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Information on EC 1.7.5.1 - nitrate reductase (quinone)
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1.7.5.1 nitrate reductase (quinone)IUBMB Comments
A membrane-bound enzyme which supports anaerobic respiration on nitrate under anaerobic conditions and in the presence of nitrate. Contains the bicyclic form of the molybdo-bis(molybdopterin guanine dinucleotide) cofactor, iron-sulfur clusters and heme b. Escherichia coli expresses two forms NarA and NarZ, both being comprised of three subunits.
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Word Map
- 1.7.5.1
-
denitrification
-
denitrify
- quinols
-
dissimilatory
- chlorate
- narj
-
narghji
-
molybdoenzyme
-
nitrate-reducing
- menaquinol
-
nitrate-dependent
-
q-site
- stigmatellin
-
menasemiquinone
-
hyscore
- menadiol
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Synonyms
membrane-bound nitrate reductase, narghi, nitrate reductase a, nitrate reductase z, quinol-nitrate oxidoreductase, quinol/nitrate oxidoreductase, quinol:nitrate oxidoreductase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
EC 1.7.99.4
-
-
formerly, part transferred
-
MSMEG_5140
NaR1
NarG
NarGHI
nitrate reducatse A
nitrate reductase A
nitrate reductase Z
Pden_4236
quinol:nitrate oxidoreductase
SCO6532
SCO6533
SCO6534
SCO6535
NarGHI
-
-
nitrate reductase A
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
nitrate + a quinol = nitrite + a quinone + H2O
-
-
-
-
nitrate + a quinol = nitrite + a quinone + H2O
electrons flow in the overall thermodynamically downhill direction from menaquinol (MQ) or ubiquinol (UQ) through the two hemes of NarI, the four [Fe-S] clusters of NarH, and then through the single [4Fe-4S] cluster of NarG to the Mo-bisPGD cofactor, where nitrate is reduced to nitrite
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PATHWAY SOURCE
PATHWAYS
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SYSTEMATIC NAME
IUBMB Comments
nitrite:quinone oxidoreductase
A membrane-bound enzyme which supports anaerobic respiration on nitrate under anaerobic conditions and in the presence of nitrate. Contains the bicyclic form of the molybdo-bis(molybdopterin guanine dinucleotide) cofactor, iron-sulfur clusters and heme b. Escherichia coli expresses two forms NarA and NarZ, both being comprised of three subunits.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
nitrate + 2,3-dimethoxy-5-methyl-6-decyl-1,4-benzoquinol
nitrite + 2,3-dimethoxy-5-methyl-6-decyl-1,4-benzoquinone + H2O
-
i.e. decylubiquinol
-
-
?
nitrate + 2-hydroxy-3-(3-methyl-2-butenyl)-1,4-naphthoquinol
nitrite + 2-hydroxy-3-(3-methyl-2-butenyl)-1,4-naphthoquinone + H2O
nitrate + 5-hydroxy-2-methyl-1,4-naphthoquinol
nitrite + 5-hydroxy-2-methyl-1,4-naphthoquinone + H2O
-
-
-
-
?
nitrate + 5-hydroxy-2-methyl-naphthalene-1,4-diol
nitrite + 5-hydroxy-2-methyl-naphthalene-1,4-dione + H2O
nitrate + menaquinol
nitrite + menaquinone + H2O
-
only the membrane-bound, not the solubilized form of the enzyme, can accept electrons from a menaquinone analog, menadione, whereas both forms can accept electrons from methylviologen. In vivo quinol interacts directly with the gamma subunit that is lost during solubilization
-
-
?
nitrate + quinol
nitrite + quinone
-
NarGHI strongly stabilizes a semiquinone radical located within the dihemic anchor subunit NarI. The semiquinone is located within the quinol oxidation site QD
-
-
?
nitrite + menaquinone + H2O
nitrate + menaquinol
-
-
-
?
nitrite + naphthoquinone + H2O
nitrate + naphthoquinol
-
-
-
?
nitrate + 2-hydroxy-3-(3-methyl-2-butenyl)-1,4-naphthoquinol
nitrite + 2-hydroxy-3-(3-methyl-2-butenyl)-1,4-naphthoquinone + H2O
-
-
-
-
?
nitrate + 2-hydroxy-3-(3-methyl-2-butenyl)-1,4-naphthoquinol
nitrite + 2-hydroxy-3-(3-methyl-2-butenyl)-1,4-naphthoquinone + H2O
-
-
-
?
nitrate + 2-hydroxy-3-(3-methyl-2-butenyl)-1,4-naphthoquinol
nitrite + 2-hydroxy-3-(3-methyl-2-butenyl)-1,4-naphthoquinone + H2O
-
-
-
?
nitrate + 2-methyl-1,4-naphthoquinol
nitrite + 2-methyl-1,4-naphthoquinone + H2O
-
i.e menadiol
-
-
?
nitrate + 2-methyl-1,4-naphthoquinol
nitrite + 2-methyl-1,4-naphthoquinone + H2O
-
i.e. menadiol
-
-
?
nitrate + 2-methyl-1,4-naphthoquinol
nitrite + 2-methyl-1,4-naphthoquinone + H2O
i.e. menadiol
-
-
?
nitrate + 2-methyl-1,4-naphthoquinol
nitrite + 2-methyl-1,4-naphthoquinone + H2O
-
i.e. menadiol. As the reduction of nitrate to nitrite requires two electrons, there must necessarily be two successive bindings of quinone, with transfer of one electron to the hemes, then to the [Fe-S] cluster, to be finally accumulated at the level of the molybdenum cofactor to be able to undertake the catalytic reaction. There are two distinct reactions, depending on whether the hemes were previously reduced by menadiol or by duroquinol. A two-pathway electron transfer model for nitrate reductase A is proposed
-
-
?
nitrate + 2-methyl-1,4-naphthoquinol
nitrite + 2-methyl-1,4-naphthoquinone + H2O
-
i.e. menadiol. Electrons from menadiol oxidation are transferred initially to heme bL
-
-
?
nitrate + 5-hydroxy-1,4-naphthoquinol
nitrite + 5-hydroxy-1,4-naphthoquinone + H2O
-
i.e. juglone
-
-
?
nitrate + 5-hydroxy-1,4-naphthoquinol
nitrite + 5-hydroxy-1,4-naphthoquinone + H2O
-
i.e. reduced form of juglone
-
-
?
nitrate + 5-hydroxy-2-methyl-naphthalene-1,4-diol
nitrite + 5-hydroxy-2-methyl-naphthalene-1,4-dione + H2O
-
i.e plumbagin
-
-
?
nitrate + 5-hydroxy-2-methyl-naphthalene-1,4-diol
nitrite + 5-hydroxy-2-methyl-naphthalene-1,4-dione + H2O
-
i.e. reduced form of plumbagin
-
-
?
