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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 .
    View publication on PubMed

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
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Pseudomonas putida CBB5 A0A0M3CPH9
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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
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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 ?
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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 ?
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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
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Pseudomonas putida
Rieske nonheme iron oxygenase reductase
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Pseudomonas putida
RO reductase
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Pseudomonas putida

Temperature Optimum [┬░C]

Temperature Optimum [┬░C] Temperature Optimum Maximum [┬░C] Comment Organism
30
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assay at Pseudomonas putida

pH Optimum

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

Cofactor

Cofactor Comment Organism Structure
Ferredoxin
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Pseudomonas putida
NADH
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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