Information on EC 1.1.1.202 - 1,3-propanediol dehydrogenase

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The expected taxonomic range for this enzyme is: Bacteria

EC NUMBER
COMMENTARY hide
1.1.1.202
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RECOMMENDED NAME
GeneOntology No.
1,3-propanediol dehydrogenase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
propane-1,3-diol + NAD+ = 3-hydroxypropanal + NADH + H+
show the reaction diagram
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
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redox reaction
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reduction
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
glycerol degradation III
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Glycerolipid metabolism
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Propanoate metabolism
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SYSTEMATIC NAME
IUBMB Comments
propane-1,3-diol:NAD+ 1-oxidoreductase
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CAS REGISTRY NUMBER
COMMENTARY hide
81611-70-3
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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-
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Manually annotated by BRENDA team
E5
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Manually annotated by BRENDA team
LMG 1212t2
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Manually annotated by BRENDA team
strain VPI 3266
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Manually annotated by BRENDA team
LMG 3285
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Manually annotated by BRENDA team
strain SYU 21132
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Manually annotated by BRENDA team
strain Cu, derivative of ATCC 200721
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Manually annotated by BRENDA team
DSM2026
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Manually annotated by BRENDA team
strain M5a1
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Manually annotated by BRENDA team
strain TUAC01, gene dhaT
UniProt
Manually annotated by BRENDA team
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UniProt
Manually annotated by BRENDA team
gene TM0920, strain MSB8
SwissProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
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growth behaviour on glucose is comparable between the wild type and a mutant strain lacking ORF lr0030. On glucose plus glycerol, the exponential growth rate of the lr_0030 mutant is lower compared to the wild type. Glycerol addition results in decreased ethanol production in the wild type, but not in lr_0030 mutant. Activity measurements using 3-hydrxypropanal as a substrate reveal lower activity of lr_0030 mutant extracts from exponential growing cells compared to wild type. During biotechnological 3-hydroxypropanal production using non-growing cells, the ratio 3-hydroxypropanal to 1,3-propanediol is approximately 7 in the wild type and lr_0030 mutant; growth behaviour on glucose is comparable between the wild type and a ORF lr1734 deletion mutant. On glucose + glycerol, the exponential growth rate of the wild type and the deletion mutant are similar. Glycerol addition results in decreased ethanol production both in the wild type and mutant. During biotechnological 3-hydroxypropanal production using non-growing cells, the ratio 3-hydroxypropanal to 1,3-propanediol is approximately 7 in the wild type, whereas this ratio is 12.5 in the mutant lacking lr_1734
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
1,2-propanediol + NAD+
2-hydroxypropanal + NADH
show the reaction diagram
1,3-propanediol + NAD+
3-hydroxypropanal + NADH
show the reaction diagram
1,3-propanediol + NAD+
3-hydroxypropanal + NADH + H+
show the reaction diagram
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-
-
-
?
1,4-butanediol + NAD+
4-hydroxybutanal + NADH
show the reaction diagram
1-butanol + NAD+
NADH + butanal
show the reaction diagram
1-propanol + NAD+
NADH + propanal
show the reaction diagram
2,3-butanediol + NAD+
? + NADH
show the reaction diagram
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-
-
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r
2-butanol + NAD+
NADH + butanone
show the reaction diagram
3-hydroxypropanal + NADH
propane-1,3-diol + NAD+
show the reaction diagram
3-hydroxypropanal + NADH + H+
propane-1,3-diol + NAD+
show the reaction diagram
3-hydroxypropanal + NADPH + H+
propane-1,3-diol + NADP+
show the reaction diagram
3-hydroxypropionaldehyde + NADH
propane-1,3-diol + NAD+
show the reaction diagram
ethanol + NAD+
NADH + ethanal
show the reaction diagram
ethylene glycol + NAD+
NADH + ?
show the reaction diagram
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-
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r
glycerol + NAD+
glyceraldehyde + NADH
show the reaction diagram
glycerol + NADH
propane-1,3-diol + NAD+
show the reaction diagram
propane-1,2-diol + NAD+
2-hydroxypropanal + NADH
show the reaction diagram
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-
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r
propane-1,3-diol + NAD+
3-hydroxypropanal + NADH
show the reaction diagram
propane-1,3-diol + NAD+
3-hydroxypropanal + NADH + H+
show the reaction diagram
propane-1,3-diol + NAD+
glycerol + NADH
show the reaction diagram
propane-1,3-diol + NAD+ + H+
3-hydroxypropanal + NADH
show the reaction diagram
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-
-
?
propane-1,3-diol + NADP+
3-hydroxypropanal + NADPH + H+
show the reaction diagram
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NADP+ is not substrate for wild-type, but for mutant D41G
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r
additional information
?
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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
1,3-propanediol + NAD+
3-hydroxypropanal + NADH + H+
show the reaction diagram
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-
-
-
?