nitrate + 5-hydroxy-2-methyl-naphthalene-1,4-diol
nitrite + 5-hydroxy-2-methyl-naphthalene-1,4-dione + H2O
-
i.e. reduced form of plumbagin
i.e. plumbagin
-
?
nitrate + duroquinol
nitrite + duroquinone + H2O
-
if quinols are used as the electron donor the enzyme operates by a two-site, enzyme-substitution mechanism
-
-
?
nitrate + quinol
nitrite + quinone + H2O
-
first enzyme involved in respiratory denitrification in prokaryotes
-
-
?
nitrate + quinol
nitrite + quinone + H2O
-
in order to use nitrate as an electron acceptor, Escherichia coli synthesises three distinct enzymes: a membrane-bound enzyme (nitrate reductase A, NarGHI) encoded by the narGHJI operon and a soluble periplasmic nitrate reductase (NapAB, EC 1.9.6.1) encoded by the napFDAGHBC operon. A second membrane-bound nitrate reductase (nitrate reductase Z, NarZYV) encoded by the NarZYWV operon is biochemically similar to NarGHI. Whereas NarGHI synthesis is induced by nitrate under anaerobic conditions, NarZYV is expressed at a cryptic level and may assist Escherichia coli in transition from aerobic to anaerobic respiration (physiological role of this isoenzyme at the onset of the stationary growth phase in rich media). NapAB is mainly expressed in the presence of low concentrations of nitrate under both aerobic and anaerobic conditions, and its expression is suppressed at high nitrate concentrations. Conversely, NarGHI is maximally expressed when nitrate concentration is elevated, and under these conditions becomes the predominant enzyme in Escherichia coli. Thus, NapAB (Ec 1.9.6.1) and NarGHI seem to function in different ranges of nitrate concentration in a complementary way to support anaerobic respiration on nitrate under anaerobic conditions and in the presence of nitrate
-
-
?
nitrate + quinol
nitrite + quinone + H2O
model of electron transfer in the nitrate reductase: electrons are provided by quinones to the NarI subunit and subsequently transferred to NarH, which eventually delivers them to the molybdenum cofactor where nitrate reduction takes place
-
-
?
nitrate + quinol
nitrite + quinone + H2O
nitrate reductase A reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force
-
-
?
nitrate + quinol
nitrite + quinone + H2O
under anaerobic conditions in the presence of nitrate, Escherichia coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (nitrate reductase A, NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. The arrangement, coordination scheme and unique environment of the redox-active prosthetic groups is revealed
-
-
?
nitrate + quinol
nitrite + quinone + H2O
-
the enzyme is essential for the fungal denitrification. The fungal formate dehydrogenase can supply electrons via quinol/quinone pool to nitrate reductase A
-
-
?
nitrate + quinol
nitrite + quinone + H2O
-
the membrane-anchored protein directs electrons from quinol oxidation at the membrane anchor, NarI, to the site of nitrate reduction in the membrane extrinsic [Fe-S] cluster and Mo-bis-MGD containing dimer, NarGH
-
-
?
nitrate + reduced benzyl viologen
nitrite + benzyl viologen
-
-
-
?
nitrate + reduced benzyl viologen
nitrite + oxidized benzyl viologen + H2O
-
-
-
-
?
nitrate + reduced benzyl viologen
nitrite + oxidized benzyl viologen + H2O
-
-
-
?
nitrate + reduced benzyl viologen
nitrite + oxidized benzyl viologen + H2O
-
when reduced viologen dyes act as the electron donor, the enzyme follows a compulsory-order, Theorell-Chance mechanism, in which it is an enzyme-nitrate complex that is reduced rather than the free enzyme
-
-
?
nitrate + reduced methyl viologen
nitrite + oxidized methyl viologen + H2O
-
-
-
-
?
nitrate + reduced methyl viologen
nitrite + oxidized methyl viologen + H2O
-
when reduced viologen dyes act as the electron donor, the enzyme follows a compulsory-order, Theorell-Chance mechanism, in which it is an enzyme-nitrate complex that is reduced rather than the free enzyme
-
-
?
nitrate + reduced methyl viologen
nitrite + oxidized methyl viologen + H2O
-
catalysis under substrate-limiting conditions clearly occurs via two pathways with distinct kinetic properties reversibly linked by a redox event. This redox event may be integral to the catalytic cycle of the active site or occur at a center, remote from the description of active-site chemistry, which serves to switch NarGH between two catalytically competent forms
-
-
?
nitrate + reduced methyl viologen
nitrite + oxidized methyl viologen + H2O
-
-
-
-
?
nitrate + tetramethyl-p-benzoquinol
nitrite + tetramethyl-p-benzoquinone + H2O
-
i.e. duroquinol
-
-
?
nitrate + tetramethyl-p-benzoquinol
nitrite + tetramethyl-p-benzoquinone + H2O
i.e. duroquinol
-
-
?
nitrate + tetramethyl-p-benzoquinol
nitrite + tetramethyl-p-benzoquinone + H2O
-
i.e. duroquinol. As the reduction of nitrate to nitrite requires two electrons, there must necessarily be two successive bindings of quinone, with transfer of one electron to the hemes, then to the [Fe-S] cluster, to be finally accumulated at the level of the molybdenum cofactor to be able to undertake the catalytic reaction. There are two distinct reactions, depending on whether the hemes were previously reduced by menadiol or by duroquinol. A two-pathway electron transfer model for nitrate reductase A is proposed
-
-
?
nitrate + ubiquinol
nitrite + ubiquinone + H2O
-
-
-
?
nitrate + ubiquinol
nitrite + ubiquinone + H2O
-
if quinols are used as the electron donor the enzyme operates by a two-site, enzyme-substitution mechanism
-
-
?
nitrite + demethylmenaquinone + H2O
nitrate + demethylmenaquinol
-
-
-
?
nitrite + demethylmenaquinone + H2O
nitrate + demethylmenaquinol
endogeneous demethylmenasemiquinone (DMSK) intermediates are stabilized in the enzyme. DMSK is formed at the NarGHI QD quinol oxidation site
-
-
?
nitrite + ubiquinone + H2O
nitrate + ubiquinol
-
-
-
?
nitrite + ubiquinone + H2O
nitrate + ubiquinol
-
-
-
?
additional information
?
