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Information on EC 1.1.1.6 - glycerol dehydrogenase
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1.1.1.6 glycerol dehydrogenaseIUBMB Comments
Also acts on propane-1,2-diol.
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Word Map
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Synonyms
CglD, dehydrogenase, glycerol, GDH, GDH2, GLD, GldA, GLDH 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
dehydrogenase, glycerol
-
-
-
-
GDH
GDH2
-
-
-
-
GLD
GldA
GLDH
-
-
-
-
glycerin dehydrogenase
-
-
-
-
glycerol dehydrogenase
glycerol NAD 2-oxidoreductase
-
-
-
-
glycerol:NAD+ 2-oxidoreductase
-
-
-
-
GlyDH
NAD-linked glycerol dehydrogenase
-
-
-
-
NAD-specific glycerol dehydrogenase
-
-
-
-
TmGlyDH
TTHADH
glycerol dehydrogenase
-
type III polyol dehydrogenase family
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
glycerol + NAD+ = glycerone + NADH + H+
-
-
-
-
glycerol + NAD+ = glycerone + NADH + H+
catalytic bi-bi mechanism; the enzyme follows an ordered Bi-Bi mechanism kinetic model and shows product inhibition
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
oxidation
-
-
-
-
redox reaction
-
-
-
-
reduction
-
-
-
-
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PATHWAY SOURCE
PATHWAYS
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SYSTEMATIC NAME
IUBMB Comments
glycerol:NAD+ 2-oxidoreductase
Also acts on propane-1,2-diol.
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CAS REGISTRY NUMBER
COMMENTARY
249285-11-8
-
9028-14-2
this number also refers to EC 1.1.99.22
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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
1,2,3-butanetriol + NAD+
1,3-dihydroxybutane-2-one + NADH
-
-
-
?
1,3-butanediol + NAD+
?
-
relative activity is 6.5% compared to oxidation of glycerol
-
-
?
3-chloro-1,2-propanediol + NAD+
?
-
130% of the activity with glycerol
-
-
?
3-mercapto-1,2-propanediol + NAD+
?
-
155% of the activity with glycerol
-
-
?
beta-glycerophosphate + NAD+
?
-
relative activity is 2% compared to oxidation of glycerol
-
-
?
diglycerol + NAD+
?
-
relative activity is 21% compared to oxidation of glycerol
-
-
?
ethanol + NAD+
acetaldehyde + NADH
-
relative activity is 1% compared to oxidation of glycerol
-
-
?
glycerol + NAD+
D-glyceraldehyde + NADH + H+
-
no activity with NADP+. The enzyme shows much higher activity towards glycerol as compared to short chain primary and secondary alcohols. The thermostable enzyme is highly stereospecific in oxidation of glycerol and converts glycerol into D-glyceraldehyde
-
-
r
hydroxy-2-propanone + NADH
propylene glycol + NAD+
-
relative activity is 27% compared to oxidation of glycerol
-
-
?
i-inositol + NAD+
?
-
relative activity is 18% compared to oxidation of glycerol
-
-
?
isopropanol + NAD+
acetone + NADH
-
relative activity is 17% compared to oxidation of glycerol
-
-
?
sorbitol + NAD+
?
-
relative activity is 3% compared to oxidation of glycerol
-
-
?
(2R,3R)-2,3-butanediol + NAD+
(3R)-acetoin + NADH
-
-
more than 99% enantiomeric excess of R-product
-
r
(2R,3R)-2,3-butanediol + NAD+
(3R)-acetoin + NADH
-
-
more than 99% enantiomeric excess of R-product
-
r
(2R,3R)-2,3-butanediol + NAD+
? + NADH
-
better substrate than glycerol
-
-
?
(2R,3R)-2,3-butanediol + NAD+
? + NADH
-
better substrate than glycerol
-
-
?
(R)-1,2-propanediol + NAD+
? + NADH
-
better substrate than glycerol
-
-
?
(R)-1,2-propanediol + NAD+
hydroxyacetone + NADH
-
the enzyme prefers the R-enantiomer
-
-
r
(R)-1,2-propanediol + NAD+
hydroxyacetone + NADH
Thermotoga maritima MSB8 / DSM 3109 / ATCC 43589
-
the enzyme prefers the R-enantiomer
-
-
r
1,2-propanediol + NAD+
hydroxyacetone + NADH
-
105% of the activity with glycerol
-
-
-
1,2-propanediol + NAD+
hydroxyacetone + NADH
-
relative activity is 116% compared to oxidation of glycerol
-
-
-
1,2-propanediol + NAD+
hydroxyacetone + NADH
-
relative activity is 116% compared to oxidation of glycerol
-
-
-
1,2-propanediol + NAD+
hydroxyacetone + NADH
-
as active as glycerol
-
-
-
1,2-propanediol + NAD+
hydroxyacetone + NADH
-
1,2-propanediol represses the global activator HilA that induces an invasive phenotype and repression of HilA could be weakened by glycerol dehydrogenase activity
-
-
?
1,3-butanediol + NAD+
4-hydroxy-2-butanone + NADH + H+
-
-
-
-
?
1,3-butanediol + NAD+
4-hydroxy-2-butanone + NADH + H+
-
-
-
-
?
1,3-dichloro-2-propanol + NAD+
1,3-dichloro-2-propanone + NADH
-
-
-
-
?
1,3-dichloro-2-propanol + NAD+
1,3-dichloro-2-propanone + NADH
-
-
-
-
?
1,3-propanediol + NAD+
?
-
relative rate of oxidation is 18% compared to oxidation of glycerol
-
-
?
1,3-propanediol + NAD+
?
-
relative rate of oxidation is 37% compared to oxidation of glycerol
-
-
?
1,4-butanediol + NAD+
?
-
relative activity is 0.3% compared to oxidation of glycerol
-
-
?
1,4-butanediol + NAD+
?
