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Literature summary for 1.5.8.4 extracted from

  • Augustin, P.; Hromic, A.; Pavkov-Keller, T.; Gruber, K.; Macheroux, P.
    Structure and biochemical properties of recombinant human dimethylglycine dehydrogenase and comparison to the disease-related H109R variant (2016), FEBS J., 283, 3587-3603 .
    View publication on PubMedView publication on EuropePMC
Search for more literature for 1.5.8.4

Cloned(Commentary)

Cloned (Comment) Organism
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 Homo sapiens
expressed in Komagataella phaffii KM71H cells Homo sapiens
expression in Komagataella phaffii, i.e. Pichia pastoris Homo sapiens

Crystallization (Commentary)

Crystallization (Comment) Organism
crystallization of the wild-type enzyme and determination of the structure to 3.1A resolution, microbatch method using different commercial crystallization screens Homo sapiens
microbatch method using 10% (w/v) PEG 20000 and 20% (v/v) PEG MME 550 Homo sapiens
wild-type, to 3.1 resolution Homo sapiens

Protein Variants

Protein Variants Comment Organism
H109R rare natural variant, mutation leads to decreased protein stability, cofactor saturation, and substrate affinity Homo sapiens
H109R rare natural variant, suffers from decreased protein stability, cofactor saturation, and substrate affinity and causes dimethylglycine dehydrogenase deficiency leading to increased blood and urinary dimethylglycine concentrations Homo sapiens
H109R the mutation causes dimethylglycine dehydrogenase deficiency leading to increased blood and urinary dimethylglycine concentrations Homo sapiens

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.3
-
 oxidized 2,6-dichlorophenolindophenol wild-type, pH 7.8, 25°C Homo sapiens
0.3
-
 N,N-dimethylglycine 25°C, pH 7.8, artificial electron acceptor: 2,6-dichlorophenolindophenol, wild-type enzyme Homo sapiens
0.3
-
 N,N-dimethylglycine wild type enzyme, with 2,6-dichlorophenolindophenol as cosubstrate, at 25°C and pH 7.8 in 50 mM HEPES/NaOH with 150 mM NaCl Homo sapiens
1.4
-
 Ferrocene wild-type, pH 7.8, 25°C Homo sapiens
1.4
-
 N,N-dimethylglycine 25°C, pH 7.8, artificial electron acceptor: ferrocene, wild-type enzyme Homo sapiens
1.4
-
 N,N-dimethylglycine wild type enzyme, with ferrocene as cosubstrate, at 25°C and pH 7.8 in 50 mM HEPES/NaOH with 150 mM NaCl Homo sapiens
4.7
-
 N,N-dimethylglycine 25°C, pH 7.8, artificial electron acceptor: 2,6-dichlorophenolindophenol, mutant enzyme H109R Homo sapiens
4.7
-
 N,N-dimethylglycine mutant enzyme H109R, with 2,6-dichlorophenolindophenol as cosubstrate, at 25°C and pH 7.8 in 50 mM HEPES/NaOH with 150 mM NaCl Homo sapiens
4.7
-
 oxidized 2,6-dichlorophenolindophenol mutant H109R, pH 7.8, 25°C Homo sapiens
32.2
-
 N,N-dimethylglycine 25°C, pH 7.8, artificial electron acceptor: ferrocene, mutant enzyme H109R Homo sapiens
32.2
-
 N,N-dimethylglycine mutant enzyme H109R, with ferrocene as cosubstrate, at 25°C and pH 7.8 in 50 mM HEPES/NaOH with 150 mM NaCl Homo sapiens
32.2
-
 Ferrocene mutant H109R, pH 7.8, 25°C Homo sapiens

Localization

Localization Comment Organism GeneOntology No. Textmining
mitochondrial matrix
-
 Homo sapiens 5759
-
mitochondrion
-
 Homo sapiens 5739
-

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
N,N-dimethylglycine + 5,6,7,8-tetrahydrofolate + electron-transfer flavoprotein Homo sapiens the enzyme takes part in choline degradation, one-carbon metabolism and electron transfer to the respiratory chain sarcosine + 5,10-methylenetetrahydrofolate + reduced electron-transfer flavoprotein
-
 ?
N,N-dimethylglycine + FAD + H2O Homo sapiens
-
 sarcosine + formaldehyde + FADH2
-
 ?

Organism

Organism UniProt Comment Textmining
Homo sapiens Q9UI17
-
-

Purification (Commentary)

Purification (Comment) Organism
-
 Homo sapiens
Ni-Sepharose 6 column chromatography and MonoQ column chromatography Homo sapiens

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
N,N-dimethylglycine + 5,6,7,8-tetrahydrofolate + electron-transfer flavoprotein the enzyme takes part in choline degradation, one-carbon metabolism and electron transfer to the respiratory chain Homo sapiens sarcosine + 5,10-methylenetetrahydrofolate + reduced electron-transfer flavoprotein
-
 ?
N,N-dimethylglycine + 5,6,7,8-tetrahydrofolate + electron-transfer flavoprotein ferrocene or 2,6-dichlorophenolindophenol are used as artificial electron acceptor Homo sapiens sarcosine + 5,10-methylenetetrahydrofolate + reduced electron-transfer flavoprotein
-
 ?
N,N-dimethylglycine + FAD + H2O
-
 Homo sapiens sarcosine + formaldehyde + FADH2
-
 ?
N,N-dimethylglycine + ferricenium + H2O
-
 Homo sapiens sarcosine + formaldehyde + ferrocene
-
 ?
N,N-dimethylglycine + H2O + ferrocene
-
 Homo sapiens sarcosine + formaldehyde + ?
-
 ?
N,N-dimethylglycine + H2O + oxidized 2,6-dichlorophenolindophenol
-
 Homo sapiens sarcosine + formaldehyde + reduced 2,6-dichlorophenolindophenol
-
 ?

