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Enzyme Nomenclature
Information on EC 1.2.1.46 - formaldehyde dehydrogenase
for references in articles please use BRENDA:EC1.2.1.46
Word Map on EC 1.2.1.46
- 1.2.1.46
- methanol
-
gsh-dependent
- s-hydroxymethylglutathione
-
dissimilation
- boidinii
- hyphomicrobium
-
1.2.1.1
- s-formylglutathione
-
methanol-grown
-
methanol-utilizing
- industry
- degradation
- biotechnology
- analysis
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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
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EC NUMBER 
COMMENTARY 
1.2.1.46
-
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RECOMMENDED NAME
GeneOntology No.
formaldehyde dehydrogenase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
formaldehyde + NAD+ + H2O = formate + NADH + 2 H+
-
-
-
-
formaldehyde + NAD+ + H2O = formate + NADH + 2 H+
Pseudomonas aeruginosa FDH has a conserved glutathione-independent ping pong mechanism of formaldehyde oxidization
formaldehyde + NAD+ + H2O = formate + NADH + 2 H+
the catalytic reaction proceeds by a Ping Pong mechanism as designated by the Michaelis-Menten model of bi-substrate enzymatic kinetics
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formaldehyde + NAD+ + H2O = formate + NADH + 2 H+
Pseudomonas aeruginosa FDH has a conserved glutathione-independent ping pong mechanism of formaldehyde oxidization
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
oxidation
redox reaction
reduction
oxidation
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-
-
-
redox reaction
-
-
-
-
reduction
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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SYSTEMATIC NAME
IUBMB Comments
formaldehyde:NAD+ oxidoreductase
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CAS REGISTRY NUMBER
COMMENTARY
9028-84-6
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
physiological function
additional information
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analysis of the influence of the crystallinity of titanium dioxide (TiO2) filmson the quantity and activity of the immobilized formaldehyde dehydrogenase, interactions between the FDH and TiO2thin film surfaces , overview. TiO2films with high crystallinity, which are annealed at 550°C, show higher enzyme immobilization and activity compared with the non-annealed TiO2film
evolution
formaldehyde dehydrogenase (FDH) is a member of the zinc-containing medium-chain alcohol dehydrogenase family
evolution
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the enzyme is a member of zinc-containing medium-chain alcohol dehydrogenase family
evolution
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formaldehyde dehydrogenase (FDH) is a member of the zinc-containing medium-chain alcohol dehydrogenase family
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physiological function
the enzyme oxidizes toxic formaldehyde to formate using NAD+ as an electron carrier
physiological function
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the enzyme oxidizes toxic formaldehyde to less active formate using NAD+ as a cofactor. The enzyme requires only NAD+ as the electron carrier, and addition of glutathione has no effect on the catalytic activity, indicating glutathione-independent catalysis
physiological function
-
the enzyme oxidizes toxic formaldehyde to formate using NAD+ as an electron carrier
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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
S-hydroxymethylglutathione + NAD+ + H2O
S-formylglutathione + NADH + H+
-
-
-
-
?
formaldehyde + H2O + NAD+
formate + NADH + H+
-
-
-
-
?
formaldehyde + NAD+ + H2O
formate + NADH
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required for growth on methanol as carbon source or methylamine as nitrogen source, reaction provides energy as NADH and protects against a toxic excess of formaldehyde
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-
?
formaldehyde + NAD+ + H2O
formate + NADH
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required for growth on methanol as carbon source or methylamine as nitrogen source, reaction provides energy as NADH and protects against a toxic excess of formaldehyde
-
-
?
formaldehyde + NAD+ + H2O
formate + NADH
-
-
-
-
-
formaldehyde + NAD+ + H2O
formate + NADH
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enzyme of creatinine metabolism
-
-
-
formaldehyde + NAD+ + H2O
formate + NADH
removal of toxic formaldehyde
-
-
?
formaldehyde + NAD+ + H2O
formate + NADH
-
enzyme of creatinine metabolism
-
-
-
formaldehyde + NAD+ + H2O
formate + NADH + H+
-
-
-
-
?
formaldehyde + NAD+ + H2O
formate + NADH + H+
-
key enzyme of formaldehyde metabolism in microorganisms
-
-
?
additional information
?
-
-
no substrates are propionaldehyde, n-butyraldehyde, isobutyraldehyde, valeraldehyde, acetaldehyde, benzaldehyde
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-
-
additional information
?
-
-
specificity, best substrate: formaldehyde
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-
-
additional information
?
-
-
reduced activity with increasing length of alkyl groups of aldehydes
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-
-
additional information
?
-
-
no activity with n-butyraldehyde or n-valeraldehyde
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-
-
additional information
?
-
-
specificity, best substrate: formaldehyde
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-
-
additional information
?
-
-
reduced activity with increasing length of alkyl groups of aldehydes
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-
-
additional information
?