-
relative activity 17% compared to oxidation of glycerol
-
-
?
2,3-butanediol + NAD+
3-hydroxybutane-2-one + NADH
-
as active as glycerol
-
-
-
DL-alpha-glycerophosphate + NAD+
?
-
oxidation at 16% compared to oxidation of glycerol
-
-
?
DL-alpha-glycerophosphate + NAD+
?
-
relative activity 11%compared to oxidation of glycerol
-
-
?
DL-glyceraldehyde + NAD+
3-hydroxypyruvaldehyde + NADH
-
relative rate of reduction is 14%compared to reduction of dihydroxyacetone
-
-
?
DL-glyceraldehyde + NAD+
3-hydroxypyruvaldehyde + NADH
-
-
-
-
?
DL-glyceraldehyde + NAD+
3-hydroxypyruvaldehyde + NADH
-
-
-
?
ethanediol + NAD+
glycolaldehyde + NADH
-
-
reduction at concentration of 50 mM
r
ethanediol + NAD+
glycolaldehyde + NADH
-
-
reduction at concentration of 50 mM
r
ethylene glycol + NAD+
?
-
relative activity is 20% compared to oxidation of glycerol
-
-
?
glycerol + NAD+
dihydroxyacetone + NADH
-
Glycerol dehydrogenase was immobilised in a polycarbamoyl sulfonate-hydrogel to be used as a sensor for glycerol. Glycerol oxidation leads to the reduction of NAD+ to NADH and electrons are transferred to ferricyanide on an electrode surface
-
-
?
glycerol + NAD+
dihydroxyacetone + NADH
-
the reaction is performed in reverse micelles harboring glycerol and NAD+ in a solution of isooctane containing 250 mM diocytlsulfosuccinate
-
-
?
glycerol + NAD+
dihydroxyacetone + NADH
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the reaction is performed in reverse micelles harboring glycerol and NAD+ in a solution of isooctane containing 250 mM diocytlsulfosuccinate
-
-
?
glycerol + NAD+
glycerone + NADH + H+
activity of the enzyme is confirmed by proteome analysis and enzyme assays with cell extract glycerol-grown cells
-
-
?
glycerol + NAD+
glycerone + NADH + H+
-
-
-
r
glycerol + NAD+
glycerone + NADH + H+
no activity detected with NADP+
-
-
?
glycerol + NAD+
glycerone + NADH + H+
no activity detected with NADP+
-
-
?
glycerol + NAD+
glycerone + NADH + H+
-
glycerone reduction is the dominant reaction
i.e. 1,3-dihydroxypropranone
-
r
glycerol + NAD+
glycerone + NADH + H+
-
-
-
-
r
glycerol + NAD+
glycerone + NADH + H+
-
glycerone reduction is the dominant reaction
i.e. 1,3-dihydroxypropranone
-
r
glycerol + NADP+
glyceraldehyde + NADPH + H+
-
activity observed with pentan-1-ol, 3-methyl-butan-1-ol, 1-decanol, low activity as ethanol dehydrogenase with NAD+ or NADPH+ as cofactor
-
-
?
glycerol + NADP+
glyceraldehyde + NADPH + H+
-
activity observed with pentan-1-ol, 3-methyl-butan-1-ol, 1-decanol, low activity as ethanol dehydrogenase with NAD+ or NADPH+ as cofactor
-
-
?
glycerol-alpha-monochlorohydrin + NAD+
?
-
relative rate of oxidation is 71% compared to oxidation of glycerol
-
-
?
glycerol-alpha-monochlorohydrin + NAD+
?
-
relative rate of oxidation is 26% compared to oxidation of glycerol
-
-
?
meso-2,3-butanediol + NAD+
(3S)-acetoin + NADH
-
-
more than 99% enantiomeric excess of S-product
-
-
meso-2,3-butanediol + NAD+
(3S)-acetoin + NADH
-
-
more than 99% enantiomeric excess of S-product
-
-
methylglyoxal + NADH
lactaldehyde + NAD+
-
relative rate of reduction is 56% compared to reduction of dihydroxyacetone
-
-
?
additional information
?
-
-
ability of the enzyme to use glycerol from biodiesel waste as substrate, overview
-
-
-
additional information
?
-
-
efficiency of a cofactor regeneration enzyme co-expressed with a glycerol dehydrogenase for the production of 1,3-dihydroxyacetone. In vitro biotransformation of glycerol is achieved with the cell-free extracts containing recombinant glycerol dehydrogenase from Escherichia coli, lactate dehydrogenase form Bacillus subtilis, or NADH oxidase LpNox1 from Lactobacillus pentosus, giving1,3-dihydroxyacetone, overview
-
-
-
additional information
?
-
the enzyme is also active with substrates 4-chloroacetoacetate, 3-chloroacetylpyridine, 4-chloroacetophenone, and acetophenone, substrate specificities of enzyme with bound Zn2+, Mn2+, or Mg2+, overview
-
-
-
additional information
?
-
the enzyme is also active with substrates 4-chloroacetoacetate, 3-chloroacetylpyridine, 4-chloroacetophenone, and acetophenone, substrate specificities of enzyme with bound Zn2+, Mn2+, or Mg2+, overview
-
-
-
additional information
?
-
-
high specificity of enzyme for secondary alcohols in R-configuration
-
-
-
additional information
?
-
-
no substrate: 1,3-propanediol, ethanol, 1-propanol, 2-propanol, propionic acid, 1,4-butanediol, sorbitol, L-iditol. Stereospecificity for R-form
-
-
-
additional information
?
-
-
high specificity of enzyme for secondary alcohols in R-configuration
-
-
-
additional information
?
-
-
no substrate: 1,3-propanediol, ethanol, 1-propanol, 2-propanol, propionic acid, 1,4-butanediol, sorbitol, L-iditol. Stereospecificity for R-form
-
-
-
additional information
?