-
-
Escherichia coli expresses two different membrane-bound respiratory nitrate reductases, nitrate reductase A (NRA) and nitrate reductase Z (NRZ). The two enzymes are encoded by distinct operons located within two different loci on the Escherichia coli chromosome. The narGHJI operon, encoding nitrate reductase A, is located in the chlC locus at 27 min, along with several functionally related genes: narK, encoding a nitrate/nitrite antiporter, and the narXL operon, encoding a nitrate-activated, two component regulatory system. The narZYWV operon, encoding nitrate reductase Z, is located in the chlZ locus located at 32.5 min, a region which includes a narK homologue, narU, but no apparent homologue to the narXL operon. The two membrane-bound enzymes have similar structures and biochemical properties and are capable of reducing nitrate using normal physiological substrates. The homology of the amino acid sequences of the peptides encoded by the two operons is extremely high but the intergenic regions share no related sequences. The expression of both the narGHJI operon and the narK gene are positively regulated by two transacting factors Fnr and NarL-phosphate, activated respectively by anaerobiosis and nitrate, while the narZYWV operon and the narU gene are constitutively expressed. Nitrate reductase A, which accounts for 98% of the nitrate reductase activity when fully induced, is clearly the major respiratory nitrate reductase in Escherichia coli
-
-
?
additional information
?
-
-
nitrate reductase Z expression is regulated in a manner opposite to that of nitrate reductase A. The narGHJZ operon is aerobically repressed, strongly induced by nitrate and positively regulated by the fnr gene product. The expression of narZ is anaerobically repressed, induced weakly, if at all, by nitrate and negatively regulated by the fnr gene product. The opposing regulation of these two enzymes suggests that a function of nitrate reductase Z may be to catalyse the immediate flow of electrons to nitrate during an aerobic/anaerobic transition when the bacterium is grown in the presence of nitrate
-
-
?
additional information
?
-
-
NRZ is expressed at a low level that is not influenced by anaerobiosis or nitrate. The NRZ operon is controlled mainly at the level of transcription and is induced 10fold at the onset of stationary phase in rich media. Expression of NRZ nitrate reductase is highly growth phase dependent and is controlled by the alternative vegetative sigma factor RpoS. RpoS-mediated regulation of NRZ may be an important physiological adaptation that allows the cell to use nitrate under stress-associated conditions
-
-
?
additional information
?
-
-
bromate and chlorate are substrates of the enzyme
-
-
?
additional information
?
-
-
the holoenzyme has two independent and spatially distinct active sites, one for quinol oxidation and the other for nitrate reduction
-
-
?
additional information
?
-
structure-function relationships of quinone reactivity
-
-
?
additional information
?
-
structure-function relationships of quinone reactivity
-
-
?
additional information
?
-
structure-function relationships of quinone reactivity
-
-
?
additional information
?
-
-
structure-function relationships of quinone reactivity
-
-
?
additional information
?
-
-
nitrate reductase Z is synthesized in small amounts, the expression of its structural genes does not seem to be induced by nitrate, repressed by oxygen or activated by the product of the fnr gene. The nitrate reductase Z in mutant LCB79/pLCB14 couples formate oxidation with nitrate reduction probably via quinones and type-b cytochromes
-
-
?
additional information
?
-
-
nitrate reductase Z is able to use both nitrate and chlorate as substrate
-
-
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
nitrite + demethylmenaquinone + H2O
nitrate + demethylmenaquinol
-
-
-
?
nitrate + quinol
nitrite + quinone + H2O
-
first enzyme involved in respiratory denitrification in prokaryotes
-
-
?
nitrate + quinol
nitrite + quinone + H2O
-
in order to use nitrate as an electron acceptor, Escherichia coli synthesises three distinct enzymes: a membrane-bound enzyme (nitrate reductase A, NarGHI) encoded by the narGHJI operon and a soluble periplasmic nitrate reductase (NapAB, EC 1.9.6.1) encoded by the napFDAGHBC operon. A second membrane-bound nitrate reductase (nitrate reductase Z, NarZYV) encoded by the NarZYWV operon is biochemically similar to NarGHI. Whereas NarGHI synthesis is induced by nitrate under anaerobic conditions, NarZYV is expressed at a cryptic level and may assist Escherichia coli in transition from aerobic to anaerobic respiration (physiological role of this isoenzyme at the onset of the stationary growth phase in rich media). NapAB is mainly expressed in the presence of low concentrations of nitrate under both aerobic and anaerobic conditions, and its expression is suppressed at high nitrate concentrations. Conversely, NarGHI is maximally expressed when nitrate concentration is elevated, and under these conditions becomes the predominant enzyme in Escherichia coli. Thus, NapAB (Ec 1.9.6.1) and NarGHI seem to function in different ranges of nitrate concentration in a complementary way to support anaerobic respiration on nitrate under anaerobic conditions and in the presence of nitrate
-
-
?
nitrate + quinol
nitrite + quinone + H2O
model of electron transfer in the nitrate reductase: electrons are provided by quinones to the NarI subunit and subsequently transferred to NarH, which eventually delivers them to the molybdenum cofactor where nitrate reduction takes place
-
-
?
nitrate + quinol
nitrite + quinone + H2O
nitrate reductase A reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force
-
-
?
nitrate + quinol
nitrite + quinone + H2O
under anaerobic conditions in the presence of nitrate, Escherichia coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (nitrate reductase A, NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. The arrangement, coordination scheme and unique environment of the redox-active prosthetic groups is revealed
-
-
?
nitrate + quinol
nitrite + quinone + H2O
-
the enzyme is essential for the fungal denitrification. The fungal formate dehydrogenase can supply electrons via quinol/quinone pool to nitrate reductase A
-
-
?
nitrate + quinol
nitrite + quinone + H2O
-
the membrane-anchored protein directs electrons from quinol oxidation at the membrane anchor, NarI, to the site of nitrate reduction in the membrane extrinsic [Fe-S] cluster and Mo-bis-MGD containing dimer, NarGH
-
-
?
nitrite + ubiquinone + H2O
nitrate + ubiquinol
-
-
-
?
nitrite + ubiquinone + H2O
nitrate + ubiquinol
-
-
-
?
additional information
?
-
-
Escherichia coli expresses two different membrane-bound respiratory nitrate reductases, nitrate reductase A (NRA) and nitrate reductase Z (NRZ). The two enzymes are encoded by distinct operons located within two different loci on the Escherichia coli chromosome. The narGHJI operon, encoding nitrate reductase A, is located in the chlC locus at 27 min, along with several functionally related genes: narK, encoding a nitrate/nitrite antiporter, and the narXL operon, encoding a nitrate-activated, two component regulatory system. The narZYWV operon, encoding nitrate reductase Z, is located in the chlZ locus located at 32.5 min, a region which includes a narK homologue, narU, but no apparent homologue to the narXL operon. The two membrane-bound enzymes have similar structures and biochemical properties and are capable of reducing nitrate using normal physiological substrates. The homology of the amino acid sequences of the peptides encoded by the two operons is extremely high but the intergenic regions share no related sequences. The expression of both the narGHJI operon and the narK gene are positively regulated by two transacting factors Fnr and NarL-phosphate, activated respectively by anaerobiosis and nitrate, while the narZYWV operon and the narU gene are constitutively expressed. Nitrate reductase A, which accounts for 98% of the nitrate reductase activity when fully induced, is clearly the major respiratory nitrate reductase in Escherichia coli
-
-
?
additional information
?
