Information on EC 1.5.8.4 - dimethylglycine dehydrogenase

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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria

EC NUMBER
COMMENTARY hide
1.5.8.4
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RECOMMENDED NAME
GeneOntology No.
dimethylglycine dehydrogenase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
N,N-dimethylglycine + 5,6,7,8-tetrahydrofolate + electron-transfer flavoprotein = sarcosine + 5,10-methylenetetrahydrofolate + reduced electron-transfer flavoprotein
show the reaction diagram
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
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oxidative deamination
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redox reaction
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reduction
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
glycine betaine degradation I
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glycine betaine degradation II (mammalian)
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creatinine degradation
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Glycine, serine and threonine metabolism
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Metabolic pathways
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SYSTEMATIC NAME
IUBMB Comments
N,N-dimethylglycine,5,6,7,8-tetrahydrofolate:electron-transferflavoprotein oxidoreductase (demethylating,5,10-methylenetetrahydrofolate-forming)
A flavoprotein, containing a histidyl(Npi)-(8alpha)FAD linkage at position 91 in the human protein. An imine intermediate is channeled from the FAD binding site to the 5,6,7,8-tetrahydrofolate binding site through a 40 A tunnel [5,8,9]. In the absence of 5,6,7,8-tetrahydrofolate the enzyme forms formaldehyde [5,9].
CAS REGISTRY NUMBER
COMMENTARY hide
37256-30-7
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
monkey
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Manually annotated by BRENDA team
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UniProt
Manually annotated by BRENDA team
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
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rare natural mutation H109R, causes dimethylglycine dehydrogenase deficiency leading to increased blood and urinary dimethylglycine concentrations
metabolism
physiological function
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dimethylglycine dehydrogenase expression suppresses metastasis through the Akt signaling pathway; DMGDH suppresses migration, invasion and metastasis both in vitro and in vivo. In a DMGDH over-expressing cell line, the phosphorylation of Akt-308/473 is significantly suppressed; the enzyme suppresses metastasis in hepatocellular carcinoma
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
5,10-methenyltetrahydrofolate + FADH2
5,10-methylene tetrahydrofolate + FAD
show the reaction diagram
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epsilon-N-methyl-L-lysine + acceptor + H2O
formaldehyde + L-lysine + reduced acceptor
show the reaction diagram
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-
?
N,N-dimethylglycine + 5,6,7,8-tetrahydrofolate + electron-transfer flavoprotein
sarcosine + 5,10-methylenetetrahydrofolate + reduced electron-transfer flavoprotein
show the reaction diagram
N,N-dimethylglycine + acceptor + H2O
sarcosine + formaldehyde + reduced acceptor
show the reaction diagram
N,N-dimethylglycine + electron-transfer flavoprotein + H2O
sarcosine + formaldehyde + reduced electron-transfer flavoprotein
show the reaction diagram
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-
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?
N,N-dimethylglycine + electron-transfer flavoprotein + H2O
sarcosine + formaldehyde + reduced electron-transfer flavoprotein + H2O2
show the reaction diagram
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?
N,N-dimethylglycine + FAD + H2O
sarcosine + formaldehyde + FADH2
show the reaction diagram
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?
N,N-dimethylglycine + ferricenium + H2O
sarcosine + formaldehyde + ferrocene
show the reaction diagram
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?
N,N-dimethylglycine + ferricenium hexafluorophosphate + H2O
sarcosine + formaldehyde + reduced ferricenium hexafluorophosphate
show the reaction diagram
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-
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?
N,N-dimethylglycine + H2O + FAD
sarcosine + formaldehyde + FADH2
show the reaction diagram
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N,N-dimethylglycine + H2O + ferrocene
sarcosine + formaldehyde + ?
show the reaction diagram
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?
N,N-dimethylglycine + H2O + oxidized 1-methoxy-5-methylphenazinium methylsulfate
sarcosine + formaldehyde + reduced 1-methoxy-5-methylphenazinium methylsulfate
show the reaction diagram
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-
-
-
?