-
-
enzyme TtGlyDH preferentially catalyzes 1,3-dihydroxypropranone reduction rather than alcohol compound oxidation. Glycerol oxidization activity is faintly detected in the presence of a high concentration of glycerol (137 mM). No activity is detected with primary alcohols or diols. The highest glycerol oxidation activity is observed at the optimal growth temperature of 60°C in Tris-HCl buffer (50 mM, pH 8.0). Maximum DHA reduction activity is also observed at 60°C, and TtGlyDH exhibits the highest activity in an acetate buffer, compared with 91% maximum activity in an imidazole buffer at the same pH of 6.0
-
-
-
additional information
?
-
-
enzyme TtGlyDH preferentially catalyzes 1,3-dihydroxypropranone reduction rather than alcohol compound oxidation. Glycerol oxidization activity is faintly detected in the presence of a high concentration of glycerol (137 mM). No activity is detected with primary alcohols or diols. The highest glycerol oxidation activity is observed at the optimal growth temperature of 60°C in Tris-HCl buffer (50 mM, pH 8.0). Maximum DHA reduction activity is also observed at 60°C, and TtGlyDH exhibits the highest activity in an acetate buffer, compared with 91% maximum activity in an imidazole buffer at the same pH of 6.0
-
-
-
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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
glycerol + NAD+
glycerone + NADH + H+
A6TGD6
-
-
-
r
glycerol + NAD+
glycerone + NADH + H+
-
-
-
-
r
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
N6-carboxymethyl-NAD+
-
wild-type enzyme TmGlyDH shows little activity with N6-carboxymethyl-NAD+ (N6-CM-NAD), an NAD+ analogue modified for easy immobilization to amino groups, but the double mutation V44A/K157G increases catalytic efficiency with N6-CMNAD+ by 10fold. kinetics with N6-CM-NAD+ and modelling, overview. N6-CM-NAD+ is immobilized on cyanogen bromide-activated Sepharose 4b
additional information
-
the enzyme's atypical dinucleotide binding motif (GGG motif) and basic residue Arg43 are both related to dinucleotide binding
-
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Co2+
-
presence of Mn2+ enhances the enzyme activity by 31.4%
Cu2+
-
presence of Mn2+ enhances the enzyme activity by 37.0%
K+
Li+
Mg2+
improvement of stability, activity, and substrate promiscuity of glycerol dehydrogenase substituted by divalent metal ions Mn2+ and Mg2+, overview. The activity of Mn-GDH and Mg-GDH improves several folds in comparison to the native GDH. The activity of substituted GDH towards non-natural substrates, 4-chloroacetoacetate, 3-chloroacetylpyridine, p-chloroacetophenone, and acetophenone is 30folds higher than native GDH. Manganese substitution increases the half-life of GDH by 6folds at 60°C and 70°C
Mn2+
NH4+
Rb+
Zn2+
additional information
Mn2+
-
improvement of activity by the substitution of a zinc ion with a manganese ion, accelerating the release of dioxyacetone; the enzyme demonstrates an improvement in activity by the substitution of a zinc ion with a manganese ion. Mn-GDH obeys a compulsory ordered-Bi-Bi mechanism
Mn2+
-
activates, polyethyleneimines-immobilized enzyme PEI-Mn2+-GDH exhibits a 2.9fold increase in activity compared with free GDH
Mn2+
improvement of stability, activity, and substrate promiscuity of glycerol dehydrogenase substituted by divalent metal ions Mn2+ and Mg2+, overview
Mn2+
-
presence of Mn2+ enhances the enzyme activity by 79.5%
NH4+
-
activates, 4fold increase in Vmax produced by NH4Cl in the direction of glycerol oxidation, and 70fold reduction in the Km for dihydroxyaceton and 2fold increase in the Vmax with 30 mM NH4Cl added to the dihydroxyaceton reduction reaction
Zn2+
-
a zinc-dependent metalloenzyme, improvement of activity by the substitution of a zinc ion with a manganese ion; glycerol dehydrogenase from Klebsiella pneumoniae sp. is a zinc-dependent metalloenzyme. The enzyme demonstrates an improvement in activity by the substitution of a zinc ion with a manganese ion
Zn2+
glycerol dehydrogenase from Klebsiella pneumoniae is a zinc-dependent metalloenzyme
Zn2+
-
active-site zinc responsible for coordinating glycerol in the active site of the enzyme. The active site is highly conserved and contains a zinc ion coordinated by two histidines and an aspartate
additional information
-
comparison of the binding energy of enzyme ternary complex for Mn-GDH and Zn-GDH; the equilibrium constants for each ligand-binding are calculated by using the forward and reverse rate constants. By profiling the binding rate and energy for substrate and product with enzyme, the rate accelerating step is determined
additional information
-
the natural GDH-bound Zn2+ are substituted with several divalent metal ions and the enzyme activity is significantly altered. Cu2+, Ni2+, Zn2+, Mn2+, Mg2+ and Ca2+ are used to investigate the effects of metal ions on GDH activity. Only Mn2+ improves the GDH activity by 1.1fold, whereas the other five metal ions inhibit the enzyme to varying degrees at high concentrations
additional information
bifunctional role of metal ions in GDH in catalysis and structure stabilization
additional information
-
three highly conserved enzyme residues, Asp171, His254, and His271, are associated with metal ion binding
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1,3-Propanediol
-
competitive inhibitor versus glycerol in direction of glycerol oxidation, noncompetitive inhibitor versus NAD+, competitive inhibitor versus dihydroxyacetone in direction of glycerol reduction, noncompetitive inhibitor versus NADH
2-amino-2-(hydroxymethyl)-1,3-propanediol
-
strong inhibition, IC50 2 mM
catechol
-
i.e. 1,2-butanediol, inactivation, enzyme regains activity after removal of alcohol
ethanol
-
10% v/v: 25-75% loss of activity, depending on substrate, enzyme regains activity after removal of alcohol
isobutanol
-