-
-
nitrate reductase Z expression is regulated in a manner opposite to that of nitrate reductase A. The narGHJZ operon is aerobically repressed, strongly induced by nitrate and positively regulated by the fnr gene product. The expression of narZ is anaerobically repressed, induced weakly, if at all, by nitrate and negatively regulated by the fnr gene product. The opposing regulation of these two enzymes suggests that a function of nitrate reductase Z may be to catalyse the immediate flow of electrons to nitrate during an aerobic/anaerobic transition when the bacterium is grown in the presence of nitrate
-
-
?
additional information
?
-
-
NRZ is expressed at a low level that is not influenced by anaerobiosis or nitrate. The NRZ operon is controlled mainly at the level of transcription and is induced 10fold at the onset of stationary phase in rich media. Expression of NRZ nitrate reductase is highly growth phase dependent and is controlled by the alternative vegetative sigma factor RpoS. RpoS-mediated regulation of NRZ may be an important physiological adaptation that allows the cell to use nitrate under stress-associated conditions
-
-
?
additional information
?
-
-
nitrate reductase Z is synthesized in small amounts, the expression of its structural genes does not seem to be induced by nitrate, repressed by oxygen or activated by the product of the fnr gene. The nitrate reductase Z in mutant LCB79/pLCB14 couples formate oxidation with nitrate reduction probably via quinones and type-b cytochromes
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
cytochrome bD
-
NarI is strongly associated with heme bD, Lys86 is required for its stabilization
-
cytochrome bH
-
both heme bL and heme bH are crucial components in the electron-transfer pathway from the subunit NarI through subunit NarH to the catalytic subunit NarG. Without heme bL electrons cannot be transferred from menaquinol to heme bH. On the other hand, in the absence of heme bH, electrons cannot be transferred from the reduced heme bL to the catalytic dimer NarGH. A complex of menadione radical anion associated with the enzyme, is formed during the process of heme reduction by menadiol
-
cytochrome bL
-
both heme bL and heme bH are crucial components in the electron-transfer pathway from the subunit NarI through subunit NarH to the catalytic subunit NarG. Without heme bL electrons cannot be transferred from menaquinol to heme bH. On the other hand, in the absence of heme bH, electrons cannot be transferred from the reduced heme bL to the catalytic dimer NarGH. A complex of menadione radical anion associated with the enzyme, is formed during the process of heme reduction by menadiol
-
demethylmenaquinone
DMKH2, endogeneous demethylmenasemiquinone (DMSK) intermediates are stabilized in the enzyme
heme b
-
the anchor subunit NarI contains two b-type hemes. Electron transfer out of NarI is mediated by two hemes, one of relatively low midpoint potential Em (heme bL), and one of relatively high Em (heme bH)
quinone
heme bD is distal to NarGH and constitutes part of the quinone binding and oxidation site (Q-site) through the axially coordinating His66 residue and one of the heme bD propionate groups. Bound quinone participates in hydrogen bonds with both the imidazole of His66 and the heme propionate
[4Fe-4S]-center
a single tetranuclear iron-sulfur [4Fe-4S] cluster, known as FS0, is bound to subunit NarG. NarH contains three [4Fe-4S] clusters (FS1-FS3) and one trinuclear iron-sulfur cluster ([3Fe-4S], FS4)
bis(molybdopterin guanine dinucleotide)molybdenum cofactor
-
evidence for the presence of interactions between the molybdenum cofactor (Moco) biosynthetic machinery and aponitrate reductase A. The final stages of molybdenum cofactor biosynthesis occurs on a complex made up by MogA, MoeA, MobA, and MobB, which is also in charge with the delivery of the mature cofactor onto the aponitrate reductase A in a NarJ-assisted process
bis(molybdopterin guanine dinucleotide)molybdenum cofactor
structural evidence for the role of an open bicyclic form of the molybdo-bis(molybdopterin guanine dinucleotide) cofactor in the catalytic mechanism
bis(molybdopterin guanine dinucleotide)molybdenum cofactor
-
the enzyme possesses a molybdopterin guanine dinucleotide active center. Two forms of the molybdenum center, high- and low-pH, are detectable by electron paramagnetic resonance spectroscopy
bis(molybdopterin guanine dinucleotide)molybdenum cofactor
the enzyme uses a molybdo-bis(molybdopterin guanine dinucleotide) cofactor for catalytic mechanism
bis(molybdopterin guanine dinucleotide)molybdenum cofactor
-
the molybdo-bis(molybdopterin guanine dinucleotide)-binding subunit NarG is organized in four domains around the molybdo-bis(molybdopterin guanine dinucleotide) cofactor
cytochrome
-
although the spectral studies of nitrate reductase Z reveals the presence of a b-type cytochrome subunit (1.5 mol/molecule of 230000 Da), none can be detected in the SDS-PAGE
-
cytochrome
-
NarI is strongly associated with heme bD, Lys86 is required for its stabilization
-
cytochrome
-
the spectrophotometric studies indicate that reduction of the cytochrome hemes varies according to the analogue of quinone used, and in no cases is it complete
-
cytochrome b
-
partial proteolysis of the cytochrome b containing holoenzyme by trypsin results in loss of cytochrome b and in cleavage of one of the subunits of the enzyme. The cytochrome-free derivative exhibits a viologen dye dependent activity that is indistinguishable from that of the holoenzyme, but it is incapable of catalyzing the quinol-dependent reaction
-
cytochrome b
-
the enzyme contains two b-type hemes in the gamma subunit. The two b-type centres are functional parts of the enzyme
-
cytochrome c
-
NarC contains a periplasmic cytochrome c, which is required for membrane attachment and maturation of the NarG catalytic subunit of the enzyme
cytochrome c
-
the isolated preparation contains heme c in a sub-stoichiometric amount with the ability to relay electrons to the molybdenum center, suggesting that this nitrate reductase may contain heme c instead of the heme b usually found in this class of enzymes
heme
-
the reduction of NarGHI hemes by menaquinol, the reduction exhibits four phases, a transient species associated with the enzyme is kinetically correlated to the second reduction of the hemes
heme
-
