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Information on EC 1.14.13.128 - 7-methylxanthine demethylase and Organism(s) Pseudomonas putida and UniProt Accession H9N289

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IUBMB Comments
A non-heme iron oxygenase. The enzyme from the bacterium Pseudomonas putida prefers NADH over NADPH. The enzyme is specific for 7-methylxanthine . Forms part of the caffeine degradation pathway.
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Pseudomonas putida
UNIPROT: H9N289
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Word Map
The taxonomic range for the selected organisms is: Pseudomonas putida
The enzyme appears in selected viruses and cellular organisms
Synonyms
caffeine demethylase, bacterial n-demethylase, theobromine demethylase, methylxanthine n-demethylase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7-methylxanthine-specific N-demethylase
-
bacterial N-demethylase
-
caffeine demethylase
-
-
heteroxanthine demethylase
-
-
methylxanthine N-demethylase
-
N-demethylase
-
-
theobromine demethylase
-
-
SYSTEMATIC NAME
IUBMB Comments
7-methylxanthine:oxygen oxidoreductase (demethylating)
A non-heme iron oxygenase. The enzyme from the bacterium Pseudomonas putida prefers NADH over NADPH. The enzyme is specific for 7-methylxanthine [2]. Forms part of the caffeine degradation pathway.
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
7-methylxanthine + O2 + NADH + H+
xanthine + NAD+ + H2O + formaldehyde
show the reaction diagram
-
-
-
?
caffeine + O2 + NADH + H+
theobromine + NAD+ + H2O + formaldehyde
show the reaction diagram
-
-
-
?
theophylline + O2 + NADH + H+
3-methylxanthine + NAD+ + H2O + formaldehyde
show the reaction diagram
-
-
-
?
1,3,7-trimethylxanthine + O2 + NAD(P)H + H+
3,7-dimethylxanthine + formaldehyde + NAD(P)+
show the reaction diagram
-
i.e. caffeine
i.e. theobromine
-
?
1,3,7-trimethylxanthine + O2 + NADPH + H+
1,3-dimethylxanthine + formaldehyde + NADP+ + H2O
show the reaction diagram
-
i.e. caffeine
i.e. theophylline
-
?
1,3,7-trimethylxanthine + O2 + NADPH + H+
1,7-dimethylxanthine + formaldehyde + NADP+ + H2O
show the reaction diagram
-
i.e. caffeine
i.e. paraxanthine
-
?
1,7-dimethylxanthine + 2 O2 + 2 NADH + 2 H+
xanthine + 2 NAD+ + 2 H2O + 2 formaldehyde
show the reaction diagram
-
i.e. paraxanthine, NADH is the preferred cofactor of reductase component of the N-demethylase holoenzyme (Ccr). The product 7-methylxanthine is further demethylated to xanthine. 1,7-Dimethylxanthine (paraxanthine) demethylation is 22% of the activity compared to demethylation of 7-methylxanthine. Activity is absolutely dependent of oxygen as a cosubstrate
-
-
?
1,7-dimethylxanthine + 2 O2 + 2 NADPH + 2 H+
xanthine + 2 NADP+ + 2 H2O + 2 formaldehyde
show the reaction diagram
-
i.e. paraxanthine, activity of the reductase component of the N-demethylase holoenzyme (Ccr) with NADPH is 22% of that with NADH. The enzyme also catalyzes the further demethylation of the product 7-methylxanthine to xanthine. Activity is absolutely dependent of oxygen as a cosubstrate
-
-
?
1,7-dimethylxanthine + O2 + NADH + H+
7-methylxanthine + NAD+ + H2O + formaldehyde
show the reaction diagram
-
i.e. paraxanthine, NADH is the preferred cofactor of reductase component of the N-demethylase holoenzyme (Ccr). The product 7-methylxanthine is further demethylated to xanthine. 1,7-Dimethylxanthine (paraxanthine) demethylation is 22% of the activity compared to demethylation of 7-methylxanthine. Activity is absolutely dependent of oxygen as a cosubstrate
-
-
?
1,7-dimethylxanthine + O2 + NADPH + H+
7-methylxanthine + NADP+ + H2O + formaldehyde
show the reaction diagram
-
i.e. paraxanthine, activity of the reductase component of the N-demethylase holoenzyme (Ccr) with NADPH is 22% of that with NADH. The enzyme also catalyzes the further demethylation of the product 7-methylxanthine to xanthine. Activity is absolutely dependent of oxygen as a cosubstrate
-
-
?