5% v/v: 0-50% loss of activity, depending on substrate, enzyme regains activity after removal of alcohol
methanol
-
10% v/v: 25-75% loss of activity, 5% v/v, 50-95% loss of activity, depending on substrate, enzyme regains activity after removal of alcohol
n-amyl alcohol
-
2% v/v: 0-50% loss of activity, depending on substrate, enzyme regains activity after removal of alcohol
n-butanol
-
5% v/v: 0-50% loss of activity, depending on substrate, enzyme regains activity after removal of alcohol
n-Propanol
-
5% v/v: 25-60% loss of activity, depending on substrate, enzyme regains activity after removal of alcohol
o-phthalaldehyde
-
inactivation due to intramolecular thioisoindole formation, glycerol partially protects
2-mercaptoethanol
-
strongly inhibitory at 100 mM, but slight activation in lower concentration, 1 mM
dihydroxyacetone
-
noncompetitive product inhibition; noncompetitive product inhibition with respect to NAD+
NADH
-
competitive inhibitor versus NAD+ in direction of glycerol oxidation, noncompetitive inhibitor versus glycerol
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
citrate
-
the enzyme is more active in presence of multivalent anions, citrate, phosphate or sulfate, in comparison to monovalent anions, e.g. acetate or chloride
iodoacetamide
-
at 1 mM 140% of the activity without activator, at 10 mM 220% of the activity without activator
N-ethylmaleimide
-
at 0.1 mM 145% of the activity without activator
p-chloromercuribenzoic acid
-
at 0.1 mM 133% of the activity without activator
phosphate
-
the enzyme is more active in presence of multivalent anions, citrate, phosphate or sulfate, in comparison to monovalent anions, e.g. acetate or chloride
SO42-
-
the enzyme is more active in presence of multivalent anions, citrate, phosphate or sulfate, in comparison to monovalent anions, e.g. acetate or chloride
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.07
D-glyceraldehyde
-
pH and temperature not specified in the publication
56
ethylene glycol
-
pH and temperature not specified in the publication
77.8
1,3-butanediol
-
mutant protein Q70H/D121A/G193C/E291Q/A310T, pH 9.5, 30°C
30.29
glycerol
-
pH 8.0, 60°C, recombinant enzyme
0.22
Glycerone
-
pH 6.5, 30°C, recombinant enzyme, in presence of 30 mM NH4Cl
1.08
Glycerone
-
pH 6.0, 60°C, recombinant enzyme
0.23
NAD+
Mg-GDH, pH 12.0, 45°C, recombinant enzyme
0.38
NAD+
wild-type Zn-GDH, pH 12.0, 45°C, recombinant enzyme
1.12
NAD+
Mg-GDH, pH 12.0, 45°C, recombinant enzyme
additional information
additional information
-
kinetic study with different effectors, overview
-
additional information
additional information
-
Michaelis-Menten kinetics, cooperative behavior of TmGlyDH
-
additional information
additional information
kinetic and thermodynamic analysis, Michaelis-Menten kinetics, overview
-
additional information
additional information
-
kinetic model based on an ordered bi-bi mechanism, thermodynamics, simulations, overview; kinetic modeling based on an ordered Bi-Bi mechanism, nonlinear regression-based kinetic parameter estimation. Thermodynamics, overview
-
additional information
additional information
-
kinetic study of the metal ion-chelated polyethyleneimines-immobilized enzyme
-
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
98.44
Glycerone
-
pH 6.0, 60°C, recombinant enzyme
87.2
1,3-butanediol
-
mutant protein Q70H/D121A/G193C/E291Q/A310T, pH 9.5, 30°C
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
91.15
Glycerone
-
pH 6.0, 60°C, recombinant enzyme
1.12
1,3-butanediol
-
mutant protein Q70H/D121A/G193C/E291Q/A310T, pH 9.5, 30°C
46.1
NAD+
wild-type Zn-GDH, pH 12.0, 45°C, recombinant enzyme
83.6
NAD+
Mg-GDH, pH 12.0, 45°C, recombinant enzyme
120.3
NAD+
Mg-GDH, pH 12.0, 45°C, recombinant enzyme
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
preliminary kinetic parameters of substrate and product inhibition, overview
-
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2
2-amino-2-(hydroxymethyl)-1,3-propanediol
Pichia membranifaciens
-
strong inhibition, IC50 2 mM
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.01
wild type, crude cell extract, pH not specified in the publication, temperature not specified in the publication
0.049
overexpressing cells, crude cell extract, pH not specified in the publication, temperature not specified in the publication
4.7
-
cell free extract, wild type; wild type, crude extract, pH not specified in the publication, temperature not specified in the publication
6
-
mutant protein D16N/N19A/E23D/L28M/E30N/R31N/Q45E/S46E/V48L/E49R/F52L/K53T/D54G/V58S/G78V/I79V/T82K/A83S/I88V/G108N/R139S/L142M/N145R/K155Q/L211I/G248S/V256I/H268Y/D317E/P319L, pH 9.5, 30°C
6.8
-
mutant protein A15T/D16G/V17A/N19K/E23D/Q45E/S46E/T47M/V48L/E49R/F52L/K53A/V58A/V59A/Q70H/D74N/G78D/E81G/T82N/Q83K/G86T/I88V/G108N/R139S/L142M/N145R/K155Q/V256I/L260M, pH 9.5, 30°C
7.4
-
mutant protein Q70H/D74N/G78D/E81G/T82N/Q83K/C84Y/G86T/I88V/G108N/E134A/E204K/L211I/E215K/I234V/V256I/L260M/E291D/S300C/A302S/E316G/V318I/A320T/I324L/T344D/P345S, pH 9.5, 30°C
220
-
cell free extract, recombinant strain (over-expression of gycerol dehydrogenase); recombinant strain (overexpression), crude extract, pH not specified in the publication, temperature not specified in the publication
additional information
-
assay development for NADH production by recombinant enzyme in reverse micelles, micelle size optimization, overview
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.5
9.5
10 - 11
-
the immobilized GDH changes the optimal pH from pH 11 to 10 and exhibits high activity in a relatively wide range of pH from pH 7 to 12, while free GDH only achieves high activity at pH 11
11
12
additional information
-
kinetic study of the metal ion-chelated polyethyleneimines-immobilized enzyme
8
-
oxidation of glycerol, tetraethyl ammonium chloride/tetraethylammonium hydroxide buffer
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
3 - 9
-