the spectrophotometric studies indicate that reduction of the cytochrome hemes varies according to the analogue of quinone used, and in no cases is it complete
heme
the transmembrane subunit NarI coordinates two low-spin hemes, heme bP and heme bD, which mediate electron transfer from the Q-site to the [Fe-S] clusters in NarH
heme
the membrane subunit (NarI) of Escherichia coli nitrate reductase A (NarGHI) contains two b-type hemes, both of which are the highly anisotropic low-spin type. Heme bD is distal to NarGH and constitutes part of the quinone binding and oxidation site (Q-site) through the axially coordinating His66 residue and one of the heme bD propionate groups. Bound quinone participates in hydrogen bonds with both the imidazole of His66 and the heme propionate
molybdenum bis-molybdopterin guanine dinucleotide
the enzyme binds one molybdenum-bis(molybdopterin guanine dinucleotide), i.e. Mo-bis-MGD, cofactor per subunit
molybdenum bis-molybdopterin guanine dinucleotide
the enzyme binds one molybdenum-bis(molybdopterin guanine dinucleotide), i.e. Mo-bis-MGD, cofactor per subunit
molybdenum bis-molybdopterin guanine dinucleotide
the enzyme binds one molybdenum-bis(molybdopterin guanine dinucleotide), i.e. Mo-bis-MGD, cofactor per subunit
molybdo-bis(pyranopterin guanine dinucleotide)
Mo-bisPGD cofactor, bound to subunit NarG. NarI anchors the NarGH subunits to the inside of the cytoplasmic membrane and contains two hemes b that are proximal (bP) and distal (bD) to the NarGH subunits, respectively
[4Fe-4S] cluster
the enzyme binds one [4Fe-4S] cluster per subunit
[4Fe-4S] cluster
the enzyme binds one [4Fe-4S] cluster per subunit
additional information
-
molecular characterization of a quinol binding and oxidation site (Q-site) in NarGHI
-
additional information
-
the semiquinone is located within the quinol oxidation site QD
-
additional information
-
the transmembrane subunit NarI provides the quinol binding and oxidation site (Q-site)
-
additional information
the transmembrane subunit NarI provides the quinol binding and oxidation site (Q-site)
-
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Fe
Fe2+
Mo
Molybdenum
Fe
complete coordination of the four Fe-S centers of the beta-subunit from Escherichia coli nitrate reductase
Fe
-
coordination model for the four [Fe-S] centres of the electron-transfer subunit NarH, coordination scheme of the [Fe-S] clusters, functional role of [Fe-S] centres
Fe
cysteine arrangements typical of iron-sulfur centers are found in the NarH polypeptide. This suggests that the latter is an electron transfer unit of the nitrate reductase complex
Fe
domain I of subunit NarG holds the [4Fe-4S] cluster FS0. The coordination scheme of FS0 is: His50, Cys54, Cys58, Cys93. NarH contains three [4Fe-4S] clusters, FS1, FS2, FS3 and one [3Fe-4S] cluster, FS4
Fe
domain I of the catalytic subunit NadG holds the [4Fe-4S] cluster FS0
Fe
-
the 230000 Da complex contains 13 atoms iron and 12 atoms labile sulfur/molecules
Fe
-
the catalytic subunit of Escherichia coli nitrate reductase A contains a [4Fe-4S] cluster with a high-spin ground state
Fe
-
the four iron-sulfur centers of nitrate reductase A belong to two classes with markedly different redox potentials. The high-potential group comprises a [3Fe-4S] and a [4Fe-4S] cluster whose midpoint potentials are +60 mV and +80 mV, respectively. Although these centers are magnetically isolated, they are coupled by a significant anticooperative redox interaction of about 50 mV. The [4Fe-4S]1+ center occurs in two different conformations as shown by its composite EPR spectrum. The low-potential group contains two [4Fe-4S] clusters with more typical redox potentials (-200 mV and -400 mV). In the fully reduced state, the three [4Fe-4S]1+ centers are magnetically coupled. The iron-sulfur centers nitrate reductase Z and nitrate reductase A, exhibit essentially the same characteristics, except that the midpoint potentials of the high-potential centers of nitrate reductase Z appear negatively shifted by about 100 mV. A correspondence between the high-potential iron-sulfur clusters of the two enzymes can be proposed
Fe2+
the enzyme binds one [4Fe-4S] cluster per subunit
Mo
-
the enzyme contains a molybdenum cofactor. The enzyme-specific chaperone NarJ coordinates assembly and molybdenum cofactor acquisition of the heterotrimeric enzyme during the biogenesis process
Mo
the enzyme uses a molybdo-bis(molybdopterin guanine dinucleotide) cofactor for catalytic mechanism
Mo
-
the enzyme possesses a molybdopterin guanine dinucleotide active center. Two forms of the molybdenum center, high- and low-pH, are detectable by electron paramagnetic resonance spectroscopy
Molybdenum
the enzyme contains one molybdenum-bis(molybdopterin guanine dinucleotide) cofactor per subunit
Molybdenum
the enzyme contains one molybdenum-bis(molybdopterin guanine dinucleotide) cofactor per subunit
Molybdenum
the enzyme contains one molybdenum-bis(molybdopterin guanine dinucleotide) cofactor per subunit
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
diethyl dicarbonate
-
the quinol-dependent, but not the viologen dye dependent, activity is inhibited irreversibly by exposure to diethyl pyrocarbonate
additional information
-
p-chloromercuribenzoate (0.5 mM) or 2-heptyl-4-hydroxyquinolin N-oxide (1 mM) are almost without effect on the purified enzyme tested with reduced viologen as electron donor
-
2-n-heptyl-4-hydroxyquinoline N-oxide
-
the quinol-dependent, but not the viologen dye dependent, activity is inhibited reversibly by treatment with 2-n-heptyl-4-hydroxyquinoline N-oxide
2-n-heptyl-4-hydroxyquinoline N-oxide
-
has significant effects on the reduction kinetics of NarGHIH56R and NarGHIH205Y
2-n-heptyl-4-hydroxyquinoline N-oxide
-
quinol-binding-site inhibitor, elicits a much stronger inhibitory effect than stigmatellin on the reoxidation of the hemes
Stigmatellin
-
has significant effects on the reduction kinetics of NarGHIH56R and NarGHIH205Y
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Communicable Diseases
In silico prediction of silver nitrate nanoparticles and Nitrate Reductase A (NAR A) interaction in the treatment of infectious disease causing clinical strains of E. coli.
Cystic Fibrosis
Membrane-bound nitrate reductase is required for anaerobic growth in cystic fibrosis sputum.
Tuberculosis
Functional analysis of molybdopterin biosynthesis in mycobacteria identifies a fused molybdopterin synthase in Mycobacterium tuberculosis.
