Literature summary for 1.14.13.B34 extracted from

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 (2019), J. Mol. Biol., 431, 3647-3661 .

Search for more literature for 1.14.13.B34

Cloned(Commentary)

Cloned (Comment)	Organism
gene ndmD, recombinant overexpression of N-terminally MBP-tagged NdmD, coexpression with NdmC and NdmE	Pseudomonas putida

Organism

Organism	UniProt	Comment	Textmining
Pseudomonas putida	A0A0M3CPH9	-	-
Pseudomonas putida CBB5	A0A0M3CPH9	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant N-terminally MBP-tagged NdmD by affinity chromatography, ion exchange chromatography, and gel filtration, copurification with NdmC and NdmE	Pseudomonas putida

Source Tissue

Source Tissue	Comment	Organism	Textmining
cell culture	soil bacterium Pseudomonas putida strain CBB5 can use caffeine (1,3,7-trimethylxanthine) as a sole carbon and nitrogen source	Pseudomonas putida	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
additional information	the enzyme NdmD shows cytochrome c reductase (ccr, EC 1.1.1.2) activity. NdmD also is the RO reductase that forms a stable ternary complex with NdmC and NdmE (NdmCDE). Since NdmC detaches the N-7 methyl group from methylxanthine derivatives, the NdmCDE complex is responsible for the last N-demethylation step of caffeine to xanthine. But NdmD is also needed by both demethylases NdmA and NdmB for electron transport from NADH to the oxygen activation site, as a demethylase reductase. Therefore, it is expected that transient interaction would exist between them	Pseudomonas putida	?	-	-
additional information	the enzyme NdmD shows cytochrome c reductase (ccr, EC 1.1.1.2) activity. NdmD also is the RO reductase that forms a stable ternary complex with NdmC and NdmE (NdmCDE). Since NdmC detaches the N-7 methyl group from methylxanthine derivatives, the NdmCDE complex is responsible for the last N-demethylation step of caffeine to xanthine. But NdmD is also needed by both demethylases NdmA and NdmB for electron transport from NADH to the oxygen activation site, as a demethylase reductase. Therefore, it is expected that transient interaction would exist between them	Pseudomonas putida CBB5	?	-	-

Subunits

Subunits	Comment	Organism
More	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	Pseudomonas putida

Synonyms

Synonyms	Comment	Organism
NdmD	-	Pseudomonas putida
Rieske nonheme iron oxygenase reductase	-	Pseudomonas putida
RO reductase	-	Pseudomonas putida

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
30	-	assay at	Pseudomonas putida

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.5	-	assay at	Pseudomonas putida

Cofactor

Cofactor	Comment	Organism	Structure
Ferredoxin	-	Pseudomonas putida
NADH	-	Pseudomonas putida

General Information

General Information	Comment	Organism
evolution	NdmD is an FNR-type family member and is classified as a type 1A reductase in the two-component system, which is composed of a FMN-binding domain, NADH-binding domain, and C-terminal plant-type ferredoxin domain. There is an additional Rieske domain at the N-terminus of NdmD, which is a unique feature compared with other RO reductases	Pseudomonas putida
metabolism	Rieske nonheme iron oxygenases (ROs) catalyze the initial oxygenation reaction of aromatic compounds by enantio- and regiospecific reactions. The type of RO in Pseudomonas putida strain CBB5, consists of the monooxygenasesNdmA, NdmB, and NdmC, which specifically detach methyl groups from the N-1, N-3, and N-7 positions of methylxanthine derivatives, respectively. The N-demethylation of caffeine to xanthine occurs via three steps: NdmA and NdmB catalyze the initial two steps of N-demethylation, and the intermediate product, 7-methylxanthine, is further catalyzed to xanthine by an unusual RO-reductase complex, the NdmCDE heterotrimer. Heterohexamerization of NdmA and NdmB under physiological conditions. NdmD is the RO reductase that forms a stable ternary complex with NdmC and NdmE (NdmCDE). Since NdmC detaches the N-7 methyl group from methylxanthine derivatives, the NdmCDE complex is responsible for the last N-demethylation step of caffeine to xanthine. But NdmD is also needed by both NdmA and NdmB for electron transport from NADH to the oxygen activation site. Therefore, it is expected that transient interaction would exist between them. Electron transfer pathway from the ferredoxin domain of NdmD to caffeine in the catalytic site of NdmA. Enzyme complex structure analysis structure-function analysis, overview	Pseudomonas putida
additional information	analysis of the binary structure of NdmA with the ferredoxin domain of NdmD, which is the first structural information for the plant-type ferredoxin domain in a complex state. Interaction analysis of NdmD with NdmA, B, and C, detailed overview	Pseudomonas putida
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	Pseudomonas putida

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Release 2023.1 (January 2023)