dihydroxyaceton reduction reaction, activity range, profile overview
4.8 - 7.8
-
pH 4.8: about 40% of maximal activity, pH 7.8: about 50% of maximal activity, reduction of dihydroxyacetone
5.5 - 9
-
pH 5.5: about 70% of maximal activity, pH 9.0: about 45% of maximal activity, reduction of dihydroxyacetone
6 - 11
6.8 - 11
-
the initial rate of reaction increases upon increasing the pH from pH 6.8 to 11.0, past pH 11.0 the initial rate falls rapidly, oxidation of glycerol
7 - 10
8 - 10.5
-
pH 8.0: about 40% of maximal activity, pH 10.5: about 70% of maximal activity, oxidation of glycerol
9 - 11
-
pH 9.0: maximal activity, pH 11.0.: nearly inactive, oxidation of glycerol
9 - 12
-
pH 9.0: about 45% of maximal activity, pH 11-12: maximal activity, oxidation of glycerol
7 - 10
-
pH 7.0: about 60% of maximal activity, pH 10.0: about 85% of maximal activity, oxidation of glycerol
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
45
50
60
80
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
kinetic study of the metal ion-chelated polyethyleneimines-immobilized enzyme
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
4.7
calculated; theoretical value
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
-
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
soluble, isolation from crude cell extract
brenda
-
soluble, isolation from crude cell extract; soluble, isolation from crude cell extract; soluble, isolation from crude cell extract
-
brenda
-
soluble, isolation from crude cell extract
brenda
-
soluble, isolation from crude cell extract
brenda
-
soluble, isolation from crude cell extract
brenda
-
soluble, isolation from crude cell extract
-
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
metabolism
physiological function
additional information
evolution
-
the enzyme belongs to the medium-chain dehydrogenase/reductase, MDRase, superfamily
evolution
-
the Serratia marcescens enzyme belongs to the type III Fe-ADH superfamily, three consecutive glycine residues belong to a 14-amino acid residue motif (GDK motif) as the coenzyme NAD(H) binding site, and three conserved histidine residues belong to a 16-residue segment that is homologous to the 15-residue stretch as the binding site of metal
evolution
-
the enzyme belongs to the Fe-ADH family. The GXGXXG motif is not present in TtGlyDH or other members of the Fe-ADH family, the GGG motif forms a more flexible turn and provides enough space to accommodate the pyrophosphate moiety of dinucleotides
evolution
-
NAD+-linked GDHs are members of the medium-chain alcohol dehydrogenase family, most of which are metalloenzymes; the NAD+-linked GDHs are members of the medium-chain alcohol dehydrogenase family, most of which are metalloenzymes
evolution
-
the Serratia marcescens enzyme belongs to the type III Fe-ADH superfamily, three consecutive glycine residues belong to a 14-amino acid residue motif (GDK motif) as the coenzyme NAD(H) binding site, and three conserved histidine residues belong to a 16-residue segment that is homologous to the 15-residue stretch as the binding site of metal
-
evolution
-
the enzyme belongs to the Fe-ADH family. The GXGXXG motif is not present in TtGlyDH or other members of the Fe-ADH family, the GGG motif forms a more flexible turn and provides enough space to accommodate the pyrophosphate moiety of dinucleotides
-
metabolism
-
in Escherichia coli, the enzyme catalyzes the first step in fermentative glycerol metabolism to produce dihydroxyacetone, biochemical transformation pathway of glycerol, overview
metabolism
-
glycerol is one of the key metabolites for propionic acid synthesis in Propionibacterium jensenii. It is a precursor for metabolic pathways for propionic acid, lactic acid, and acetic acid biosynthesis in Propionibacterium
metabolism
anaerobic fermentative metabolism of glycerol: proteome analysis as well as enzyme assays performed in cell-free extracts demonstrate that glycerol is degraded via glyceraldehyde-3-phosphate, which is further metabolized through the lower part of glycolysis leading to formation of mainly ethanol and hydrogen
metabolism
-
glycerol is one of the key metabolites for propionic acid synthesis in Propionibacterium jensenii. It is a precursor for metabolic pathways for propionic acid, lactic acid, and acetic acid biosynthesis in Propionibacterium
-
physiological function
-
GroDHase is mainly involved in Gro utilization as a carbon and energy source
physiological function
-
glycerol dehydrogenase is the enzyme responsible for the oxidation of glycerol to dihydroxyacetone. This permits its entrance into the glycolytic pathway
physiological function
-
glycerol dehydrogenases (GlyDHs) are essential for glycerol metabolism in vivo, catalyzing its reversible reduction to 1,3-dihydroxypropranone
physiological function
-
glycerol dehydrogenases (GlyDHs) are essential for glycerol metabolism in vivo, catalyzing its reversible reduction to 1,3-dihydroxypropranone
-
additional information
-
molecular modeling and site-directed mutagenesis analyses demonstrate that TtGlyDH has an atypical dinucleotide binding motif (GGG motif) and a basic residue Arg43, both related to dinucleotide binding
additional information
-
mechanistic study of manganese-substituted glycerol dehydrogenase using a kinetic and thermodynamic analysis, overview. The binding energy of enzyme ternary complex for Mn-GDH and GDH derived from kinetic parameters indicates that metal ion substitution accelerates the release of dioxyacetone. The metal ion plays a role in catalysis enhancement
additional information
-
molecular modeling and site-directed mutagenesis analyses demonstrate that TtGlyDH has an atypical dinucleotide binding motif (GGG motif) and a basic residue Arg43, both related to dinucleotide binding
-
Show AA Sequence and Transmembrane Helices (2741 entries)
Please use the AA Sequence and Transmembrane Helices Search for a specific query.
