x * 47000, SDS-PAGE, native enzyme
47681
-
x * 43000, SDS-PAGE, x * 47681, recombinant His-tagged enzyme, MALDI-TOF mass spectrometry
48178
-
2 * 48178, calculated from amino acid sequence
48292
4 * 48292, MALDI-TOF mass spectrometry
48294
4 * 48294, calculated from amino acid sequence
48960
x * 48960, calculated from amino acid sequence
121000
-
gel filtration
150000
-
gel filtration
184000
-
gel filtration
185000
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
homotetramer
tetramer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hanging drop vapor diffusion method, using 10% (w/v) PEG 8000, 0.1 M HEPES pH 6.0 and 0.2 M sodium acetate
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hanging-drop vapor diffusion method
mutant enzyme H101N in complex with L-rhamnose and D-allose, vapor diffusion method, using 7-8% (w/v) polyethylene glycol 20000 and 50 mM MES buffer (pH 6.3)
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purified L-RhI alone and in complexes with L-rhamnose and D-allose, X-ray diffraction structure determination and analysis at 1.97-2.0 A resolution
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purified recombinant His-tagged L-RhI by hanging-drop vapour-diffusion method, 0.002 ml of 20 mg/ml protein in 20 mM Tris-HCl, pH 8.0, is mixed with 0.002 ml reservcoir solution containing 7-8% w/v PEG 20 000 and 50 mM MES buffer, pH 6.3, equilibration against 0.5 ml reservoir solution, X-ray diffraction structure determination and analysis at 2.0 A resolution
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the structures of Mn2+-bound L-rhamnose isomerase, of the mutant S329K in complex with D-psicose or L-rhamnose, and of the mutant D327N in complex with D-psicose or L-rhamnulose are determined at resolutions of 1.8, 1.6, 1.95, 1.9, and 1.7 A, respectively
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wild type and mutant enzymes S329F, S329K, S329L, and S329A in complex with L-rhamnose, D-psicose or D-allose, droplet vapor diffusion method, using 6-9.25% (w/v) polyethylene glycol 20000, 50 mM MES buffer, pH 6.1-6.3, at 20°C
-
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4 - 11
the enzyme is stable at pH values ranging from 4.0 to 11.0 with more than 80% remaining activity and retains more than 90% activity after a 6 h incubation at 80°C and pH 7.0-8.0. The enzyme activity is fully retained at pH 7-8, 32% remaining at pH 9.0, but becomes inactivated in the pH range from 4.0 to 6.0
727653
5 - 11
5 - 9
the enzyme is stable at pH values ranging from 5.0 to 9.0
715213
7 - 10
purified recombinant enzyme, stable
677768
7 - 11
-
4°C, 24 h, pH 7: about 30% loss of activity, pH 9: stable, pH 11: about 10% loss of activity, free enzyme
2633
8
the half-lives of the free and immobilized enzymes are 28 and 112 h at pH 8.0 and 75°C in the presence of 1 mM Mn2+
727230
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37
-
50 h stable, partially purified enzyme
40 - 70
the activity is fully retained after 2 h incubation at 40-70°C
60
60 min, purified recombinant enzyme, pH 7.0, 90% remaining activity
60 - 80
-
the enzyme shows 100% activity for 10 h at 60°C, the half-life of the enzyme is more than 900 min, about 25 min, and 5 min at 60°C, 70°C, and 80°C, respectively
65
60 min, purified recombinant enzyme, pH 7.0, 50% remaining activity
75
the half-lives of the free and immobilized enzymes are 28 and 112 h at pH 8.0 and 75°C in the presence of 1 mM Mn2+
75 - 95
-
the half-lives of the enzyme at 75°C, 80°C, 85°C, 90°C and 95°C are 773 h, 347 h, 187 h, 118 h, and 65 h, respectively
80 - 90
the enzyme shows good thermostability and retains more than 90% activity after a 6 h incubation at 80°C and pH 7.0-8.0. The enzyme is stable at 85°C for 4 h. However, the enzyme activity drops sharply to 30% after 2 h at 90°C, and the half-life at 90°C is around 65 min
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
immobilized enzyme is stable even after repeated use over 20 d at 40°C
-
immobilized enzyme retains about 90% of the initial activity even after five repeated uses in a batch reaction
-
the cross-linked enzyme shows a catalytic half-life of 2 months
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-15°C, stable
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
heat treatment, nucleic acid precipitation, and Q-Sepharose column chromatography
heat treatment, nucleic acid precipitation, and Q-Sepharose ion-exchange chromatography
His-Trap column chromatography
-
His-Trap HP column chromatography, and gel filtration
native enzyme by anion exchange, hydrophobic interaction, and again anion exchange chromatography to apparent homogeneity, recombinant His6-tagged enzyme 3.87fold from Escherichia coli strain JM109 by nickel affinity chromatography to homogeneity
Ni-NTA column chromatography
recombinant His-tagged enzyme
-
recombinant His6-tagged enzyme from Escherichia coli by nickel affinity chromatography and dialysis
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
a plasmid, pOI-02, encoding the L-RhI gene, is used
-
expressed in Escherichia coli BL21(DE3) cells
-
expressed in Escherichia coli BL21-CodonPlus (DE3)-RIL cells
expressed in Escherichia coli ER2566 cells
expressed in Escherichia coli JM109 cells
-
expression in Escherichia coli JM 109
-
expression of His6-tagged enzyme in Escherichia coli
-
gene L-rhi, DNA and amino acid sequence determination and analysis, expression of the soluble His6-tagged enzyme in Escherichia coli strain JM109
overexpression in Escherichia coli
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
H101N
-
the enzymatic activity of the mutant is decreased
S329A
-
mutant showing reduced catalytic efficiency compared to the wild type enzyme
S329F
-
mutant showing reduced catalytic efficiency compared to the wild type enzyme
S329L
-
mutant showing reduced catalytic efficiency compared to the wild type enzyme
additional information
-
cross-linking of the enzyme with glutaraldehyde and L-lysine, for usage in production of D-allose from D-piscose, overview
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
food industry
industry
synthesis
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