3,7-dimethylxanthine + O2 + NAD(P)H + H+
monomethylxanthine + formaldehyde + NADP+
show the reaction diagram
-
theobromine demethylase
-
-
?
3-methylxanthine + O2 + NADH + H+
xanthine + NAD+ + H2O + formaldehyde
show the reaction diagram
-
3-methylxanthine demethylation is 12% of the activity compared to demethylation of 7-methylxanthine. Activity is absolutely dependent of oxygen as a cosubstrate
-
-
?
7-methylxanthine + O2 + NAD(P)H + H+
xanthine + formaldehyde + NADP+
show the reaction diagram
-
heteroxanthine demethylase, substrate-selective
-
-
?
7-methylxanthine + O2 + NAD(P)H + H+
xanthine + NAD(P)+ + H2O + formaldehyde
show the reaction diagram
-
part of the caffeine degradation pathway in Pseudomonas putida
-
-
?
7-methylxanthine + O2 + NADH + H+
xanthine + NAD+ + H2O + formaldehyde
show the reaction diagram
7-methylxanthine + O2 + NADPH + H+
xanthine + NADP+ + H2O + formaldehyde
show the reaction diagram
-
-
-
-
?
caffeine + 2 O2 + 2 NADH + 2 H+
7-methylxanthine + 2 NAD+ + 2 H2O + 2 formaldehyde
show the reaction diagram
-
i.e. 1,3,7-trimethylxanthine. Caffeine demethylation is 7% of the activity compared to demethylation of 7-methylxanthine. Activity is absolutely dependent of oxygen as a cosubstrate
-
-
?
caffeine + 3 O2 + 3 NADH + 3 H+
xanthine + 3 NAD+ + 3 H2O + 3 formaldehyde
show the reaction diagram
-
i.e. 1,3,7-trimethylxanthine. Caffeine demethylation is 7% of the activity compared to demethylation of 7-methylxanthine. Activity is absolutely dependent of oxygen as a cosubstrate
-
-
?
caffeine + O2 + NADH + H+
1,7-dimethylxanthine + NAD+ + H2O + formaldehyde
show the reaction diagram
-
i.e. 1,3,7-trimethylxanthine. Caffeine demethylation is 7% of the activity compared to demethylation of 7-methylxanthine. Activity is absolutely dependent of oxygen as a cosubstrate
-
-
?
caffeine + O2 + NADH + H+
theobromine + NAD+ + H2O + formaldehyde
show the reaction diagram
-
i.e. 1,3,7-trimethylxanthine. Caffeine demethylation is 7% of the activity compared to demethylation of 7-methylxanthine. Activity is absolutely dependent of oxygen as a cosubstrate
-
-
?
theobromine + 2 O2 + 2 NADH + 2 H+
xanthine + 2 NAD+ + 2 H2O + 2 formaldehyde
show the reaction diagram
-
i.e. 3,7-dimethylxanthine. Theobromine demethylation is 13% of the activity compared to demethylation of 7-methylxanthine. Activity is absolutely dependent of oxygen as a cosubstrate
-
-
?
theobromine + O2 + NADH + H+
3-methylxanthine + NAD+ + H2O + formaldehyde
show the reaction diagram
-
i.e. 3,7-dimethylxanthine. Theobromine demethylation is 13% of the activity compared to demethylation of 7-methylxanthine. Activity is absolutely dependent of oxygen as a cosubstrate
-
-
?
theobromine + O2 + NADH + H+
7-methylxanthine + NAD+ + H2O + formaldehyde
show the reaction diagram
-
i.e. 3,7-dimethylxanthine. Theobromine demethylation is 13% of the activity compared to demethylation of 7-methylxanthine. Activity is absolutely dependent of oxygen as a cosubstrate
-
-
?
theophylline + 2 O2 + 2 NADH + 2 H+
xanthine + 2 NAD+ + 2 H2O + 2 formaldehyde
show the reaction diagram
-
1,3-dimethylxanthine. Theophylline demethylation is 3% of the activity compared to demethylation of 7-methylxanthine. Activity is absolutely dependent of oxygen as a cosubstrate
-
-
?