Please use the AA Sequence and Transmembrane Helices Search for a specific query.
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PDB
SCOP
CATH
UNIPROT
ORGANISM
Schizosaccharomyces pombe (strain 972 / ATCC 24843)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
38000
38742
x * 38742 , calculated, 367 amino acid residues
39000
39500
39800
-
8 * 40000, recombinant His-tagged enzyme, SDS-PAGE, 8 * 39800, about, sequence calculation
40000
336000 - 390000
40000
-
8 * 40000, recombinant His-tagged enzyme, SDS-PAGE, 8 * 39800, about, sequence calculation
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
homotetramer
monomer
octamer
tetramer
additional information
?
x * 38742 , calculated, 367 amino acid residues
octamer
-
8 * 40000, recombinant His-tagged enzyme, SDS-PAGE, 8 * 39800, about, sequence calculation
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CRYSTALLIZATION/commentary
ORGANISM
UNIPROT
LITERATURE
crystal obtained by hanging-drop vaour-diffusion method, S305C mutant
-
preliminary X-ray characterization; sitting drop vapor-diffusion method
hanging drop vapour diffusion, mixing of 0.001 ml 6 mg/ml protein in 150 mM ammonium acetate, 50 mM sodium chloride, 20 mM Tris, pH 7.4, 5% glycerol with 0.001 ml reservoir solution containing 5-10% PEG 3350, 0.2 M calcium acetate, and 4% glycerol, X-ray diffraction structure determination and analysis at 1.90 A resolution, molecular replacement using PDB entry 1jpu as a search model
-
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
A15T/D16G/V17A/N19K/E23D/Q45E/S46E/T47M/V48L/E49R/F52L/K53A/V58A/V59A/Q70H/D74N/G78D/E81G/T82N/Q83K/G86T/I88V/G108N/R139S/L142M/N145R/K155Q/V256I/L260M
-
mutant selected from a DNA shuffling library (Escherichia coli, Salmonella enterica, Klebsiella pneumoniae)
D121A
-
D121 can potentially hinder the proper binding of substrate 1,3-butanediol due to steric hindrance
D16N/N19A/E23D/L28M/E30N/R31N/Q45E/S46E/V48L/E49R/F52L/K53T/D54G/V58S/G78V/I79V/T82K/A83S/I88V/G108N/R139S/L142M/N145R/K155Q/L211I/G248S/V256I/H268Y/D317E/P319L
-
mutant selected from a DNA shuffling library (Escherichia coli, Salmonella enterica, Klebsiella pneumoniae)
Q70H/D121A/G193C/E291Q/A310T
-
mutant selected from a DNA shuffling library (Escherichia coli, Salmonella enterica, Klebsiella pneumoniae) and site-directed mutation D121A
Q70H/D74N/G78D/E81G/T82N/Q83K/C84Y/G86T/I88V/G108N/E134A/E204K/L211I/E215K/I234V/V256I/L260M/E291D/S300C/A302S/E316G/V318I/A320T/I324L/T344D/P345S
-
mutant selected from a DNA shuffling library (Escherichia coli, Salmonella enterica, Klebsiella pneumoniae)
Q70H/G193C/E291Q/A310T
-
mutant selected from a DNA shuffling library (Escherichia coli, Salmonella enterica, Klebsiella pneumoniae)
I154A
-
site-directed mutagenesis, the mutant shows altered activity with cofactor derivative N6-CM-NAD+ immobilized on Sepharose beads compared to the wild-type enzyme
I154A/K157G
-
site-directed mutagenesis, the mutant shows altered activity with cofactor derivative N6-CM-NAD+ immobilized on Sepharose beads compared to the wild-type enzyme
I154A/K157N
-
site-directed mutagenesis, the mutant shows altered activity with cofactor derivative N6-CM-NAD+ immobilized on Sepharose beads compared to the wild-type enzyme
K157G
-
site-directed mutagenesis, the mutant shows altered activity with cofactor derivative N6-CM-NAD+ immobilized on Sepharose beads compared to the wild-type enzyme
K157N
-
site-directed mutagenesis, the mutant shows altered activity with cofactor derivative N6-CM-NAD+ immobilized on Sepharose beads compared to the wild-type enzyme
V44A
-
site-directed mutagenesis, the mutant shows altered activity with cofactor derivative N6-CM-NAD+ immobilized on Sepharose beads compared to the wild-type enzyme
V44A/I154A
-
site-directed mutagenesis, the mutant shows altered activity with cofactor derivative N6-CM-NAD+ immobilized on Sepharose beads compared to the wild-type enzyme
V44A/K157G
-
site-directed mutagenesis, the mutant shows altered activity with cofactor derivative N6-CM-NAD+ immobilized on Sepharose beads compared to the wild-type enzyme; site-directed mutagenesis, wild-type enzyme TmGlyDH shows little activity with N6-carboxymethyl-NAD+ (N6-CM-NAD), an NAD+ analogue modified for easy immobilization to amino groups, but the double mutation V44A/K157G increases catalytic efficiency with N6-CMNAD+ by 10fold
V44A/K157N
-
site-directed mutagenesis, the mutant shows altered activity with cofactor derivative N6-CM-NAD+ immobilized on Sepharose beads compared to the wild-type enzyme
I154A
Thermotoga maritima MSB8 / DSM 3109 / ATCC 43589
-
site-directed mutagenesis, the mutant shows altered activity with cofactor derivative N6-CM-NAD+ immobilized on Sepharose beads compared to the wild-type enzyme
-
K157N
Thermotoga maritima MSB8 / DSM 3109 / ATCC 43589
-
site-directed mutagenesis, the mutant shows altered activity with cofactor derivative N6-CM-NAD+ immobilized on Sepharose beads compared to the wild-type enzyme
-
V44A
Thermotoga maritima MSB8 / DSM 3109 / ATCC 43589
-
site-directed mutagenesis, the mutant shows altered activity with cofactor derivative N6-CM-NAD+ immobilized on Sepharose beads compared to the wild-type enzyme
-
V44A/K157G
Thermotoga maritima MSB8 / DSM 3109 / ATCC 43589
-