-
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no activity with n-butyraldehyde or n-valeraldehyde
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-
-
additional information
?
-
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no activity for methanol or ethanol
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-
-
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
formaldehyde + NAD+ + H2O
formate + NADH
-
required for growth on methanol as carbon source or methylamine as nitrogen source, reaction provides energy as NADH and protects against a toxic excess of formaldehyde
-
-
?
formaldehyde + NAD+ + H2O
formate + NADH
-
required for growth on methanol as carbon source or methylamine as nitrogen source, reaction provides energy as NADH and protects against a toxic excess of formaldehyde
-
-
?
formaldehyde + NAD+ + H2O
formate + NADH
-
enzyme of creatinine metabolism
-
-
-
formaldehyde + NAD+ + H2O
formate + NADH
P46154
removal of toxic formaldehyde
-
-
?
formaldehyde + NAD+ + H2O
formate + NADH
-
enzyme of creatinine metabolism
-
-
-
formaldehyde + NAD+ + H2O
formate + NADH + H+
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key enzyme of formaldehyde metabolism in microorganisms
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
NAD+
tightly but not covalently bound to protein, one molecule bound per subunit
NAD+
NAD+-binding mode analysis, with two bound zinc ions per monomer of the tetrameric enzyme
additional information
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substrate specificity is regulated by modifin, FDH oxidizes formaldehyde exclusively and only in the presence of modifin, whereas a range of aldehydes and alcohols are oxidized in the absence of modifin, modifin cannot be replaced by glutathione
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additional information
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pyrroloquinoline quinone may be the bound cofactor
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additional information
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processes formaldehyde in a highly selective manner and without need for NAD(P). The dlFalDH cofactor is an unidentified quinone
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ca2+
Zinc
Zn2+
Ca2+
-
plays an important role in the active centre of DL-FDH and for the sensing purpose
Ca2+
-
is required for the stabilization of the tetrameric structure of dlFalDH and for its optimal functionality
Zinc
-
zinc metalloenzyme, 2 zinc atoms per subunit, one participates in catalytic activity, the other is involved in maintaining the native conformation of the enzyme
Zinc
-
active-site zinc-liganding amino acids: Cys-47 and His-68; structural zinc-liganding amino acids: Cys-97, Cys-100, Cys-103, Cys-111
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
SDS
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1 mM, over 50% loss of activity for the free enzyme, about 10% loss of activity for the immobilized enzymes
2,2'-bipyridine
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reversible inactivation, formation of an enzyme-Zn-bipyridine complex
additional information
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down-regulation of the dlFalDH production in correlation with the absence of methylamine hydrochloride consumption
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additional information
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biosensor output signal decreases substantially with the increase of borate buffer concentration. Sensitivity of the biosensor in 2.5 mM Tris-HCl buffer is decreased dramatically
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
methanol
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cultivation on 1% methanol provides the highest level of enzyme synthesis for recipient and overproducing strains
additional information
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culture in the fed-batch mode in the bioreactor and active methylamine consumption positively affect dlFalDH productivity
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additional information
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best sensitivity of the biosensor is observed in 2.5 mM borate buffer, pH 8.4
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additional information
the enzyme from Pseudomonas putida is an exception in that it does not depend on glutathione for catalysis
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additional information
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the enzyme from Pseudomonas aeruginosa does not depend on glutathione for catalysis. The enzyme requires only NAD+ as the electron carrier, and addition of glutathione has no effect on the catalytic activity, indicating glutathione-independent catalysis
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.18
formaldehyde
-
KM value of the used FdDH in solution from the wild strains
0.438
formaldehyde
-
enzyme immobilized on phenyl-functionalized MPS-4, pH 7.0, 22°
10.6
formaldehyde
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enzyme immobilized on methyl-functionalized MPS-4, pH 7.0, 22°
119.9
formaldehyde
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immobilized enzyme in a bioactive layer on the transducer surface, apparent Michaelis-Menten constant derived from the formaldehyde calibration curves is 120 mM with a linear detection range for formaldehyde up to 20 mM
0.0017
S-hydroxymethylglutathione
-
oxidation of S-hydroxymethylglutathione, formaldehyde dehydrogenase
0.038
S-hydroxymethylglutathione
-
oxidation of S-hydroxymethylglutathione, R368L mutant
2.65
S-hydroxymethylglutathione
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oxidation of S-hydroxymethylglutathione, E67L mutant
