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Information on EC 1.5.3.10 - dimethylglycine oxidase and Organism(s) Arthrobacter globiformis and UniProt Accession Q9AGP8

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EC Tree
     1 Oxidoreductases
         1.5 Acting on the CH-NH group of donors
             1.5.3 With oxygen as acceptor
                1.5.3.10 dimethylglycine oxidase
IUBMB Comments
A flavoprotein (FAD). The enzyme, characterized from the bacterium Arthrobacter globiformis, contains two active sites connected by a large "reaction chamber". An imine intermediate is transferred between the sites, eliminating the production of toxic formaldehyde. In the absence of folate the enzyme does form formaldehyde. Does not oxidize sarcosine. cf. EC 1.5.8.4, dimethylglycine dehydrogenase.
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Arthrobacter globiformis
UNIPROT: Q9AGP8
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The taxonomic range for the selected organisms is: Arthrobacter globiformis
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Synonyms
dimethylglycine oxidase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimethylglycine dehydrogenase
dmg
-
-
-
-
N,N-dimethylglycine:oxygen oxidoreductase (demethylating)
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
N,N-dimethylglycine + 5,6,7,8-tetrahydrofolate + O2 = sarcosine + 5,10-methylenetetrahydrofolate + H2O2
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
redox reaction
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-
-
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oxidation
-
-
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reduction
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-
-
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oxidative demethylation
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-
-
-
PATHWAY SOURCE
PATHWAYS
-
-
SYSTEMATIC NAME
IUBMB Comments
N,N-dimethylglycine,5,6,7,8-tetrahydrofolate:oxygen oxidoreductase (demethylating,5,10-methylenetetrahydrofolate-forming)
A flavoprotein (FAD). The enzyme, characterized from the bacterium Arthrobacter globiformis, contains two active sites connected by a large "reaction chamber". An imine intermediate is transferred between the sites, eliminating the production of toxic formaldehyde. In the absence of folate the enzyme does form formaldehyde. Does not oxidize sarcosine. cf. EC 1.5.8.4, dimethylglycine dehydrogenase.
CAS REGISTRY NUMBER
COMMENTARY hide
74870-79-4
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
N,N-dimethylglycine + H2O + O2
sarcosine + formaldehyde + H2O2
show the reaction diagram
involved in tetrahydrofolate-dependent assimilation of methyl groups
-
?
N,N-dimethylglycine + 5,6,7,8-tetrahydrofolate + O2
sarcosine + 5,10-methylenetetrahydrofolate + H2O2
show the reaction diagram
-
-
-
-
?
N,N-dimethylglycine + H2O + O2
sarcosine + formaldehyde + H2O2
show the reaction diagram
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
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-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
N,N-dimethylglycine + H2O + O2
sarcosine + formaldehyde + H2O2
show the reaction diagram
involved in tetrahydrofolate-dependent assimilation of methyl groups
-
?
N,N-dimethylglycine + H2O + O2
sarcosine + formaldehyde + H2O2
show the reaction diagram
-
-
-
-
?
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
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-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
flavin
8alpha-N1-histidyl flavin
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NaCl
-
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
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
glycine betaine
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2
N,N-dimethylglycine
-
1.39 - 142
N,N-dimethylglycine
0.041 - 0.117
O2
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
14.3
N,N-dimethylglycine
-
0.047 - 13.6
N,N-dimethylglycine
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
9.5
-
DMGO1 and DMGO2
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
DMGO_ARTGO
830
0
89985
Swiss-Prot
-
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
88000
x * 88000, SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 88000, SDS-PAGE
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 hide
LITERATURE
D552A
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mutation leads to increased formaldehyde release
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
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
to homogeneity, recombinant enzyme
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
expression in Escherichia coli
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expression of wild-type and mutant enzymes in Escherichia coli
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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
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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
Manually annotated by BRENDA team
Leys, D.; Basran, J.; Scrutton, N.S.
Channelling and formation of 'active' formaldehyde in dimethylglycine oxidase
EMBO J.
22
4038-4048
2003
Arthrobacter globiformis
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team