theophylline + O2 + NADH + H+
1-methylxanthine + NAD+ + H2O + formaldehyde
show the reaction diagram
-
1,3-dimethylxanthine. Theophylline demethylation is 3% of the activity compared to demethylation of 7-methylxanthine. Activity is absolutely dependent of oxygen as a cosubstrate
-
-
?
theophylline + O2 + NADH + H+
3-methylxanthine + NAD+ + H2O + formaldehyde
show the reaction diagram
-
1,3-dimethylxanthine. Theophylline demethylation is 3% of the activity compared to demethylation of 7-methylxanthine. Activity is absolutely dependent of oxygen as a cosubstrate
-
-
?
additional information
?
-
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
7-methylxanthine + O2 + NADH + H+
xanthine + NAD+ + H2O + formaldehyde
show the reaction diagram
-
-
-
?
caffeine + O2 + NADH + H+
theobromine + NAD+ + H2O + formaldehyde
show the reaction diagram
-
-
-
?
1,3,7-trimethylxanthine + O2 + NAD(P)H + H+
3,7-dimethylxanthine + formaldehyde + NAD(P)+
show the reaction diagram
-
i.e. caffeine
i.e. theobromine
-
?
1,3,7-trimethylxanthine + O2 + NADPH + H+
1,3-dimethylxanthine + formaldehyde + NADP+ + H2O
show the reaction diagram
-
i.e. caffeine
i.e. theophylline
-
?
1,3,7-trimethylxanthine + O2 + NADPH + H+
1,7-dimethylxanthine + formaldehyde + NADP+ + H2O
show the reaction diagram
-
i.e. caffeine
i.e. paraxanthine
-
?
7-methylxanthine + O2 + NAD(P)H + H+
xanthine + NAD(P)+ + H2O + formaldehyde
show the reaction diagram
-
part of the caffeine degradation pathway in Pseudomonas putida
-
-
?
7-methylxanthine + O2 + NADH + H+
xanthine + NAD+ + H2O + formaldehyde
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NADH
NdmA enzyme is a Rieske (2Fe-2S) non-heme iron monooxygenase that requires a partner reductase, NdmD, to transfer electrons from NADH
[2Fe-2S]-center
NdmA enzyme is a Rieske (2Fe-2S) non-heme iron monooxygenase that requires a partner reductase, NdmD, to transfer electrons from NADH
NAD(P)H
-
dependent on
NADPH
-
activity of Ccr (reductase component of the N-demethylase holoenzyme) with NADPH is 22% of that with NADH
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Fe2+
NdmA enzyme is a Rieske (2Fe-2S) non-heme iron monooxygenase
Ca2+
-
1 mM, activation to 123% of control
Fe2+
-
preincubation of Ndm for 15 min with 1 mM Fe2+, followed by desalting, increases the iron content to 20.1 mol per mol hexameric N-demethylase component (Ndm) of the N-demethylase holoenzyme. After this treatment, Ndm specific activity increases about 6fold (when 50 mM Fe2+ is present in the enzyme reaction mixture). N-Demethylase component (Ndm) of the N-demethylase holoenzyme is deduced to be a Rieske [2Fe-2S]-domain containing non-haem iron oxygenase
Mg2+
-
1 mM, activation to 132% of control
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Ag+
-
0.2 mM, complete inhibition
Co2+
-
0.2 mM, 40% inhibition
Cu2+
-
0.2 mM, complete inhibition
Fe2+
-
1 mM, 37% inhibition
Hg2+
-
1 mM, 98% inhibition
Sn2+
-
0.2 mM, 17% inhibition
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.037
Caffeine
pH and temperature not specified in the publication
0.0504
1,7-dimethylxanthine
-
pH 7.5, 30°C, kinetic parameters for two-subunit N-demethylase component (Ndm), in the presence of saturating amounts of Ccr (reductase component with cytochrome c reductase activity) and 50 mM Fe2+
1.1
3,7-Dimethylxanthine
-
theobromine demethylase, pH and temperature not specified in the publication
0.0153 - 0.0638
7-methylxanthine
0.113
O2
-
pH and temperature not specified in the publication
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3.17
Caffeine
pH and temperature not specified in the publication
0.27
1,7-dimethylxanthine
-
pH 7.5, 30°C, kinetic parameters for two-subunit N-demethylase component (Ndm), in the presence of saturating amounts of Ccr (reductase component with cytochrome c reductase activity) and 50 mM Fe2+
0.16 - 1.58
7-methylxanthine
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
85.68
Caffeine
pH and temperature not specified in the publication
5.4
1,7-dimethylxanthine
-
pH 7.5, 30°C, kinetic parameters for two-subunit N-demethylase component (Ndm), in the presence of saturating amounts of Ccr (reductase component with cytochrome c reductase activity) and 50 mM Fe2+
