Any feedback?
Literature summary for 1.14.13.B34 extracted from
- Identification and characterization of oxidoreductase component (NdmD) of methylxanthine oxygenase system in Pseudomonas sp. NCIM 5235 (2018), Appl. Microbiol. Biotechnol., 102, 7913-7926 .
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| gene ndmD, genetic organization of caffeine-degrading genes and its isolation and of the ndmD gene, recombinant expression of His-tagged wild-type and mutant NdmDs in Escherichia coli strain BL21 | Pseudomonas sp. NCIM 5235 |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| additional information | to determine the role of N-terminal Rieske domain in NdmD reductase activity, two deletion constructs DELTA114NdmD and DELTA250NdmD are made. Cytochrome c reductase (ccr) activity of the NdmD constructs and demethylase activity of NdmA in the presence of NdmD constructs show that there is no significant difference in the catalytic activity of NdmD upon deletion of its N-terminal Rieske domain | Pseudomonas sp. NCIM 5235 |
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| Co2+ | 67% inhibition | Pseudomonas sp. NCIM 5235 |  |
| Cu2+ | complete inhibition | Pseudomonas sp. NCIM 5235 | |
| Ni2+ | 42% inhibition | Pseudomonas sp. NCIM 5235 | |
| Zn2+ | 35% inhibition | Pseudomonas sp. NCIM 5235 | |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| additional information | - |
additional information | Michaelis-Menten kinetics | Pseudomonas sp. NCIM 5235 |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| additional information | Mg2+ and Mn2+ do not cause any significant change in enzyme activity | Pseudomonas sp. NCIM 5235 |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Pseudomonas sp. NCIM 5235 | A0A2U9IY48 | isolated from coffee plantation soil in Ooty, India | - |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant His-tagged NdmD 3.63fold from Escherichia coli strain BL21 by nickel affinity chromatography | Pseudomonas sp. NCIM 5235 |
Source Tissue
| Source Tissue | Comment | Organism | Textmining |
|---|---|---|---|
| cell culture | strain NCIM 5235 can utilize caffeine as sole source of carbon and nitrogen for growth | Pseudomonas sp. NCIM 5235 | - |
Specific Activity [micromol/min/mg]
| Specific Activity Minimum [µmol/min/mg] | Specific Activity Maximum [µmol/min/mg] | Comment | Organism |
|---|---|---|---|
| 23.88 | - |
purified recombinant enzyme, pH 8.0, 25°C, substrate cytochrome c | Pseudomonas sp. NCIM 5235 |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| additional information | enzyme NdmD shows broad substrate specificity with highest catalytic efficiency towards cytochrome c. The enzyme NdmD shows cytochrome c reductase (ccr, EC 1.1.1.2) activity towards three different substrates cytochrome c, DCPIP, and potassium ferricyanide,, kinetics overviews. NdmD also assists as an oxidoreductase the demethylase activity of NdmA, NdmB, and NdmC, overview. NdmD is the reductase component of the different methylxanthine demethylases. NdmD does not catalyze caffeine demethylation but only acts as a reductase | Pseudomonas sp. NCIM 5235 | ? | - |
- |
|
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| ? | x * 65000, about, recombinant His-tagged NdmD, SDS-PAGE | Pseudomonas sp. NCIM 5235 |
| More | 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 Rieske domain present in NdmD serves to function as an electron transfer domain during catalysis by NdmC as it lacks its own Rieske domain. Enzyme domain structure, overview | Pseudomonas sp. NCIM 5235 |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| NdmD | - |
Pseudomonas sp. NCIM 5235 |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 35 | - |
- |
Pseudomonas sp. NCIM 5235 |
Temperature Range [°C]
| Temperature Minimum [°C] | Temperature Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 15 | 45 | activity range, a drastic drop in activity is observed above 40°C, 16% of maximal activity at 45°C | Pseudomonas sp. NCIM 5235 |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 8 | - |
- |
Pseudomonas sp. NCIM 5235 |
pH Range
| pH Minimum | pH Maximum | Comment | Organism |
|---|---|---|---|
| 6 | 10 | 40% of maximal activity at pH 6.0, 60% at pH 10.0 | Pseudomonas sp. NCIM 5235 |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| NAD(P)H | - |
Pseudomonas sp. NCIM 5235 | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| 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 | Pseudomonas sp. NCIM 5235 |
| 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 | Pseudomonas sp. NCIM 5235 |
| 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 | Pseudomonas sp. NCIM 5235 |
| 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 | Pseudomonas sp. NCIM 5235 |
| 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 | Pseudomonas sp. NCIM 5235 |
Use of this online version of BRENDA is free under the CC BY 4.0 license. See terms of use for full details.
Release 2023.1 (January 2023)
Legal
Curated at
Member of
