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Literature summary for 1.9.6.1 extracted from

  • Cerqueira, N.M.; Gonzalez, P.J.; Fernandes, P.A.; Moura, J.J.; Ramos, M.J.
    Periplasmic nitrate reductase and formate dehydrogenase similar molecular architectures with very different enzymatic activities (2015), Acc. Chem. Res., 48, 2875-2884 .
    View publication on PubMed
Search for more literature for 1.9.6.1

Protein Variants

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

Inhibitors Comment Organism Structure
Dithionite
-
 Methylotenera mobilis

Localization

Localization Comment Organism GeneOntology No. Textmining
periplasm
-
 Desulfovibrio desulfuricans
-
-
periplasm
-
 Methylotenera mobilis
-
-

Metals/Ions

Metals/Ions Comment Organism Structure
Fe2+
-
 Desulfovibrio desulfuricans
Mo(VI) coordinates a cysteine and a sulfido residue Desulfovibrio desulfuricans
Molybdenum
-
 Methylotenera mobilis

Natural Substrates/ Products (Substrates)

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

Organism UniProt Comment Textmining
Desulfovibrio desulfuricans P81186
-
-
Methylotenera mobilis C6WXA3
-
-
Methylotenera mobilis JLW8 C6WXA3
-
-

Reaction

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
a

Substrates and Products (Substrate)

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

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 [°C] Temperature Optimum Maximum [°C] Comment Organism
22
-
 assay at room temperature Methylotenera mobilis

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.5
-
 assay at Methylotenera mobilis

Cofactor

Cofactor Comment Organism Structure
cytochrome c
-
 Desulfovibrio desulfuricans
cytochrome c
-
 Methylotenera mobilis
molybdenum cofactor
-
 Desulfovibrio desulfuricans

General Information

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