3-hydroxypropanal + NADH + H+
propane-1,3-diol + NAD+
show the reaction diagram
3-hydroxypropionaldehyde + NADH
propane-1,3-diol + NAD+
show the reaction diagram
glycerol + NADH
propane-1,3-diol + NAD+
show the reaction diagram
propane-1,3-diol + NAD+
3-hydroxypropanal + NADH
show the reaction diagram
propane-1,3-diol + NAD+
glycerol + NADH
show the reaction diagram
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the enzyme is important in vivo for convertion of glycerol into propane-1,3-diol
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r
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K+
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highest levels of activity in presence of 100 mM K+
Ni2+
located near active site, crystallization data. The activity with 1,3-propanediol is highly dependent on the presence of Ni2+
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1,10-phenanthroline
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2,2'-dipyridyl
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reactivation by Mn2+ or Fe2+
8-hydroxyquinoline
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EDTA
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50 mM is necessary to obtain a 50% inhibition of enzymatic activity
glycerol
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at high concentration above 40 g/l, overview
imidazole
activity is reduced down to 32% in the presence of 1 mM imidazole and addition of 250 mM results in complete inactivity
additional information
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
fumarate
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25% activation of the enzyme, enhances the production of 1,3-propanediol from glycerol and the glycerol consumption in vivo
glycerol
isopropyl-beta-D-thiogalactoside
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inducer of gene expression, results in the increased activity of PDOR in LB medium
isopropyl-D-thiogalactoside
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DhaT activity in the AK strain harboring pBR-dhaT-orfWX remarkably increases in the presence of isopropyl-D-thiogalactoside, although the activity is not proportional to the concentration of the inducer
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
11.5
1,2-propanediol
pH 9.0, 60C
26.7
1,3-Propanediol
pH 9.0, 60C
10.05
3-hydroxypropanal
pH 8.0, 37C
26 - 29
glyceraldehyde
300 - 700
glycerol
0.05 - 0.48
NAD+
0.013 - 0.48
NADH
0.97
NADP+
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mutant D41G, pH 7.4, 37C
0.14
NADPH
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mutant D41G, pH 7.4, 37C
1.25 - 18
Propane-1,3-diol
0.17 - 11
propionaldehyde
additional information
additional information
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mathematical description and modelling of reaction and reaction kinetics, overview
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
51.99 - 82.33
NAD+
90.64 - 411.6
NADH
11.83
NADP+
Klebsiella pneumoniae
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mutant D41G, pH 7.4, 37C
187.4
NADPH
Klebsiella pneumoniae
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mutant D41G, pH 7.4, 37C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.01
1,2-propanediol
4.9 - 260
NAD+
12.9 - 6043
NADH
12.2
NADP+
Klebsiella pneumoniae
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mutant D41G, pH 7.4, 37C
10
1338
NADPH
Klebsiella pneumoniae
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mutant D41G, pH 7.4, 37C
5
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
12.09
glycerol
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pH 9.0, 25C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.37
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wild-type Clostridium butyricum strain VPI 3266
1.1
pH 9.0, 60C
1.2
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recombinant enzyme in Clostridium acetobutylicum mutant strain DG1
3.8
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native enzyme
9.6
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recombinant enzyme
49.5
reduction of 3-hydroxypropanal, pH 8.0, 37C
77.9
oxidation of propane-1,3-diol, pH 10.5, 25C
additional information
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nucleotide pools of wild-type Clostridium butyricum strain VPI 3266 and recombinant Clostridium acetobutylicum mutant strain DG1
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.2
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3-hydroxypropanal + NADH
7
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propane-1,3-diol + NAD+
9.07
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3-hydroxypropanal + NADH
9.5
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recombinant enzyme
9.7
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assay at
9.72
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propane-1,3-diol + NADH
10.5
oxidation of alcohol
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 8.5
more than 80% of maximum activity for reduction of aldehyde
7
less than 10% of maximum activity for oxidation reaction
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30
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recombinant enzyme
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.2
calculated
5.9
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sequence calculation
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
43000
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gel filtration and PAGE
74000
gel filtration
180000
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gel filtration
328000
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gel filtration
331000
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gel filtration, sedimentation coefficient
355000
384200
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gel filtration
415000
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sequence analysis
446000
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dynamic light scattering analysis of the purified protein in solution
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
decamer
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crystallography or gel filtration
hexamer or octamer
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6 * or 8 * 45000, SDS-PAGE
monomer
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1 * 43000, calculated
octamer
tetramer
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4 * 42000, SDS-PAGE
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
selenomethionine-labeled protein, to 2.4 A resolution. space group P32
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by vapor diffusion in sitting drops at 20C, at 2.7 A resolution. The enzyme shows a decameric structure, formed by a pentamer of dimers, which is the catalytic form of the enzyme. Dimers are associated by strong ionic interactions that are responsible for the highly stable in vivo packing of the enzyme. The decameric arrangement is related to the cooperativity between monomers