Synonyms

Synonyms Comment Organism
DMGDH
-
 Homo sapiens

Temperature Stability [°C]

Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
47
-
 melting point of mutant enzyme H109R Homo sapiens
47
-
 melting point, mutant H109R Homo sapiens
52
-
 melting temperature Homo sapiens
52
-
 melting point of wild-type enzyme Homo sapiens
52
-
 melting point, wild-type Homo sapiens

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.73
-
 oxidized 2,6-dichlorophenolindophenol wild-type, pH 7.8, 25°C Homo sapiens
0.73
-
 N,N-dimethylglycine wild type enzyme, with 2,6-dichlorophenolindophenol as cosubstrate, at 25°C and pH 7.8 in 50 mM HEPES/NaOH with 150 mM NaCl Homo sapiens
0.733
-
 N,N-dimethylglycine 25°C, pH 7.8, artificial electron acceptor: 2,6-dichlorophenolindophenol, wild-type enzyme Homo sapiens
1.5
-
 N,N-dimethylglycine 25°C, pH 7.8, artificial electron acceptor: 2,6-dichlorophenolindophenol, mutant enzyme H109R Homo sapiens
1.52
-
 N,N-dimethylglycine mutant enzyme H109R, with 2,6-dichlorophenolindophenol as cosubstrate, at 25°C and pH 7.8 in 50 mM HEPES/NaOH with 150 mM NaCl Homo sapiens
1.52
-
 oxidized 2,6-dichlorophenolindophenol mutant H109R, pH 7.8, 25°C Homo sapiens
3.55
-
 Ferrocene wild-type, pH 7.8, 25°C Homo sapiens
3.55
-
 N,N-dimethylglycine 25°C, pH 7.8, artificial electron acceptor: ferrocene, wild-type enzyme Homo sapiens
3.55
-
 N,N-dimethylglycine wild type enzyme, with ferrocene as cosubstrate, at 25°C and pH 7.8 in 50 mM HEPES/NaOH with 150 mM NaCl Homo sapiens
9.07
-
 N,N-dimethylglycine mutant enzyme H109R, with ferrocene as cosubstrate, at 25°C and pH 7.8 in 50 mM HEPES/NaOH with 150 mM NaCl Homo sapiens
9.07
-
 Ferrocene mutant H109R, pH 7.8, 25°C Homo sapiens
9.1
-
 N,N-dimethylglycine 25°C, pH 7.8, artificial electron acceptor: ferrocene, mutant enzyme H109R Homo sapiens

Cofactor

Cofactor Comment Organism Structure
FAD
-
 Homo sapiens
FAD flavoprotein Homo sapiens
FAD A280/A450 ratios of the highly pure protein fractions are between 14-16 and 20-25 for wild-type and mutant H109R, respectively. The redox potential for the reduction of FAD is -93 mV Homo sapiens
tetrahydrofolate
-
 Homo sapiens

General Information

General Information Comment Organism
malfunction rare natural mutation H109R, causes dimethylglycine dehydrogenase deficiency leading to increased blood and urinary dimethylglycine concentrations Homo sapiens
metabolism the enzyme takes part in choline degradation, one-carbon metabolism and electron transfer to the respiratory chain Homo sapiens

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
0.18
-
 N,N-dimethylglycine mutant enzyme H109R, with ferrocene as cosubstrate, at 25°C and pH 7.8 in 50 mM HEPES/NaOH with 150 mM NaCl Homo sapiens
0.18
-
 Ferrocene mutant H109R, pH 7.8, 25°C Homo sapiens
0.28
-
 N,N-dimethylglycine 25°C, pH 7.8, artificial electron acceptor: ferrocene, mutant enzyme H109R Homo sapiens
0.32
-
 N,N-dimethylglycine 25°C, pH 7.8, artificial electron acceptor: 2,6-dichlorophenolindophenol, mutant enzyme H109R Homo sapiens
0.33
-
 N,N-dimethylglycine mutant enzyme H109R, with 2,6-dichlorophenolindophenol as cosubstrate, at 25°C and pH 7.8 in 50 mM HEPES/NaOH with 150 mM NaCl Homo sapiens
0.33
-
 oxidized 2,6-dichlorophenolindophenol mutant H109R, pH 7.8, 25°C Homo sapiens
2.28
-
 Ferrocene wild-type, pH 7.8, 25°C Homo sapiens
2.28
-
 N,N-dimethylglycine wild type enzyme, with ferrocene as cosubstrate, at 25°C and pH 7.8 in 50 mM HEPES/NaOH with 150 mM NaCl Homo sapiens
2.43
-
 oxidized 2,6-dichlorophenolindophenol wild-type, pH 7.8, 25°C Homo sapiens
2.43
-
 N,N-dimethylglycine wild type enzyme, with 2,6-dichlorophenolindophenol as cosubstrate, at 25°C and pH 7.8 in 50 mM HEPES/NaOH with 150 mM NaCl Homo sapiens
2.44
-
 N,N-dimethylglycine 25°C, pH 7.8, artificial electron acceptor: 2,6-dichlorophenolindophenol, wild-type enzyme Homo sapiens
2.54
-
 N,N-dimethylglycine 25°C, pH 7.8, artificial electron acceptor: ferrocene, wild-type enzyme Homo sapiens