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Information on EC 1.5.3.10 - dimethylglycine oxidase
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1.5.3.10 dimethylglycine oxidaseIUBMB Comments
A flavoprotein (FAD). Does not oxidize sarcosine.
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Word Map
- 1.5.3.10
- arthrobacter
- globiformis
- sarcosine
- amine
- formaldehyde
-
t-protein
- tetrahydrofolate
- flavoprotein
- fad
- betaine
-
folate-binding
- folate
-
folinic
-
methylene
-
heterotetrameric
-
tetrahydrofolate-binding
-
stopped-flow
-
charge-transfer
- sulfite
-
half-reaction
-
multiwavelength
-
folate-dependent
- l-proline
-
iminium
- oxidases
- aminomethyltransferase
-
tetrahydrofolate-dependent
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Synonyms
dimethylglycine dehydrogenase, DMGO, DMGO1, DMGO2, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
dimethylglycine dehydrogenase
DMGO
DMGO1
DMGO2
dimethylglycine dehydrogenase
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-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
N,N-dimethylglycine + H2O + O2 = sarcosine + formaldehyde + H2O2
a flavoprotein, FAD
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-
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N,N-dimethylglycine + H2O + O2 = sarcosine + formaldehyde + H2O2
A flavoprotein, FAD. Does not oxidize sarcosine
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N,N-dimethylglycine + H2O + O2 = sarcosine + formaldehyde + H2O2
reaction mechanism, substrate binding structures, bifunctional enzyme catalyzing the formation of 5,10-methylne tetrahydrofolate and the oxidation of N,N-dimethylglycine, active site structures, Tyr259 and His225 are involved in catalysis
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N,N-dimethylglycine + H2O + O2 = sarcosine + formaldehyde + H2O2
tetrahydrofolate-binding site of enzyme is highly specific for reduced folate compounds and enhances the nucleophilic character of the tetrahydrofolate N10 position
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
oxidation
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-
-
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oxidative demethylation
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-
-
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redox reaction
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-
-
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reduction
-
-
-
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PATHWAY SOURCE
PATHWAYS
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SYSTEMATIC NAME
IUBMB Comments
N,N-dimethylglycine:oxygen oxidoreductase (demethylating)
A flavoprotein (FAD). Does not oxidize sarcosine.
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CAS REGISTRY NUMBER
COMMENTARY
74870-79-4
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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
5,10-methenyltetrahydrofolate + reduced N,N-dimethylglycine
5,10-methylene tetrahydrofolate + oxidized N,N-dimethylglycine
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-
-
-
?
additional information
?
-
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bifunctional enzyme catalyzing the formation of 5,10-methylene tetrahydrofolate and the oxidation of N,N-dimethylglycine, folate binding and active site, a large channel connects both active sites, the channeling is kinetically controlled by terahydrofolate binding, overview
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-
?
N,N-dimethylglycine + H2O + O2
sarcosine + formaldehyde + H2O2
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-
-
-
?
N,N-dimethylglycine + H2O + O2
sarcosine + formaldehyde + H2O2
involved in tetrahydrofolate-dependent assimilation of methyl groups
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?
N,N-dimethylglycine + H2O + O2
sarcosine + formaldehyde + H2O2
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the oxidation of dimethylglycine is coupled to the synthesis of 5,10-methylenetetrahydrofolate through an unusual substrate channeling mechanism. Uncoupling of the active sites can be achieved by mutagenesis or deletion of the 5,10-methylenetetrahydrofolate synthase site and this leads to accumulation of intracellular formaldehyde. Channeling occurs by nonbiased diffusion of the labile intermediate through a large solvent cavity connecting both active sites
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-
?
N,N-dimethylglycine + H2O + O2
sarcosine + formaldehyde + H2O2
-
-
-
-
?
N,N-dimethylglycine + H2O + O2
sarcosine + formaldehyde + H2O2
-
-
-
?
N,N-dimethylglycine + H2O + O2
sarcosine + formaldehyde + H2O2
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-
-
?
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NATURAL SUBSTRATE
NATURAL 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
additional information
?
-
-
bifunctional enzyme catalyzing the formation of 5,10-methylene tetrahydrofolate and the oxidation of N,N-dimethylglycine, folate binding and active site, a large channel connects both active sites, the channeling is kinetically controlled by terahydrofolate binding, overview
-
-
?
N,N-dimethylglycine + H2O + O2
sarcosine + formaldehyde + H2O2
-
-
-
-
?
N,N-dimethylglycine + H2O + O2
sarcosine + formaldehyde + H2O2
involved in tetrahydrofolate-dependent assimilation of methyl groups
-
?
N,N-dimethylglycine + H2O + O2
sarcosine + formaldehyde + H2O2
-
-
-
-
?
N,N-dimethylglycine + H2O + O2
sarcosine + formaldehyde + H2O2
-
-
-
?