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homology modeling with cofactors NADH and NADPH
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purified recombinant His-tagged enzyme, sitting-drop vapour diffusion, 22C, 0.0015 ml of 55 mg/ml protein in 50 mM HEPES, pH 7.4, 150 mM NaCl, 1 mM MnCl2 and 2 mM DTT, is mixed with an equal volume of reservoir solution containing 0.1 M MES, pH 6.5, with 12% w/v PEG 20000, and 10 mM CaCl2, 8-24 h, X-ray diffraction structure determination and analysis at 2.7 A resolution
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to 3.2 A resolution. The electron density map around the active site shows no sign of a bound co-factor, but the active site metal could be located and identified as Ni2+
purified recombinant His-tagged protein in 20 mM Tris, pH 7.9, 150 mM NaCl, 0.25 mM TCEP, by nandroplet vapour diffusion method, cyrstallization buffer contains 20% PEG 300, 5% w/v PEG 8000, 10% glycerol, and 0.1 M Tris-HCl, pH 8.5, X-ray diffraction structure determination and analysis at 1.3 A resolution, modeling of 2 enzyme molecules, residues 1-359, complexed with 2 molecules of NADP+, 2 ions of Fe2+, 2 molecules of Tris, and 895 water molecules
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 7
most stable within this range
721395
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50
60 min, inactivation
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, Mn2+-DTT-HEPES buffer, stable for 3 days, 82% loss of activity after 3 weeks
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OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
inactivated by oxidation during aerobic metabolism
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389488
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
by centrifugation, nickel affinity column and gel filtration
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recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
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recombinant protein
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recombinant soluble enzyme from Escherichia coli strain BL21(DE3)
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recombinant tagged selenomethionine-labeled enzyme from Escherichia coli by nickel affinity, ion exchange, and gel filtration chromatography and ultrafiltration
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
all genes of the dha regulon, including the gene for 1,3-propanediol oxidoreductase of Klebsiella pneumoniae mobilized by the plasmid RP4:mini Mu and transferred to Escherichia coli
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expression in Clostridium acetobutylicum mutant strain DG1 from plasmid pSPD5, subcloning in Escherichia coli
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expression in Escherichia coli
gene dhaT, cloning from genomic DNA, DNA sequence determination, inducible high-level expression of the mostly soluble enzyme in Escherichia coli strain BL21(DE3)
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gene dhaT, DNA and amino acid sequence determination and analysis, sequence comparisons
gene dhaT, expression of the N-terminally His-tagged in Escherichia coli strain BL21(DE3)
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gene dhaT, high level co-expression of the 1,3-PD oxidoreductase with glycerol dehydratase, encoded by gene dhaB, and glycerol dehydratase reactivating factor, encoded by gene gdrAB, in Escherichia coli strain BL21 (DE3) using two incompatible plasmids, fed-batch fermentation of recombinant bacteria. The NADPH-linked alcohol dehydrogenase, which is encoded by yqhD, a gene from Escherichia coli, can non-specifically catalyze 3-hydroxypropionaldehyde converting to 1,3-propanediol with sufficient activity, overview
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gene TM0920, expression of soluble N-terminally MGSDKIHHHHHH-tagged selenomethionine-labeled enzyme in Escherichia coli methionine auxotrophic strain DL41
genes for the production of propane-1,3-diol in Clostridium butyricum, dhaB1 and dhaB2, which encode the vitamin B12-independent glycerol dehydratase DhaB1 and its activating factor, DhaB2, respectively, tandemly arrayed with the Escherichia coli yqhD gene, which encodes the 1,3-propanediol oxidoreductase isoenzyme YqhD. Heterologous expression of the propane-1,3-diol operon under the control of the temperature-sensitive lambda phage PLPR promoter regulated by the cIts857 repressor, from plasmid pDY220, in Escherichia coli K-12 ER2925
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overexpression in Escherichia coli
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overexpression of gene dhaT encoding PDOR (from vector pETPkan-dhaT) and transformed into Klebsiella pneumoniae
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plasmid including Escherichia coli yqhD introduced into Klebsiella pneumoniae AK mutant strain defective in in 1,3-PD oxidoreductase activity (DhaT)
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plasmid pUC18K-dhaT transformed into Klebsiella pneumoniae KG1
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plasmids pUC18 K-dhaT and pUC18 K-gdh, carrying the genes dhaT encoding PDOR and gdh encoding glycerol dehydrogenase, respectively, transformed into a propane-1,3-diol native producer Klebsiella pneumoniae KG1
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recombinant plasmids containing dhaT expressed in Klebsiella pneumoniae Cu, and the mutant strains AK and AR
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the dhaD gene encoding glycerol dehydrogenase (GDH) and dhaT gene encoding 1,3-propanediol oxidoreductase (PDOR) inserted into pTD plasmid and overexpressed in Klebsiella pneumoniae ACCC 10082
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the dhaT gene coding for 1,3-PD dehydrogenase inserted into vector pET-YSBLIC and transformed into Escherichia coli BL21(DE3)
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D41A
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mutation for relaxation of the coenzyme specificity, weakens the repulsion between Asp41 and the phosphate group esterified to the 2-hydroxyl group of the ribose at the adenine end of NADPH
D41G
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mutation for relaxation of the coenzyme specificity, weakens the repulsion between Asp41 and the phosphate group esterified to the 2-hydroxyl group of the ribose at the adenine end of NADPH
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
industry
synthesis
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