0.0048
S-nitrosoglutathione
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reduction of S-nitrosoglutathione, formaldehyde dehydrogenase
additional information
additional information
-
Km for NAD+ with various aldehydes and alcohols
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additional information
additional information
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bi-substrate kinetics modelling
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.177
formaldehyde
-
enzyme immobilized on phenyl-functionalized MPS-4, pH 7.0, 22°
0.247
formaldehyde
-
enzyme immobilized on methyl-functionalized MPS-4, pH 7.0, 22°
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.023
formaldehyde
-
enzyme immobilized on methyl-functionalized MPS-4, pH 7.0, 22°
0.404
formaldehyde
-
enzyme immobilized on phenyl-functionalized MPS-4, pH 7.0, 22°
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7
-
FdDH specific activity in cell-free extract of Tf 11-6, cultivated in methanol medium supplemented with 10 mM formaldehyde
additional information
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.5
8.4
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best sensitivity of the biosensor output signal is observed in 2.5 mM borate buffer, pH 8.4
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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PDB
SCOP
CATH
ORGANISM
UNIPROT
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
42000
150000
250000
42000
-
4 * 42000, recombinant protein, expressed in Escherichia coli, SDS-PAGE, calculation from gene sequence
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
homotetramer
-
4 * 44000, recombinant His-tagged enzyme, SDS-PAGE, 4 * 43252, recombinant His-tagged enzyme, mass spectrometry
tetramer
additional information
tetramer
the active form with each monomer (350-400 amino-acid residues) consisting of catalytic and coenzyme binding domains together with two bound zinc ions
tetramer
-
the active form with each monomer (350-400 amino-acid residues) consisting of catalytic and coenzyme binding domains together with two bound zinc ions
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tetramer
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4 * 42000, recombinant protein, expressed in Escherichia coli, SDS-PAGE, calculation from gene sequence
additional information
three-dimensional structure modelling and analysis
additional information
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three-dimensional structure modelling and analysis
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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
formaldehyde dehydrogenase-adenosine 5'-diphosphate ribose and E67L-NADH binary complexes are determined
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purified recombinant enzyme, sitting drop vapour diffusion method, mixing of 0.001 ml of 15 mg/ml FDH protein and 4 mg/ml NAD+ in 10 mM Tris-HCl, pH 8.0, and 1 mM DTT, with 0.001 ml of reservoir solution containing 0.1 M Bis-Tris, pH 5.5, and 1.8 M ammonium sulfate, at 18°C, method optimization, X-ray diffraction structure determination and analysis at 2.7 A resolution, molecular replacement method, and modelling
purified recombinant His-tagged enzyme, sitting drop vapor diffusion method, mixing of 0.001 ml of 15 mg/ml protein in 10 mM Tris-HCl. pH 8.0, and 1 mM DTT with 0.001 ml of reservoir solution containing 0.1 M Bis-Tris, pH 5.5, and 1.8 M ammonium sulfate, at 18°C, X-ray diffraction structure determination and analysis at 2.7 A resolution, molecular replacement method, and modelling
-
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
FDH is not stable at a pH below 6.5, but shows higher stability in an alkaline pH domain
690067
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30 - 65
-
at 65°C, the enzyme retains about 60% of its highest activity (assay time of ca. 5 min), which is equal to the level of FdDH activity at 30°C
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ORGANIC SOLVENT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Methanol
-
5%, high loss of activity for the free enzyme, while the immobilzed enzymes are stable
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
14 h and 1 mM during 22 h, the storage stability of the developed biosensors is found to be longer than 18 days at 4°C
-
4°C, Nafion membrane-immobilized enzyme, more than 6 months, remains stable
-
the developed sensors demonstrate a good operational stability at comparatively low formaldehyde concentrations of 2 mM during
-
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
by two-step anion-exchange chromatography and precipitation by 80% (NH4)2SO4, precipitate, 3.8fold purified
-
FdDH ss isolated from the cell-free extract by a two-step ion exchange chromatography
-
recombinant His-tagged enzyme 94.1fold from Escherichia coli strain BL21(DE3)/pG-TF2 by nickel affinity chromatography dialysis, anion exchange chromatography, and gelfiltration
-
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3)/pG-TF2 by nickel affinity chromatography dialysis, anion exchange chromatography, and dialysis against crystallization buffer
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
construction of a recombinant yeast clone originated from the recipient strain of thermotolerant methylotrophic yeast Hansenula polymorpha which is a NAD+- and glutathione dependent FdDH over-producer
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FLD1 gene with its own promoter is recloned into LEU2-containing integrative plasmid pYT1 devoid of the autonomously replicating sequence to be used for multicopy integration of the gene into chromosome of the recipient strain NCYC 495
