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 (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 | 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 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 | Comment | Organism | GeneOntology No. | Textmining |
---|---|---|---|---|
mitochondrial matrix | - |
Homo sapiens | 5759 | - |
mitochondrion | - |
Homo sapiens | 5739 | - |
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 | UniProt | Comment | Textmining |
---|---|---|---|
Homo sapiens | Q9UI17 | - |
- |
Purification (Comment) | Organism |
---|---|
- |
Homo sapiens |
Ni-Sepharose 6 column chromatography and MonoQ column chromatography | Homo sapiens |
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 | Comment | Organism |
---|---|---|
DMGDH | - |
Homo sapiens |
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 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 | 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 | 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 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 |