site-directed mutagenesis, the mutant shows altered activity with cofactor derivative N6-CM-NAD+ immobilized on Sepharose beads compared to the wild-type enzyme; site-directed mutagenesis, wild-type enzyme TmGlyDH shows little activity with N6-carboxymethyl-NAD+ (N6-CM-NAD), an NAD+ analogue modified for easy immobilization to amino groups, but the double mutation V44A/K157G increases catalytic efficiency with N6-CMNAD+ by 10fold
-
additional information
additional information
-
efficiency of a cofactor regeneration enzyme co-expressed with a glycerol dehydrogenase for the production of 1,3-dihydroxyacetone. In vitro biotransformation of glycerol is achieved with the cell-free extracts containing recombinant glycerol dehydrogenase from Escherichia coli, lactate dehydrogenase form Bacillus subtilis, or NADH oxidase LpNox1 from Lactobacillus pentosus, giving1,3-dihydroxyacetone, coexpression of all enzymes in Escherichia coli strain BL21(DE3)
additional information
-
the glycerol dehydrogenase gene from Klebsiella pneumoniae is fused to codon-optimized NADH oxidase gene from Lactobacillus brevis. Gene fusion of glycerol dehydrogenase (GDH) and NOX forms a bifunctional multienzyme for bioconversion of glycerol coupled with coenzyme regeneration
additional information
-
bioinspired immobilization of glycerol dehydrogenase by metal ion-chelated polyethyleneimines (PEI) as artificial polypeptides. Nanoparticles with diameters from 250–650 nm are prepared that exhibit a 1.4fold enhancement catalytic efficiency. The oligomeric GDH assemblies are coated and stabilized by the excessive manganese-chelated PEIs, which further prevents the disassociation of the GDH subunits, metal-mediated oligomeric assemblies of the enzyme. Half-life of immobilized GDH is enhanced by 5.6folds in aqueous phase at 85°C. Formation of multi-level interactions in the PEI-metal-GDH complex, mechanism, overview. A potential technique for multimeric enzyme immobilization with the advantages of low cost, easy operation, high activity reservation, and high stability. The activity of PEI-Mn2+-GDH gradually decreases over 5 cycles. PEI-Mn2+-GDH retains 71% and 53% of its initial activity after cycling through 3 and 5 successive reactions, respectively. The decrease in the activity of the recycled catalyst may be due to the leakage of GDH
additional information
-
bioinspired immobilization of glycerol dehydrogenase by metal ion-chelated polyethyleneimines (PEI) as artificial polypeptides. Nanoparticles with diameters from 250–650 nm are prepared that exhibit a 1.4fold enhancement catalytic efficiency. The oligomeric GDH assemblies are coated and stabilized by the excessive manganese-chelated PEIs, which further prevents the disassociation of the GDH subunits, metal-mediated oligomeric assemblies of the enzyme. Half-life of immobilized GDH is enhanced by 5.6folds in aqueous phase at 85°C. Formation of multi-level interactions in the PEI-metal-GDH complex, mechanism, overview. A potential technique for multimeric enzyme immobilization with the advantages of low cost, easy operation, high activity reservation, and high stability. The activity of PEI-Mn2+-GDH gradually decreases over 5 cycles. PEI-Mn2+-GDH retains 71% and 53% of its initial activity after cycling through 3 and 5 successive reactions, respectively. The decrease in the activity of the recycled catalyst may be due to the leakage of GDH; the glycerol dehydrogenase gene from Klebsiella pneumoniae is fused to codon-optimized NADH oxidase gene from Lactobacillus brevis. Gene fusion of glycerol dehydrogenase (GDH) and NOX forms a bifunctional multienzyme for bioconversion of glycerol coupled with coenzyme regeneration
-
additional information
-
recombinant co-overexpression of enzymes glycerol dehydrogenase, malate dehydrogenase, and fumarate hydratase from Klebsiella pneumoniae subsp. pneumoniae strain ATCC 12657 in Propionibacterium jensenii leads to increased increased propionic acid production. The transcription levels of the corresponding enzymes in the engineered strains are 2.85 to 8.07fold higher than those in the wild type. The coexpression of GDH and MDH increases the propionic acid titer from 26.95 g/liter in wild-type to 39.43 g/liter in the engineered strains. Fed-batch culture kinetics of propionic acid production from glycerol, overview
additional information
-
recombinant co-overexpression of enzymes glycerol dehydrogenase, malate dehydrogenase, and fumarate hydratase from Klebsiella pneumoniae subsp. pneumoniae strain ATCC 12657 in Propionibacterium jensenii leads to increased increased propionic acid production. The transcription levels of the corresponding enzymes in the engineered strains are 2.85 to 8.07fold higher than those in the wild type. The coexpression of GDH and MDH increases the propionic acid titer from 26.95 g/liter in wild-type to 39.43 g/liter in the engineered strains. Fed-batch culture kinetics of propionic acid production from glycerol, overview
-
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.5
additional information
-
immobilization of the enzyme by metal ion-chelated polyethyleneimines greatly broadens the pH adaptability of GDH from strong alkaline into alkalescence
741417
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30 - 50
purified recombinant enzyme, pH 12.0, quite stable over 150 min
50
55
-
recombinant enzyme, maintaining 70% activity after 2 h
60
60 - 70
-
recombinant enzyme, maintaining over 80% activity after 30 min
60
-
recombinant enzyme, maintaining 65% activity after 2 h
70
80
-