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00008
2-n-heptyl-4-hydroxyquinoline N-oxide
Escherichia coli
-
pH 7, substrate: 2-hydroxy-3-(3-methyl-2-butenyl)-1,4-naphthoquinol
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
i.e. respiratory nitrite reductase subunit NarG
UniProt
brenda
respiratory nitrate reductase 1 alpha chain
UniProt
brenda
-
395164, 658071, 674425, 674613, 695649, 696060, 696079, 696200, 696201, 696212, 696375, 696520, 697207, 697691, 697693, 697708, 700254, 700372
-
-
brenda
narH: P11349, narG: P09152, narI: P11350
SwissProt
brenda
P09152: alpha-chain, P11349: beta-chain, P0AF26: delta-chain
SwissProt
brenda
i.e. respiratory nitrite reductase subunit NarG
UniProt
brenda
nitrate reductase 1 alpha subunit
UniProt
brenda
respiratory nitrate reductase 1 alpha chain
UniProt
brenda
O86717 i.e. catalytic subunit NarG, O86716 i.e. beta chain NarH, O86714 i.e. gamma chain NarI, O86715 i.e. delta chain NarJ
O86717; O86716; O86714; O86715
UniProt
brenda
O86717 i.e. catalytic subunit NarG, O86716 i.e. beta chain NarH, O86714 i.e. gamma chain NarI, O86715 i.e. delta chain NarJ
O86717; O86716; O86714; O86715
UniProt
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
O86717; O86716; O86714; O86715
about 12% of the activity in spores. The bcc-aa3 supercomplex is not essential for isoform Nar2 activity or Nar3 synthesis in mycelium
brenda
-
about 12% of the activity in spores. The bcc-aa3 supercomplex is not essential for isoform Nar2 activity or Nar3 synthesis in mycelium
-
brenda
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
NarG and NarH are cytoplasmic subunits
brenda
the transmembrane subunit NarI anchors narGH to the cytoplasmic side of the membrane
-
brenda
-
nitrate reductase A (encoded by narGHJI operon) and nitrate reductase Z (encoded by narZYWv operon) are membrane-bound
brenda
-
the enzyme-specific chaperone NarJ controls the quality of the enzyme addressed to the membrane via binding to the N-terminal tail of the iron-sulfur containing subunit NarG
brenda
the membrane-intrinsic subunit NarI anchors NarGH to the membrane through a predominantly hydrophobic interface with both subunits
brenda
the NarI subunit anchors the NarGH subunits to the inside of the cytoplasmic membrane
brenda
-
alpha and beta polypeptides, and therefore the active site for nitrate reduction, are located on the cytoplasmic side of the membrane. The gamma polypeptide is the only subunit which is embedded in the membrane
brenda
-
the membrane-anchored protein directs electrons from quinol oxidation at the membrane anchor, NarI, to the site of nitrate reduction in the membrane extrinsic [Fe-S] cluster and Mo-bis-MGD containing dimer, NarGH
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
quinone site variants Lys86 and Gly65, Q-site inhibitor HOQNO, and their effects on heme bD, overview
metabolism
physiological function
additional information
metabolism
nitrate enters the periplasm through porins where it is reduced to nitrite by the periplasmic nitrate reductase (Nap) or it is further transported into the bacterial cytosol by NarK and serves as an electron acceptor for nitrate reductase A (NarG). Periplasmic nitrite is further converted to NH3 by the periplasmic nitrite reductase (Nrf). Electrons required for these reactions can be transferred to the quinone (Q) pool by NADH:ubiquinone oxidoreductase (Nuo) in a reaction coupled to energy-conserving proton translocation
metabolism
nitrate enters the periplasm through porins where it is reduced to nitrite by the periplasmic nitrate reductase (Nap) or it is further transported into the bacterial cytosol by NarK and serves as an electron acceptor for nitrate reductase A (NarG). Periplasmic nitrite is further converted to NH3 by the periplasmic nitrite reductase (Nrf). Electrons required for these reactions can be transferred to the quinone (Q) pool by NADH:ubiquinone oxidoreductase (Nuo) in a reaction coupled to energy-conserving proton translocation
metabolism
nitrate enters the periplasm through porins where it is reduced to nitrite by the periplasmic nitrate reductase (Nap) or it is further transported into the bacterial cytosol by NarK and serves as an electron acceptor for nitrate reductase A (NarG). Periplasmic nitrite is further converted to NH3 by the periplasmic nitrite reductase (Nrf). Electrons required for these reactions can be transferred to the quinone (Q) pool by NADH:ubiquinone oxidoreductase (Nuo) in a reaction coupled to energy-conserving proton translocation
metabolism
-
demethylmenasemiquinone and menasemiquinone bind in a similar and strongly asymmetric manner through a short H-bond, caused by slightly inequivalent contributions from two beta-methylene protons of the isoprenoid side chain. Their large isotropic hyperfine coupling constants are consistent with both a specific highly asymmetric binding mode of (demethyl)menasemiquinone and a near in-plane orientation of its isoprenyl chain at Cbeta relative to the aromatic ring, which differs by about 90° to that predicted for free or NarGHI-bound menaquinol
metabolism
O86717; O86716; O86714; O86715
in resting spores the Nar1 nitrate reductase requires a functional cytochrome bcc-aa3 supercomplex to reduce nitrate. Mutants lacking the complete qcr-cta genetic locus show no Nar1-dependent nitrate reduction
metabolism
NarJ serves as a chaperone for both the anaerobic respiratory nitrate reductase (NarG) and the assimilatory nitrate reductase NasC (cf. EC 1.7.1.1), the latter of which is active during both aerobic and anaerobic nitrate assimilation. Both NasC and NarG are inactive in the absence of NarJ. 50% of NarJ binds in a 1:1 complex with NasC and the remaining 50% binds in a 1:1 complex with NarG
metabolism
-
in resting spores the Nar1 nitrate reductase requires a functional cytochrome bcc-aa3 supercomplex to reduce nitrate. Mutants lacking the complete qcr-cta genetic locus show no Nar1-dependent nitrate reduction
-
metabolism
-
NarJ serves as a chaperone for both the anaerobic respiratory nitrate reductase (NarG) and the assimilatory nitrate reductase NasC (cf. EC 1.7.1.1), the latter of which is active during both aerobic and anaerobic nitrate assimilation. Both NasC and NarG are inactive in the absence of NarJ. 50% of NarJ binds in a 1:1 complex with NasC and the remaining 50% binds in a 1:1 complex with NarG
-
metabolism
-
nitrate enters the periplasm through porins where it is reduced to nitrite by the periplasmic nitrate reductase (Nap) or it is further transported into the bacterial cytosol by NarK and serves as an electron acceptor for nitrate reductase A (NarG). Periplasmic nitrite is further converted to NH3 by the periplasmic nitrite reductase (Nrf). Electrons required for these reactions can be transferred to the quinone (Q) pool by NADH:ubiquinone oxidoreductase (Nuo) in a reaction coupled to energy-conserving proton translocation
-
physiological function
-
