BRENDA - Enzyme Database show
show all sequences of 1.9.6.1

Periplasmic nitrate reductase and formate dehydrogenase similar molecular architectures with very different enzymatic activities

Cerqueira, N.M.; Gonzalez, P.J.; Fernandes, P.A.; Moura, J.J.; Ramos, M.J.; Acc. Chem. Res. 48, 2875-2884 (2015)

Data extracted from this reference:

Engineering
Amino acid exchange
Commentary
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
Commentary
Organism
Structure
Dithionite
-
Methylotenera mobilis
Localization
Localization
Commentary
Organism
GeneOntology No.
Textmining
periplasm
-
Methylotenera mobilis
-
-
periplasm
-
Desulfovibrio desulfuricans
-
-
Metals/Ions
Metals/Ions
Commentary
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
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
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
Primary Accession No. (UniProt)
Commentary
Textmining
Desulfovibrio desulfuricans
P81186
-
-
Methylotenera mobilis
C6WXA3
-
-
Methylotenera mobilis JLW8
C6WXA3
-
-
Reaction
Reaction
Commentary
Organism
2 ferrocytochrome + 2 H+ + nitrate = 2 ferricytochrome + nitrite
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 and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2 ferrocytochrome + 2 H+ + nitrate
-
741478
Desulfovibrio desulfuricans
2 ferricytochrome + nitrite
-
-
-
?
2 ferrocytochrome + 2 H+ + nitrate
-
741478
Methylotenera mobilis
2 ferricytochrome + nitrite
-
-
-
r
2 ferrocytochrome + 2 H+ + nitrate
-
741478
Methylotenera mobilis JLW8
2 ferricytochrome + nitrite
-
-
-
r
2 reduced methyl viologen + 2 H+ + nitrate
artificial electron acceptor
741478
Methylotenera mobilis
2 oxidized methyl viologen + nitrite
-
-
-
r
2 reduced methyl viologen + 2 H+ + nitrate
artificial electron acceptor
741478
Methylotenera mobilis JLW8
2 oxidized methyl viologen + nitrite
-
-
-
r
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
22
-
assay at room temperature
Methylotenera mobilis
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.5
-
assay at
Methylotenera mobilis
Cofactor
Cofactor
Commentary
Organism
Structure
cytochrome c
-
Methylotenera mobilis
cytochrome c
-
Desulfovibrio desulfuricans
molybdenum cofactor
-
Desulfovibrio desulfuricans
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
cytochrome c
-
Methylotenera mobilis
cytochrome c
-
Desulfovibrio desulfuricans
molybdenum cofactor
-
Desulfovibrio desulfuricans
Engineering (protein specific)
Amino acid exchange
Commentary
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 (protein specific)
Inhibitors
Commentary
Organism
Structure
Dithionite
-
Methylotenera mobilis
Localization (protein specific)
Localization
Commentary
Organism
GeneOntology No.
Textmining
periplasm
-
Methylotenera mobilis
-
-
periplasm
-
Desulfovibrio desulfuricans
-
-
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Fe2+
-
Desulfovibrio desulfuricans
Mo(VI)
coordinates a cysteine and a sulfido residue
Desulfovibrio desulfuricans
Molybdenum
-
Methylotenera mobilis
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
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
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2 ferrocytochrome + 2 H+ + nitrate
-
741478
Desulfovibrio desulfuricans
2 ferricytochrome + nitrite
-
-
-
?
2 ferrocytochrome + 2 H+ + nitrate
-
741478
Methylotenera mobilis
2 ferricytochrome + nitrite
-
-
-
r
2 ferrocytochrome + 2 H+ + nitrate
-
741478
Methylotenera mobilis JLW8
2 ferricytochrome + nitrite
-
-
-
r
2 reduced methyl viologen + 2 H+ + nitrate
artificial electron acceptor
741478
Methylotenera mobilis
2 oxidized methyl viologen + nitrite
-
-
-
r
2 reduced methyl viologen + 2 H+ + nitrate
artificial electron acceptor
741478
Methylotenera mobilis JLW8
2 oxidized methyl viologen + nitrite
-
-
-
r
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
22
-
assay at room temperature
Methylotenera mobilis
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.5
-
assay at
Methylotenera mobilis
General Information
General Information
Commentary
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
General Information (protein specific)
General Information
Commentary
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
Other publictions for EC 1.9.6.1
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
741478
Cerqueira
Periplasmic nitrate reductase ...
Desulfovibrio desulfuricans, Methylotenera mobilis, Methylotenera mobilis JLW8
Acc. Chem. Res.
48
2875-2884
2015