N,N-dimethylglycine + H2O + oxidized 2,6-dichlorophenolindophenol
sarcosine + formaldehyde + reduced 2,6-dichlorophenolindophenol
show the reaction diagram
N,N-dimethylglycine + oxidized ferricenium hexafluorophosphate + H2O
sarcosine + formaldehyde + reduced ferricenium hexafluorophosphate + H2O2
show the reaction diagram
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?
N,N-dimethylglycine + tetrahydropteroylpentaglutamate + acceptor
sarcosine + 5,10-methylene tetrahydropteroylpentaglutamate + reduced acceptor
show the reaction diagram
N-methyl-L-alanine + acceptor + H2O
formaldehyde + L-alanine + reduced acceptor
show the reaction diagram
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?
sarcosine + acceptor + H2O
glycine + formaldehyde + reduced acceptor
show the reaction diagram
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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
5,10-methenyltetrahydrofolate + FADH2
5,10-methylene tetrahydrofolate + FAD
show the reaction diagram
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N,N-dimethylglycine + 5,6,7,8-tetrahydrofolate + electron-transfer flavoprotein
sarcosine + 5,10-methylenetetrahydrofolate + reduced electron-transfer flavoprotein
show the reaction diagram
Q9UI17
the enzyme takes part in choline degradation, one-carbon metabolism and electron transfer to the respiratory chain
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?
N,N-dimethylglycine + electron-transfer flavoprotein + H2O
sarcosine + formaldehyde + reduced electron-transfer flavoprotein
show the reaction diagram
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?
N,N-dimethylglycine + electron-transfer flavoprotein + H2O
sarcosine + formaldehyde + reduced electron-transfer flavoprotein + H2O2
show the reaction diagram
Q5RKL4
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?
N,N-dimethylglycine + FAD + H2O
sarcosine + formaldehyde + FADH2
show the reaction diagram
Q9UI17
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?
N,N-dimethylglycine + H2O + FAD
sarcosine + formaldehyde + FADH2
show the reaction diagram
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N,N-dimethylglycine + tetrahydropteroylpentaglutamate + acceptor
sarcosine + 5,10-methylene tetrahydropteroylpentaglutamate + reduced acceptor
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
tetrahydrofolate
Tetrahydropteroylpentaglutamate
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additional information
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1-methoxy-5-methylphenazinium methylsulfate can act as electron acceptor; 2,6-dichlorophenolindophenol can act as electron acceptor
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Nonheme iron
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Dimethylthetin
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Methoxyacetate
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competitive inhibitor at low substrate concentrations
additional information
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.05
dimethylglycine
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1.4 - 32.2
Ferrocene
0.039 - 32.2
N,N-dimethylglycine
0.3 - 4.7
oxidized 2,6-dichlorophenolindophenol
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3.55 - 9.07
Ferrocene
0.01 - 9.1
N,N-dimethylglycine
0.73 - 1.52
oxidized 2,6-dichlorophenolindophenol
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.18 - 2.28
Ferrocene
0.18 - 2.54
N,N-dimethylglycine
0.33 - 2.43
oxidized 2,6-dichlorophenolindophenol
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.0068
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mutant H109R, pH 7.5, 25°C
0.157 - 0.268
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0.165
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wild-type, pH 7.5, 25°C
0.24
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purified recombinant enzyme from soluble fraction
129
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potassium phosphate fraction
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8.5 - 9
8.5
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recombinant and native enzyme
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
45
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recombinant and native enzyme
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
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detectable levels of expression demonstrated at the RNA and protein level
Manually annotated by BRENDA team
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hepatocellular carcinoma
Manually annotated by BRENDA team
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detectable levels of expression demonstrated at the RNA and protein level
Manually annotated by BRENDA team
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predominant expression of the enzyme
Manually annotated by BRENDA team
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detectable levels of expression demonstrated at the RNA and protein level
Manually annotated by BRENDA team
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detectable levels of expression demonstrated at the RNA and protein level
Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
94000
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His-tagged pMe2GlyDH, SDS-PAGE