the recombinant enzyme, 40% activity remaining after 25 min, 20% activity remaining after 150 min
85
-
metal ion-chelated polyethyleneimine-immobilized enzyme PEI-Mn2+-GDH exhibits a half-life that is enhanced by 5.6folds in aqueous phase at 85°C
additional information
thermal inactivation of GDH is not a simple first-order process, thermal deactivation kinetics, modelling, overview
50
-
the recombinant enzyme is initially more stable in the presence of DHA than in its absence, maintaining 100% activity over 120 min, but it quickly inactivates after 120 min, losing over 84% of its activity in the next 5 h
60
purified recombinant enzyme, pH 12.0, loss of about 25% activity after 100 min
70
-
metal ion-chelated polyethyleneimine-immobilized enzyme PEI-Mn2+-GDH exhibits greater heat resistance than free enzyme GDH. After incubation for 90 min at 70°C, PEI-Mn2+-GDH still presents nearly 50% of its initial activity, while free GDH is almost totally inactivated
70
purified recombinant enzyme, pH 12.0, loss of about 75% activity after 80 min
70
-
recombinant enzyme, maintaining 19% activity after 2 h
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
manganese substitution increases the half-life of GDH by 6folds at 60°C and 70°C
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-15°C, with 5% culture filtrate or 5% boiled crude cell extract, 10% Ficoll, pH 7.5, stable for 1 month
-
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PURIFICATION/commentary
ORGANISM
UNIPROT
LITERATURE
gene gldA, recombinant C-terminally His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, ultrafiltration, and dialysis
-
immobilized metal ion affinity chromatography (Co2+)
immobilized metal ion affinity chromatography (Ni2+); purity estimated from SDS-PAGE: 95%
purified by Ni-affinity chromatography; recombinant His-tagged enzyme from strain BL21(DE3) by nickel affinity chromatography
-
purified with 25fold purification and 68% yield using a single chromatographic step
-
recombinant His-tagged chimeric enzyme GDH-NOX from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
-
recombinant His-tagged enzyme from Escherichia coli strain BL21 (DE3) by immobilized metal affinity chromatography or by heat shock treatment, both resulting in about the same protein purity of over 90%
-
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
-
recombinant N-terminally His6-tagged enzyme from Escherichia coli train BL21(DE3)pLysS by nicke affinity chromatography and gel filtration
-
recombinent His-tagged enzyme from Escherichia coli strain BL21(DE3) pET-32a by nickel affinity chromatography, desalting gel filtration, and ultrafiltration
-
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CLONED/commentary
ORGANISM
UNIPROT
LITERATURE
cloning from contaminating bacteria, DNA and amino acid sequence determmination and analysis, recombinant expression of N-terminally His6-tagged enzyme in Escherichia coli train BL21(DE3)pLysS
-
coexpression of enzymes recombinant glycerol dehydrogenase from Escherichia coli, lactate dehydrogenase form Bacillus subtilis, and NADH oxidase LpNox1 from Lactobacillus pentosus in Escherichia coli strain BL21(DE3). The activities of LDH, LpNox1 and GlyDH in the cell-free extract are 98.8, 27.8 and 39.5 U/ml, respectively, overview
-
expressed in Klebsiella pneumoniae KG1; overexpressed in Klebsiella pneumoniae KG1
-
expression as His-tag fusion protein in Escherichia coli BL21 (DE3) pLysS; gene gld, expression of His-tagged enzyme in strain BL21(DE3)
-
gene gldA from Escherichia coli strain JM109, expression of His-tagged enzyme in Escherichia coli strain BL21 (DE3), subcloning in Escherichia coli TOP10 cells
-
gene gldA, DNA and amino acid sequence determination and analysis, recombinant expression in Escherichia coli strain BL21(DE3)
-
gene gldA, DNA and amino acid sequence determination and analysis, sequence comparisons and phylogenetic analysis, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
-
gene gldA, recombinant expression in Escherichia coli strain BL21(DE3); gene gldA, recombinant expression in Escherichia coli strain BL21(DE3)
-
gene gldA, recombinant expression of C-terminally His6-tagged enzyme in Escherichia coli strain BL21(DE3)
-
His-tagged version expressed in Escherichia coli BL21 STAR (DE3); N-terminal His-tag, expressed in E. coli BL21 STAR (DE3)
His-tagged version expressed in Escherichia coli BL21(DE3)
recombinant co-overexpression of enzymes glycerol dehydrogenase, malate dehydrogenase, and fumarate hydratase from Klebsiella pneumoniae subsp. pneumoniae strain ATCC 12657 in Propionibacterium jensenii leads to increased increased propionic acid production, quantittive reverse transcription PCR expression analysis
-
recombinant expression of the His-tagged enzyme encoding gene fused to the codon-optimized NADH oxidase gene nox from Lactobacillus brevis, chimeric enzyme GDH-NOX, in Escherichia coli strain BL21(DE3) resulting in bioconversion of glycerol to dihydroxyacetone in the cells
-
recombinent expression of His-tagged enzyme in Escherichia coli strain BL21(DE3) pET-32a
-
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
induced by alcohols and aliphatic or aromatic hydrocarbons when glycerol used as the only substrate; induced by n-decanol (as sole carbon source)
induced by glucose starvation, essential for glycerol assimilation
induced by alcohols and aliphatic or aromatic hydrocarbons when glycerol used as the only substrate; induced by