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FLD1 gene with the own promoter inserted into the integrative plasmid pYT1 containing LEU2 gene of Saccharomyces cerevisiae (as a selective marker). The constructed vector is used for multi-copy integration of the target gene into genome by transformation of the recipient cells of the strain NCYC 495
-
gene fdhA, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)/pG-TF2
recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)/pG-TF2. 50% of the recombinant proteins are localized in the supernatant fraction of cell-free extract, suggesting that coexpression with chaperones GroES, GroEL, and Tig has significantly improved the solubilization of Pseudomonas aeruginosa FDH in Escherichia coli
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
E67L
-
mutant shows, that Glu67 is critical for capturing the substrates for catalysis
R368L
-
mutant shows, that the predominant role of Arg-368 is in the binding of the coenzyme
additional information
additional information
-
immobilization of the purified enzyme on seven types of mesoporous silica (MPS), whose pores are from 2.4 to 31.2 nm sized, avaluatio of the enzyme activity in oxidation of formaldehyde, method overview. Enhancement of catalytic activity is obtained by immobilizing onto MPS, whose pore (mesopore) size is similar to the molecular size of enzyme FDH. FDH immobilized on phenyl-functionalized MPS-4 (MPS-4-Ph) has higher activity than FDH immobilized on non-functionalized one. Immobilized FDH on MPS-4-Ph is active for low formaldehyde concentration form 6.0 M and more sensitive than conventional formaldehyde detectors. The high-order structure of the FDH does not alter upon binding to the non-functionalized MPS surface. But FDH immobilized on functionalized-MPS is changed by hydrophobic interaction or covalent binding
additional information
-
analysis of the influence of the crystallinity of titanium dioxide (TiO2) filmson the quantity and activity of the immobilized formaldehyde dehydrogenase, overview. TiO2films with high crystallinity, which are annealed at 550°C, show higher enzyme immobilization and activity compared with the non-annealed TiO2film. Immobilization of the enzyme on the TiO2thin films, method, overview
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
analysis
biotechnology
-
development of novel formaldehyde-selective amperometric biosensors based on immobilized NAD+- and glutathione dependent formaldehyde dehydrogenase with high selectivity to formaldehyde and a low cross-sensitivity to other substances, the laboratory prototype of the sensor is applied for FA testing in some real samples of pharmaceutical (formidron), disinfectant (descoton forte) and industrial product (formalin)
degradation
industry
analysis
-
presence of enzyme can be used as a selectable marker in DNA-mediated transformations
analysis
-
presence of enzyme can be used as a selectable marker in DNA-mediated transformations
-
degradation
-
physiological significance of dlFalDH in the formaldehyde metabolism in Hyphomicrobium zavarzinii ZV 580 cultured on C1 compounds
degradation
-
physiological significance of dlFalDH in the formaldehyde metabolism in Hyphomicrobium zavarzinii ZV 580 cultured on C1 compounds
-
industry
-
construction of a formaldehyde-selective biosensor using NAD+- and glutathione-dependent recombinant formaldehyde dehydrogenase as a bio-recognition element immobilised on the surface of Si/SiO2/Si3N4 structure
industry
-
high thermostability makes FdDH potentially useful for bioanalytic purposes, namely, for formaldehyde assay in food products, wastewater, and pharmaceuticals, and for biotransformation of formaldehyde to formic acid
industry
-
development of a bi-enzyme biosensor for formaldehyde using diaphorase from Bacillus stearothermophilus, NAD+- and glutathione-dependent FDH as bio-recognition elements. Both enzymes can be immobilized on the top of a graphite electrode together with two osmium-redox polymers. Characteristics of the optimized formaldehyde biosensor are sensitivity, detection limit, and linear dynamic range
industry
-
amperometric enzyme-based sensor-system for the direct detection of formaldehyde in air, based on a native bacterial NAD+- and glutathione-independent formaldehyde dehydrogenase as biorecognition element. With the elimination of NAD+ it is much more promising to obtain a sensor device with higher long-term stability
industry
-
amperometric enzyme-based sensor-system for the direct detection of formaldehyde in air, based on a native bacterial NAD+- and glutathione-independent formaldehyde dehydrogenase as biorecognition element. With the elimination of NAD+ it is much more promising to obtain a sensor device with higher long-term stability
-
industry
-
high thermostability makes FdDH potentially useful for bioanalytic purposes, namely, for formaldehyde assay in food products, wastewater, and pharmaceuticals, and for biotransformation of formaldehyde to formic acid
-
industry
-
construction of a formaldehyde-selective biosensor using NAD+- and glutathione-dependent recombinant formaldehyde dehydrogenase as a bio-recognition element immobilised on the surface of Si/SiO2/Si3N4 structure
-
industry
-
construction of a formaldehyde-selective biosensor using NAD+- and glutathione-dependent recombinant formaldehyde dehydrogenase as a bio-recognition element immobilised on the surface of Si/SiO2/Si3N4 structure
-
industry
-
development of a bi-enzyme biosensor for formaldehyde using diaphorase from Bacillus stearothermophilus, NAD+- and glutathione-dependent FDH as bio-recognition elements. Both enzymes can be immobilized on the top of a graphite electrode together with two osmium-redox polymers. Characteristics of the optimized formaldehyde biosensor are sensitivity, detection limit, and linear dynamic range
-
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