N,N-dimethylglycine + H2O + O2
sarcosine + formaldehyde + H2O2
-
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
NaCl
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the specific activity of DMGO decreased when cells are grown in the medium with high NaCl concentration. High osmolarity inhibits the activity of the enzyme, but not in the case of the medium with glycine betaine as the sole carbon source
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1.39
N,N-dimethylglycine
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DMGO1, pH 9.0, temperature not specified in the publication
1.86
N,N-dimethylglycine
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DMGO2, pH 9.0, temperature not specified in the publication
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
metabolism
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in high-salinity media with 1 M NaCl, Arthrobacter globiformis accumulates 360 mM of glycine betaine when the main source of carbon is glucose and 180 mM glycine betaine when the sole carbon source is glycine betaine
metabolism
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in high-salinity media with 1 M NaCl, Arthrobacter globiformis accumulates 360 mM of glycine betaine when the main source of carbon is glucose and 180 mM glycine betaine when the sole carbon source is glycine betaine
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). A0A1J5PJV6_9ZZZZ
82
0
8855
TrEMBL
other Location (Reliability: 1)
A0A2S6T6P9_9PROT
443
0
48694
TrEMBL
-
A0A1J5PCX8_9ZZZZ
219
0
23744
TrEMBL
other Location (Reliability: 3)
A0A6A7SHT2_9ZZZZ
855
0
94605
TrEMBL
other Location (Reliability: 3)
A0A2P5VKU8_9PROT
141
0
15518
TrEMBL
-
A0A2P5VKQ9_9PROT
260
0
28977
TrEMBL
-
A0A2Z2P2R9_9GAMM
855
0
95279
TrEMBL
-
F0M736_PSEPM
Pseudarthrobacter phenanthrenivorans (strain DSM 18606 / JCM 16027 / LMG 23796 / Sphe3)
835
0
90838
TrEMBL
-
F5XJW8_MICPN
Microlunatus phosphovorus (strain ATCC 700054 / DSM 10555 / JCM 9379 / NBRC 101784 / NCIMB 13414 / VKM Ac-1990 / NM-1)
825
0
89339
TrEMBL
-
A0A2S6S9T6_9PROT
448
0
49724
TrEMBL
-
A0A385ZVE1_9ACTN
812
0
88600
TrEMBL
-
A0A5B8RH90_9ZZZZ
855
0
94605
TrEMBL
other Location (Reliability: 3)
A0A6J5G3W9_9BURK
390
0
42364
TrEMBL
-
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
in complex with folate compounds. N-terminal region covalently binds FAD and has dimethylglycine dehydrogenase activity
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mutant D552A in complex with tetrahydrofolate. Presence of one water molecule instead of the Asp552 side chain
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purified recombinant wild-type enzyme, sitting-drop vapour diffusion method, 0.004 ml of protein solution containing 15 mg/ml protein, mixed with 0.002 ml reservoir solution containing 15% PEG 5000 monomethylether, 0.2 M MgCl2, and 0.1 M HEPES, pH 7.5, magnesium salt can be exchanged for acetate, for complexing the crystals are soaked in a solution containing folic or folinic acid in 15% PEG 5000 monomethylether and 0.3 M NaCl for 10 min, X-ray diffraction structure determination and analysis at 1.60 A resolution
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
H225Q
Y259F
additional information
-
complete removal of 5,10-CH2-THF synthase domain through expression of a truncated version generates a mutant enzyme unable to avoid hydrolysis of the imine species generated following amine oxidation
H225Q
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site-directed mutagenesis, reduced catalytic activity compared to the wild-type enzyme
H225Q
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modest changes in kinetic parameters, no stabilization of FADH2-iminium charge-transfer complex
Y259F
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site-directed mutagenesis, reduced catalytic activity compared to the wild-type enzyme
Y259F
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able to oxidize substrate, steady-state turnover is attenuated 200fold, rate of FAD reduction is substantially impaired, no stabilization of FADH2-iminium charge-transfer complex
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
two dmg genes, dmg and dmg2, DNA and amino acid sequence determination, genetic organization, quantitative real-time pCR expression analysis
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
glycine betaine induces the expression of the dmg genes by about 300fold at 5 mM
glycine betaine induces the expression of the dmg genes by about 300fold at 5 mM
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glycine betaine induces the expression of the dmg genes by about 300fold at 5 mM
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-
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Meskys, R.; Harris, R.J.; Casaite, V.; Basran, J.; Scrutton, N.S.
Organization of the genes involved in dimethylglycine and sarcosine degradation in Arthrobacter spp. Implications for glycine betaine catabolism
Eur. J. Biochem.
268
3390-3398
2001
Arthrobacter globiformis (Q9AGP8), Arthrobacter globiformis
brenda
Mori, N.; Kawakami, B.; Tani, Y.; Yamada, H.
Purification and properties of dimethylglycine oxidase from Cylindrocarpon didymum M-1
Agric. Biol. Chem.
44
1383-1389
1980
Cylindrocarpon didymum, Cylindrocarpon didymum M-1
-
brenda
Leys, D.; Basran, J.; Scrutton, N.S.
Channelling and formation of 'active' formaldehyde in dimethylglycine oxidase
EMBO J.
22
4038-4048
2003
Arthrobacter globiformis
brenda
Scrutton, N.S.; Leys, D.
Crystal structure of DMGO provides a prototype for a new tetrahydrofolate-binding fold
Biochem. Soc. Trans.
33
776-779
2005
Arthrobacter globiformis
brenda
Basran, J.; Fullerton, S.; Leys, D.; Scrutton, N.S.
Mechanism of FAD reduction and role of active site residues His-225 and Tyr-259 in Arthrobacter globiformis dimethylglycine oxidase: analysis of mutant structure and catalytic function
Biochemistry
45
11151-11161
2006
Arthrobacter globiformis
brenda
Tralau, T.; Lafite, P.; Levy, C.; Combe, J.P.; Scrutton, N.S.; Leys, D.
An internal reaction chamber in dimethylglycine oxidase provides efficient protection from exposure to toxic formaldehyde
J. Biol. Chem.
284
17826-17834
2009
Arthrobacter globiformis
brenda
Casaite, V.; Poviloniene, S.; Meskiene, R.; Rutkiene, R.; Meskys, R.
Studies of dimethylglycine oxidase isoenzymes in Arthrobacter globiformis cells
Curr. Microbiol.
62
1267-1273
2011
Arthrobacter globiformis, Arthrobacter globiformis NRRL B-2979
brenda
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