10.17 - 24.8
7-methylxanthine
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
55.4
-
pH 7.5, 30°C, activity with paraxanthine
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6
-
caffeine demethylase
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.5 - 8
-
about 50% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30
in vivo assay, recombinant enzyme
22 - 24
-
caffeine demethylase
30 - 35
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
SwissProt
Manually annotated by BRENDA team
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
soil bacterium Pseudomonas putida strain CBB5 can use caffeine (1,3,7-trimethylxanthine) as a sole carbon and nitrogen source
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
the enzyme NdmA catalyzes NADH-dependent N1-demethylation of caffeine to theobromine and theophylline to 3-methylxanthine, and subsequently to 7-methylxanthine, and xanthine. The oxidoreductase NdmD, UniProt ID H9N291, catalyzes the oxidation of NADH and transfers electrons to NdmA and NdmB, which catalyze the N-demethylation reaction
evolution
-
catabolism of caffeine in microorganisms commences via two possible mechanisms: demethylation and oxidation. Through the demethylation route, the major metabolite formed in fungi is theophylline, whereas theobromine is the major metabolite in bacteria
metabolism
physiological function
some bacteria, such as Pseudomonas putida strain CBB5, utilize caffeine as a sole carbon and nitrogen source by degrading it through sequential N-demethylation catalyzed by five enzymes: NdmA, NdmB, NdmC, NdmD, and NdmE. Enzyme NdmC specifically detaches methyl groups from the N-7 position of methylxanthine derivatives, NdmC is a monooxygenase
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
NDMA_PSEPU
351
0
40203
Swiss-Prot
-
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
240000
-
gel filtration, two-subunit N-demethylase component (Ndm) of the N-demethylase holoenzyme
41000
-
x * 41000, theobromine demethylase, SDS-PAGE, x * 36600-43500, caffeine demethylase complex, SDS-PAGE
67000
x * 67000, SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
the enzyme occurs as a Rieske nonheme iron oxygenase (RO)-reductase complex, the NdmCDE heterotrimer. NdmCDE domain architecture analysis, NdmC contains the ligand-binding domain, and the remaining Rieske domain must be nonfunctional because the metal coordinating residues are not conserved. Instead, a potentially functional, unique Rieske domain is located at the N-terminus of NdmD. In addition to the N-terminal Rieske domain, NdmD is composed of a flavin mononucleotide (FMN)-binding domain, an NADH-binding domain, and a C-terminal plant-type ferredoxin domain. NdmE has no discernable function, but exhibits high structural similarity to many glutathione-S-transferases. NdmE might facilitate complex formation by structural alignment
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
H120A/D237A
site-directed mutagenesis, catalytically inactive mutant
additional information
production of theobromine and paraxanthine by engineered Escherichia coli expressing the enzyme NdmA and NdmN from Psseudomonas putida CBS5, method evaluation and optimization. Addition of metal ions is not required, additon of Co2+ and Zn2+ might inhibit the process
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
45
-
1 min, complete inactivation
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
stabilization can be achieved by addition of either glycerol (20%), bovine serum albumin (10 mg/ml), dithiothreitol (1 mM) or the substrate 7-methylxanthine (1 mM). Storage under nitrogen atmosphere has a stabilizing influence. The addition of caffeine (1 mM), dimethylxanthines (1 mM) and protease inhibitors (pepstatin A, PMSF, 0.1 mM) is without influence on stability
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-80°C, two-subunit N-demethylase component (Ndm) of the N-demethylase holoenzyme is stable for over 1 month
-
4°C, 5 days, two-subunit N-demethylase component (Ndm) of the N-demethylase holoenzyme is stabel for at lewast 5 days
-
4°C, pH 6.0, 94% loss of activity after 24 h
-