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5
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742645
Lopez
The periplasmic nitrate reduc ...
Salmonella enterica, Salmonella enterica SL1344 AND CAL128
Infect. Immun.
83
3470-3478
2015
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1
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6
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3
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741958
Jacques
Kinetics of substrate inhibit ...
Rhodobacter sphaeroides, Rhodobacter sphaeroides DSM 158
Biochim. Biophys. Acta
1837
1801-1809
2014
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4
1
1
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1
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1
1
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742380
Sanchez
The nitrate-sensing NasST sys ...
Bradyrhizobium japonicum, Bradyrhizobium japonicum JCM 10833
Environ. Microbiol.
16
3263-3274
2014
-
-
1
-
1
-
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1
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5
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2
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3
2
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742486
Dow
Characterization of a peripla ...
Escherichia coli
FEBS J.
281
246-260
2014
1
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1
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1
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2
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742319
Gonzalez
-
Periplasmic nitrate reductase ...
Anaeromyxobacter dehalogenans, Bradyrhizobium japonicum, Campylobacter jejuni subsp. jejuni, Campylobacter jejuni subsp. jejuni ATCC 700819, Cupriavidus necator, Cupriavidus necator H16 / ATCC 23440 / NCIB 10442 / S-10-1, Desulfitobacterium hafniense, Desulfovibrio desulfuricans, Escherichia coli, Paracoccus denitrificans, Paracoccus pantotrophus, Paracoccus pantotrophus GB17, Pseudomonas sp., Pseudomonas sp. G-179, Rhodobacter sphaeroides, Shewanella gelidimarina, Shewanella oneidensis, Wolinella succinogenes
Coord. Chem. Rev.
257
315-331
2013
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14
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28
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18
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18
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14
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14
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42
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42
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742648
Cerqueira
The sulfur shift an activatio ...
Desulfovibrio desulfuricans
Inorg. Chem.
52
10766-10772
2013
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712967
Simpson
The periplasmic nitrate reduct ...
Shewanella amazonensis, Shewanella amazonensis SB2B, Shewanella baltica, Shewanella baltica OS155, Shewanella baltica OS185, Shewanella baltica OS195, Shewanella baltica OS223, Shewanella denitrificans, Shewanella denitrificans OS217, Shewanella frigidimarina, Shewanella halifaxensis, Shewanella loihica, Shewanella loihica PV-4, Shewanella oneidensis, Shewanella oneidensis MR-1 / ATCC 700550, Shewanella pealeana, Shewanella piezotolerans, Shewanella piezotolerans WP3, Shewanella putrefaciens, Shewanella putrefaciens CN-32, Shewanella sediminis, Shewanella sp., Shewanella sp. ANA-3, Shewanella sp. MR-4, Shewanella sp. MR-7, Shewanella sp. W3-18-1, Shewanella woodyi
Microbiology
156
302-312
2010
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696917
Durvasula
Effect of periplasmic nitrate ...
Paracoccus pantotrophus
Biotechnol. Prog.
25
973-979
2009
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698636
Stewart
Catabolite repression control ...
Paracoccus pantotrophus
J. Bacteriol.
191
996-1005
2009
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699015
Hofmann
Density functional theory stud ...
Desulfovibrio desulfuricans
J. Biol. Inorg. Chem.
14
1023-1035
2009
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699199
Cerqueira
The effect of the sixth sulfur ...
Desulfovibrio desulfuricans
J. Comput. Chem.
30
2466-2484
2009
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711653
Van Alst
Compensatory periplasmic nitra ...
Pseudomonas aeruginosa
Can. J. Microbiol.
55
1133-1144
2009
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