1.14.13.B34: N-demethylase reductase

malfunction

65% loss in reductase activity of NdmD can be attributed to the fractional loss of flavin by disruption of the flavin-binding environment of FMN-binding pocket. Deletion of N-terminal Rieske domain does not disrupt flavin binding in the constructs DELTA114NdmD and DELTA250NdmD

metabolism

physiological function

additional information

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

evolution

the N-terminal Rieske domain found in NdmD is a product of domain shuffling between NdmC and NdmD during evolution and is not required for its reductase activity

evolution

metabolism

based on the sequence of a genomic fragment, caffeine demethylation enzyme system found in Pseudomonas sp. is predicted to consist of a two two-component Rieske monooxygenases namely NdmA and NdmB specific towards methyl groups at 1 and 3 positions in xanthine ring respectively and one kind of three-component Rieske monooxygenase system comprising a monooxygenase NdmC specific towards 7-methylxanthine, a reductase component NdmD and a structural protein NdmE. NdmD also acts as the reductase component for NdmA and NdmB. The Rieske domain present in NdmD serves to function as an electron transfer domain during catalysis by NdmC as it lacks its own Rieske domain. NdmC forms a large multi-subunit complex comprising 2 monomeric units of each NdmC, NdmD, and NdmE and follows the typical electron flow pattern of Rieske oxygenases. The N-terminal Rieske domain found in NdmD is a product of domain shuffling between NdmC and NdmD during evolution and is not required for its reductase activity

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

metabolism

physiological function

Pseudomonas sp. NCIM 5235 is a caffeine-degrading bacterial strain that metabolizes caffeine by sequential demethylation using methylxanthine demethylases, including 7-methylxanthine demethylase NdmC. These enzymes belong to the class of two-component Rieske oxygenases and require an oxidoreductase, NdmD, for efficient catalysis. Three oxygenases (NdmA, NdmB, and NdmC) specific towards methyl groups at 1, 3, and 7 positions in xanthine ring share a common reductase component, NdmD, analysis of NdmD parameters and function, overview. NdmD acts as the reductase component for NdmA, NdmB, and NdmC. The Rieske domain present in NdmD serves to function as an electron transfer domain during catalysis by NdmC as it lacks its own Rieske domain

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

physiological function

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

additional information

NdmD in Pseudomonas sp. has a unique domain fusion in its N-terminal that is not observed in any other Rieske oxygenase reductases reported so far. The N-terminal Rieske domain found in NdmD is a product of domain shuffling between NdmC and NdmD during evolution and is not required for its reductase activity

additional information