Protein Variants | Comment | Organism |
---|---|---|
additional information | construction of a gene nap deletion mutant, the wild-type gene is replaced by the deletion/insertion version via homologous recombination. The mutant strain can no longer grow on methanol in contrast to the wild-type | Methylotenera mobilis |
Inhibitors | Comment | Organism | Structure |
---|---|---|---|
Dithionite | - |
Methylotenera mobilis |
Localization | Comment | Organism | GeneOntology No. | Textmining |
---|---|---|---|---|
periplasm | - |
Desulfovibrio desulfuricans | - |
- |
periplasm | - |
Methylotenera mobilis | - |
- |
Metals/Ions | Comment | Organism | Structure |
---|---|---|---|
Fe2+ | - |
Desulfovibrio desulfuricans | |
Mo(VI) | coordinates a cysteine and a sulfido residue | Desulfovibrio desulfuricans | |
Molybdenum | - |
Methylotenera mobilis |
Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|
2 ferrocytochrome + 2 H+ + nitrate | Desulfovibrio desulfuricans | - |
2 ferricytochrome + nitrite | - |
? | |
2 ferrocytochrome + 2 H+ + nitrate | Methylotenera mobilis | - |
2 ferricytochrome + nitrite | - |
r | |
2 ferrocytochrome + 2 H+ + nitrate | Methylotenera mobilis JLW8 | - |
2 ferricytochrome + nitrite | - |
r |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Desulfovibrio desulfuricans | P81186 | - |
- |
Methylotenera mobilis | C6WXA3 | - |
- |
Methylotenera mobilis JLW8 | C6WXA3 | - |
- |
Reaction | Comment | Organism | Reaction ID |
---|---|---|---|
2 ferrocytochrome + 2 H+ + nitrate = 2 ferricytochrome + nitrite + H2O | sulfur-shift mechanism catalytic mechanism, detailed overview. The mechanism is defined by a change in the Mo ion coordination, which involves a first-to-second shell displacement (shift) of the sulfur from the Cys, resulting in a free coordination position that is used by the enzyme to bind the substrate with a low energy cost, molybdenum coordinates an oxygen atom from the substrate, an oxygen atom from the substrate is transferred to the Mo ion, and later released as a water molecule. The reaction requires two electrons, which are provided by external reducing species, and two protons that are obtained from the solvent either directly or indirectly mediated by residues from the enzyme catalytic pocket | Desulfovibrio desulfuricans |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
2 ferrocytochrome + 2 H+ + nitrate | - |
Desulfovibrio desulfuricans | 2 ferricytochrome + nitrite | - |
? | |
2 ferrocytochrome + 2 H+ + nitrate | - |
Methylotenera mobilis | 2 ferricytochrome + nitrite | - |
r | |
2 ferrocytochrome + 2 H+ + nitrate | - |
Methylotenera mobilis JLW8 | 2 ferricytochrome + nitrite | - |
r | |
2 reduced methyl viologen + 2 H+ + nitrate | artificial electron acceptor | Methylotenera mobilis | 2 oxidized methyl viologen + nitrite | - |
r | |
2 reduced methyl viologen + 2 H+ + nitrate | artificial electron acceptor | Methylotenera mobilis JLW8 | 2 oxidized methyl viologen + nitrite | - |
r |
Synonyms | Comment | Organism |
---|---|---|
mmol_1648 | - |
Methylotenera mobilis |
NAP | - |
Desulfovibrio desulfuricans |
NAP | - |
Methylotenera mobilis |
periplasmic nitrate reductase | - |
Desulfovibrio desulfuricans |
single subunit Nap-type periplasmic nitrate reductase | - |
Methylotenera mobilis |
Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
---|---|---|---|
22 | - |
assay at room temperature | Methylotenera mobilis |
pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
---|---|---|---|
7.5 | - |
assay at | Methylotenera mobilis |
Cofactor | Comment | Organism | Structure |
---|---|---|---|
cytochrome c | - |
Desulfovibrio desulfuricans | |
cytochrome c | - |
Methylotenera mobilis | |
molybdenum cofactor | - |
Desulfovibrio desulfuricans |
General Information | Comment | Organism |
---|---|---|
evolution | periplasmic nitrate reductase (Nap) from Desulfovibrio desulfuricans and formate dehydrogenase (Fdh) from Escherichia coli K-12, both belonging to the DMSO reductase family, subfamily I, have a very similar structure, but very different activities. The show key differences that tune them for completely different functions in living cells. Both enzymes share almost identical three-dimensional protein foldings and active sites, in terms of coordination number, geometry and nature of the ligands. The substrates of both enzymes (nitrate and formate) are polyatomic anions that also share similar charge and stereochemistry. In terms of the catalytic mechanism, both enzymes have a common activation mechanism (the sulfur-shift mechanism) that ensures a constant coordination number around the metal ion during the catalytic cycle. In spite of these similarities, they catalyze very different reactions: Nap abstracts an oxygen atom from nitrate releasing nitrite, whereas FdH catalyzes a hydrogen atom transfer from formate and releases carbon dioxide. Detailed comparison, overview. A key difference between the catalytic mechanisms of Nap and FdH is the fact that only Mo is used to reduce nitrate but in Fdhs both Mo and W are catalytically competent to oxidize formate to carbon dioxide | Desulfovibrio desulfuricans |
malfunction | a gene nap deletion mutant can no longer grow on methanol in contrast to the wild-type and shows almost abolished N2O production from nitrate | Methylotenera mobilis |
metabolism | cytochromes c encoded by genes in close proximity to the genes for XoxF proteins and methylamine dehydrogenase functions are likely involved in the metabolism with Nap, pathway overview | Methylotenera mobilis |
additional information | the enzyme shows a sulfur-shift mechanism catalytic mechanism, the active site is deeply buried and centered on the Mo atom, which is hexacoordinated to four sulfur atoms of two pyranopterin guanosine dinucleotides, one inorganic sulfur, and one S (Nap) atom from the side chain of a Cys, structure, structure overview. Above the region of the metal center, the enzyme presents an arginine residue, Arg354,that is proposed to be key for stabilization and substrate binding. The side chain of this residues probably interacts electrostatically with the substrates, compensating for the negative charge and favoring their interaction with the negatively charged active site | Desulfovibrio desulfuricans |
physiological function | the single subunit nitrate reductase (Nap) appears to be involved in both the assimilatory and the dissimilatory denitrification pathways. The role in the former is supported by the methanol growth deficiency of the mutant when nitrate is used as a nitrogen source, and the role in the latter is supported by the lack of accumulation of N2O in the mutant | Methylotenera mobilis |