the cytochrome c containing nitrate reductase plays a role in electron transport for denitrification in Thermus thermophilus, narC mutants are defective in anaerobic growth with nitrite, NO and N2O and present decreased NADH oxidation coupled to these electron acceptors
physiological function
-
mutants deficient in all three nitrate reductases narGHI, narXYZ, napFDAGHCB are capable of sustaining 48% of protoporphyrinogen IX oxidases activity and 65% of wild-type activity, respectively
physiological function
-
Streptomyces coelicolor has a high capacity for nitrate reduction both during aerobic growth and when the bacterium is incubated anaerobically. During aerobic growth in liquid medium the bacterium is able to reduce 50 mM nitrate stoichiometrically to nitrite. A mutant lacking all three NarGHJI operons fails to reduce nitrate
physiological function
under nitrate-rich conditions, the nar and nap genes encoding a membrane-bound form and a periplasmic form of nitrate reductase, as well as NO-regulated genes encoding flavohaemoglobin, flavorubredoxin and hybrid cluster protein are induced following transition from the oxic to anoxic state, and 20% of nitrate consumed in steady-state is released as N2O when nitrite has accumulated to millimolar levels. In a narG mutant lacking membrane-bound nitrate reductase, the steady-state rate of N2O production was about 30-fold lower than that of the wild-type. A combination of nitrate-sufficiency, nitrite accumulation and an active Nar-type nitrate reductase leads to NO and thence N2O production, and this can account for up to 20% of the nitrate catabolized
physiological function
the NO2- that arises from human host-derived NO3- through the enzymatic activity of Mycobacterium tuberculosis enzyme NarG inhibits bacterial growth, enhances ATP synthesis, and regulates the expression of 120 genes associated with adaptation to acid, hypoxia, oxidative and nitrosative stress, and iron deprivation. Enzyme NarG can promote growth of this intracellular pathogen in NO-producing human macrophages. Importance of NO3-/NO2- reduction in the pathogenesis. Bis-molybdopterin guanine dinucleotide, the cofactor of nitrate reductase, is required for the persistence of intracellular pathogen Mycobacterium tuberculosis in guinea pigs. The enzymatic activity of Mycobacterium tuberculosis NarG inhibits bacterial growth
physiological function
NarB, NarGHJI, dehydrogenase MSMEG_2237 and MSMEG_6816 are not required for nitrate reduction as MSMEG_4206 serves as the sole assimilatory nitrate reductase
physiological function
-
Streptomyces coelicolor has a high capacity for nitrate reduction both during aerobic growth and when the bacterium is incubated anaerobically. During aerobic growth in liquid medium the bacterium is able to reduce 50 mM nitrate stoichiometrically to nitrite. A mutant lacking all three NarGHJI operons fails to reduce nitrate
-
physiological function
-
NarB, NarGHJI, dehydrogenase MSMEG_2237 and MSMEG_6816 are not required for nitrate reduction as MSMEG_4206 serves as the sole assimilatory nitrate reductase
-
physiological function
-
under nitrate-rich conditions, the nar and nap genes encoding a membrane-bound form and a periplasmic form of nitrate reductase, as well as NO-regulated genes encoding flavohaemoglobin, flavorubredoxin and hybrid cluster protein are induced following transition from the oxic to anoxic state, and 20% of nitrate consumed in steady-state is released as N2O when nitrite has accumulated to millimolar levels. In a narG mutant lacking membrane-bound nitrate reductase, the steady-state rate of N2O production was about 30-fold lower than that of the wild-type. A combination of nitrate-sufficiency, nitrite accumulation and an active Nar-type nitrate reductase leads to NO and thence N2O production, and this can account for up to 20% of the nitrate catabolized
-
physiological function
-
the NO2- that arises from human host-derived NO3- through the enzymatic activity of Mycobacterium tuberculosis enzyme NarG inhibits bacterial growth, enhances ATP synthesis, and regulates the expression of 120 genes associated with adaptation to acid, hypoxia, oxidative and nitrosative stress, and iron deprivation. Enzyme NarG can promote growth of this intracellular pathogen in NO-producing human macrophages. Importance of NO3-/NO2- reduction in the pathogenesis. Bis-molybdopterin guanine dinucleotide, the cofactor of nitrate reductase, is required for the persistence of intracellular pathogen Mycobacterium tuberculosis in guinea pigs. The enzymatic activity of Mycobacterium tuberculosis NarG inhibits bacterial growth
-
additional information
NarGHI comprises a catalytic subunit (NarG, 140 kDa), an electron-transfer subunit (NarH, 58 kDa), and a membrane anchor subunit (NarI, 26 kDa). NarG contains a Mo-bisPGD cofactor that is the site of nitrate reduction as well as a single tetranuclear iron-sulfur ([4Fe-4S]) cluster known as FS0. NarH contains three [4Fe-4S] clusters (FS1-FS3) and one trinuclear iron-sulfur cluster ([3Fe-4S], FS4). NarI anchors the NarGH subunits to the inside of the cytoplasmic membrane and contains two hemes b that are proximal (bP) and distal (bD) to the NarGH subunits, respectively
additional information
NarGHI comprises a catalytic subunit (NarG, 140 kDa), an electron-transfer subunit (NarH, 58 kDa), and a membrane anchor subunit (NarI, 26 kDa). NarG contains a Mo-bisPGD cofactor that is the site of nitrate reduction as well as a single tetranuclear iron-sulfur ([4Fe-4S]) cluster known as FS0. NarH contains three [4Fe-4S] clusters (FS1-FS3) and one trinuclear iron-sulfur cluster ([3Fe-4S], FS4). NarI anchors the NarGH subunits to the inside of the cytoplasmic membrane and contains two hemes b that are proximal (bP) and distal (bD) to the NarGH subunits, respectively
additional information
NarGHI comprises a catalytic subunit (NarG, 140 kDa), an electron-transfer subunit (NarH, 58 kDa), and a membrane anchor subunit (NarI, 26 kDa). NarG contains a Mo-bisPGD cofactor that is the site of nitrate reduction as well as a single tetranuclear iron-sulfur ([4Fe-4S]) cluster known as FS0. NarH contains three [4Fe-4S] clusters (FS1-FS3) and one trinuclear iron-sulfur cluster ([3Fe-4S], FS4). NarI anchors the NarGH subunits to the inside of the cytoplasmic membrane and contains two hemes b that are proximal (bP) and distal (bD) to the NarGH subunits, respectively
additional information
-
NarGHI comprises a catalytic subunit (NarG, 140 kDa), an electron-transfer subunit (NarH, 58 kDa), and a membrane anchor subunit (NarI, 26 kDa). NarG contains a Mo-bisPGD cofactor that is the site of nitrate reduction as well as a single tetranuclear iron-sulfur ([4Fe-4S]) cluster known as FS0. NarH contains three [4Fe-4S] clusters (FS1-FS3) and one trinuclear iron-sulfur cluster ([3Fe-4S], FS4). NarI anchors the NarGH subunits to the inside of the cytoplasmic membrane and contains two hemes b that are proximal (bP) and distal (bD) to the NarGH subunits, respectively
additional information