97410
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pMe2GlyDH, calculated from amino acid sequence
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystallization of the wild-type enzyme and determination of the structure to 3.1A resolution, microbatch method using different commercial crystallization screens; microbatch method using 10% (w/v) PEG 20000 and 20% (v/v) PEG MME 550; wild-type, to 3.1 resolution
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crystal structure of the recombinant mature and precursor forms of enzyme and the enzyme complexed with 5,6,7,8-tetrahydrofolate. Both forms reveal similar kinetic parameters and have the same tertiary structure fold with two domains formed by N- and C-terminal halves of the protein. The active center is located in the N-terminal domain while the tetrahydrofolate binding site is located in the C-terminal domain about 40 A from the isoalloxazine ring of FAD. The folate binding site is connected with the enzyme active center via an intramolecular channel. This suggests the possible transfer of the intermediate imine of dimethylglycine from the active center to the bound 5,6,7,8-tetrahydrofolate where they can react producing a 5,10-methylenetetrahydrofolate; recombinant mature and precursor forms, in complex with tetrahydrofolate. Both forms of DMGDH reveal similar kinetic parameters and have the same tertiary structure fold with two domains formed by N- and C-terminal halves of the protein. The active center is located in the N-terminal domain while the THF binding site is located in the C-terminal domain about 40 A from the isoalloxazine ring of FAD. The folate binding site is connected with the enzyme active center via an intramolecular channel; using 0.2 M K/Na-tartrate-20% (w/v) PEG 3350 for the mature enzyme or 0.2 M NaSCN-20% (w/v) PEG 3350-0.1 M Tris pH 7.5 for the precursor
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
47
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melting point, mutant H109R; melting point of mutant enzyme H109R
52
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melting point of wild-type enzyme; melting point, wild-type; melting temperature
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-4°C, lyophilized, 1 week
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
; Ni-Sepharose 6 column chromatography and MonoQ column chromatography
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native enzyme from liver mitochondria, recombinant His-tagged enzyme from Escherichia coli 45fold by nickel affinity chromatography
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Ni2+-Sepharose column chromatography
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of in vitro synthesized 6-His-dimethylglycine dehydrogenase on nickel chelating Sepharose
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using ammonium sulfate treatment and dissolution in 7.5 mM potassium phosphate
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using gel filtration chromatography on Sephadex G-150, DEAE-cellulose chromatography, and affinity chromatography
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
development of an intracellular, heterologous expression system in Komagataella phaffii (formerly known as Pichia pastoris). Initial attempts to express the gene in Escherichia coli (BL21 DE3) yielded largely insoluble protein. The H109R variant is expressed in lower amounts compared to the wild-type enzyme; expressed in Komagataella phaffii KM71H cells; expression in Komagataella phaffii, i.e. Pichia pastoris
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expressed in Escherichia coli BL21(DE3) cells as a C-terminally 6-His-tagged fusion protein which is predominantly in its apo form
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expression in Escherichia coli
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overexpression in Escherichia coli strain JM109 as N-terminally His-tagged enzyme being equally distributed in the soluble fraction and the insoluble inclusion body fraction
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screening of a cDNA library prepared in Escherichia coli from rat liver polyA RNA in the plasmid vector peD-X
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
enzyme expression is decreased in hepatocellular carcinoma; expression is decreased in hepatocellular carcinoma
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Renatured/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
refolding by 80fold dilution after solubilization from inclusion bodies by urea treatment, 50-60% reactivation yield, overview
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
diagnostics
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the enzyme may be a valuable biomarker of hepatocellular carcinoma diagnosis
medicine
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expression of DMGDH is decreased in hepatocellular carcinoma. the enzyme can be applied as valuable biomarker for both diagnosis and prognosis; the enzyme is biomarker for both diagnosis and prognosis for hepatocellular carcinoma; the enzyme may be a valuable biomarker of hepatocellular carcinoma diagnosis
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