similar to caffeine demethylase, heteroxanthinedemethylase is also unstable and loss of activity occurs upon storage
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
native heteroxanthine demethylase partially
-
Ni-NTA column chromatography
Ni-NTA column chromatography and Sephacryl S200 gel filtration
purification of two-subunit N-demethylase component (Ndm) of the N-demethylase holoenzyme
-
recombinant His-tagged wild-type and mutant NdmC proteins by nickel affinity chromatography and gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene ndmA, recombinant expression of ndmA and ndmD genes in Escherichia coli
expressed in Escherichia coli BL21(DE3) cells
gene ndmC, recombinant overexpression of His-tagged wild-type and mutant NdmC proteins, coexpression with NdmD and NdmE
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
-
methylxanthine intermediates of caffeine catabolism obtained by the action of N-demethylases have many applications. In medicine, theobromine and theophylline are used as diuretics, vasodilators, and myocardial stimulants. Monomethylxanthines can be converted to effective caffeine derivatives by chemical derivatization and hence can serve as interesting alternatives to caffeine. Xanthine also finds pharmaceutical application in drugs for treatment of asthma. The biotechnological potential of N-demethylases therefore lies not only in general decaffeination purposes but also in specific product recovery from caffeine
pharmacology
-
methylxanthine intermediates of caffeine catabolism obtained by the action of N-demethylases have many applications. In medicine, theobromine and theophylline are used as diuretics, vasodilators, and myocardial stimulants. Monomethylxanthines can be converted to effective caffeine derivatives by chemical derivatization and hence can serve as interesting alternatives to caffeine. Xanthine also finds pharmaceutical application in drugs for treatment of asthma. The biotechnological potential of N-demethylases therefore lies not only in general decaffeination purposes but also in specific product recovery from caffeine
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Glck, M.; Lingens, F.
Heteroxanthinedemethylase, a new enzyme in the degradation of caffeine by Pseudomonas putida
Appl. Microbiol. Biotechnol.
28
59-62
1988
Pseudomonas putida
-
Manually annotated by BRENDA team
Summers, R.M.; Louie, T.M.; Yu, C.L.; Subramanian, M.
Characterization of a broad-specificity non-haem iron N-demethylase from Pseudomonas putida CBB5 capable of utilizing several purine alkaloids as sole carbon and nitrogen source
Microbiology
157
583-592
2011
Pseudomonas putida, Pseudomonas putida CBB5
Manually annotated by BRENDA team
Dash, S.S.; Gummadi, S.N.
Catabolic pathways and biotechnological applications of microbial caffeine degradation
Biotechnol. Lett.
28
1993-2002
2006
Pseudomonas putida
Manually annotated by BRENDA team
Summers, R.M.; Louie, T.M.; Yu, C.L.; Gakhar, L.; Louie, K.C.; Subramanian, M.
Novel, highly specific N-demethylases enable bacteria to live on caffeine and related purine alkaloids
J. Bacteriol.
194
2041-2049
2012
Pseudomonas putida (M1EY73), Pseudomonas putida CBB5 (M1EY73), Pseudomonas putida CBB5
Manually annotated by BRENDA team
Summers, R.M.; Seffernick, J.L.; Quandt, E.M.; Yu, C.L.; Barrick, J.E.; Subramanian, M.V.
Caffeine junkie: an unprecedented glutathione S-transferase-dependent oxygenase required for caffeine degradation by Pseudomonas putida CBB5
J. Bacteriol.
195
3933-3939
2013
Pseudomonas putida (M1EY73), Pseudomonas putida CBB5 (M1EY73)
Manually annotated by BRENDA team
Algharrawi, K.; Summers, R.; Subramanian, M.
Production of theobromine by N-demethylation of caffeine using metabolically engineered E. coli
Biocatal. Agricult. Biotechnol.
11
153-160
2017
Pseudomonas putida (H9N289), Pseudomonas putida CBB5 (H9N289)
-
Manually annotated by BRENDA team
Kim, J.H.; Kim, B.H.; Brooks, S.; Kang, S.Y.; Summers, R.M.; Song, H.K.
Structural and mechanistic insights into caffeine degradation by the bacterial N-demethylase complex
J. Mol. Biol.
431
3647-3661
2019
Pseudomonas putida (M1EY73), Pseudomonas putida CBB5 (M1EY73), Pseudomonas putida CBB5
Manually annotated by BRENDA team