structure-function relationships of quinone reactivity. The NarGHI catalytic activity measured with the demethylmenaquinol (DMKH2) analogue 1,4-naphthoquinol is comparable to that measured using the corresponding methylated methylmenaquinol (MKH2) analogue menadiol, kinetics, overview
additional information
structure-function relationships of quinone reactivity. The NarGHI catalytic activity measured with the demethylmenaquinol (DMKH2) analogue 1,4-naphthoquinol is comparable to that measured using the corresponding methylated methylmenaquinol (MKH2) analogue menadiol, kinetics, overview
additional information
structure-function relationships of quinone reactivity. The NarGHI catalytic activity measured with the demethylmenaquinol (DMKH2) analogue 1,4-naphthoquinol is comparable to that measured using the corresponding methylated methylmenaquinol (MKH2) analogue menadiol, kinetics, overview
additional information
-
structure-function relationships of quinone reactivity. The NarGHI catalytic activity measured with the demethylmenaquinol (DMKH2) analogue 1,4-naphthoquinol is comparable to that measured using the corresponding methylated methylmenaquinol (MKH2) analogue menadiol, kinetics, overview
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
129000
-
x * 129000 (alpha) + x * 66000 (beta) + x * 24000 (gamma), SDS-PAGE
138700
x * 138700 + x * 57700, x * 26500, x * 25500, the narGHJI operon that encodes the nitrate reductase encodes four polypeptides NarG (138700 Da), NarH (57700 Da), NarJ (26500 Da) and NarI (25500 Da), calculated from sequence
150000
-
1 * 150000 (alphaz) + 1 * 60000 (betaz) + a b-type cytochrome subunit, SDS-PAGE
223900
multiple isomorphous replacement and anaomalous scattering (MIRAS), crystallographic data
24000
-
x * 129000 (alpha) + x * 66000 (beta) + x * 24000 (gamma), SDS-PAGE
25500
x * 138700 + x * 57700, x * 26500, x * 25500, the narGHJI operon that encodes the nitrate reductase encodes four polypeptides NarG (138700 Da), NarH (57700 Da), NarJ (26500 Da) and NarI (25500 Da), calculated from sequence
26500
x * 138700 + x * 57700, x * 26500, x * 25500, the narGHJI operon that encodes the nitrate reductase encodes four polypeptides NarG (138700 Da), NarH (57700 Da), NarJ (26500 Da) and NarI (25500 Da), calculated from sequence
57700
x * 138700 + x * 57700, x * 26500, x * 25500, the narGHJI operon that encodes the nitrate reductase encodes four polypeptides NarG (138700 Da), NarH (57700 Da), NarJ (26500 Da) and NarI (25500 Da), calculated from sequence
60000
-
1 * 150000 (alphaz) + 1 * 60000 (betaz) + a b-type cytochrome subunit, SDS-PAGE
66000
-
x * 129000 (alpha) + x * 66000 (beta) + x * 24000 (gamma), SDS-PAGE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
heterotrimer
electron transfer can occur from the menaquinol binding site in NarI to the molybdo-bis(molybdopterin guanine dinucleotide) active site in NarG, where nitrate is reduced to nitrite
?
-
1 * 150000 (alphaz) + 1 * 60000 (betaz) + a b-type cytochrome subunit, SDS-PAGE
?
x * 138700 + x * 57700, x * 26500, x * 25500, the narGHJI operon that encodes the nitrate reductase encodes four polypeptides NarG (138700 Da), NarH (57700 Da), NarJ (26500 Da) and NarI (25500 Da), calculated from sequence
?
-
alpha and beta polypeptides are essentially peripheral polypeptides that are attached to the membrane by protein-protein interactions, presumably via the gamma polypeptide
?
-
x * 129000 (alpha) + x * 66000 (beta) + x * 24000 (gamma), SDS-PAGE
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure of NarGHI at 1.9 A resolution, crystals of native and selenomethionine-substituted NarGHI are obtained by vapor diffusion with sitting drops
sitting-drop vapor diffusion method, crystals of native and selenomethionine-substituted NarGHI, crystal structure at 1.9 A resolution
the crystal structure of Escherichia coli nitrate reductase A in complex with pentachlorophenol is determined to 2.0 A of resolution
-
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C196A
mutation results in the full loss of the four Fe-S clusters and of the Mo-cofactor, leading to inactive enzyme
C227A
mutation results in the full loss of the four Fe-S clusters and of the Mo-cofactor, leading to inactive enzyme
C263A
mutant retains significant nitrate reductase activity. EPR analysis shows that the highest redox potential [4Fe-4S] cluster (center 1) is selectively removed by the C263A mutation
C26A
mutant retains significant nitrate reductase activity. Mutation likely eliminates the lowest potential [4Fe-4S] cluster (center 4)
G65A
site-directed mutageness of subunit NarI, mutant G65A is able to support growth and retains significant quinol:nitrate oxidoreductase activity
H187Y
H205Y
-
mutant without heme bH but with heme bL, a smaller and slower heme reduction compared to that of the wild-type enzyme is observed. A transient species, likely to be associated with a semiquinone radical anion, is generated not only on reduction of the wild-type enzyme but also on reduction of NarGHIH56R and NarGHIH205Y. Compared to the wild type, no significant heme reoxidation is observed for NarGHIH56R and NarGHIH205Y. This result indicates that a single mutation removing heme bH blocks the electron-transfer pathway from the subunit NarI to the catalytic dimer NarGH
H49S
the mutant lacks catalytic activity and the FS0 [4Fe-4S] cluster and molybdo-bis(pyranopterin guanine dinucleotide) cofactor but retains the GDP moieties
H56R
-
mutant without heme bH but with heme bL, a smaller and slower heme reduction compared to that of the wild-type enzyme is observed. A transient species, likely to be associated with a semiquinone radical anion, is generated not only on reduction of the wild-type enzyme but also on reduction of NarGHIH56R and NarGHIH205Y. Compared to the wild type, no significant heme reoxidation is observed for NarGHIH56R and NarGHIH205Y. This result indicates that a single mutation removing heme bH blocks the electron-transfer pathway from the subunit NarI to the catalytic dimer NarGH
H56Y
H66Y
K86A
R94S
the mutant shows a concomitant decrease in enzyme turnover to about 30% of the wild type
H49S
-
the mutant lacks catalytic activity and the FS0 [4Fe-4S] cluster and molybdo-bis(pyranopterin guanine dinucleotide) cofactor but retains the GDP moieties
-
R94S
-
the mutant shows a concomitant decrease in enzyme turnover to about 30% of the wild type
-
additional information
-
mutant enzyme lacking the highest-potential [4Fe-4S] cluster is devoid of menadione activity, but still retains duroquinone activity
H187Y
-
mutant lacking heme bL but having heme bH, the heme reduction by menadiol is abolished
H187Y
-
mutant lacking the distal heme bD, no EPR signal of the semiquinone is observed
H187Y
-
mutant lacks the distal heme bD, no EPR signal of the semiquinone is observed
H56Y
-
a semiquinone is detected in the mutant lacking the proximal heme bP. Its thermodynamic properties and spectroscopic characteristics, as revealed by Q-band EPR and ENDOR spectroscopies, are identical to those observed in the native enzyme
H56Y
-
mutant lacks the distal heme bD, a EPR signal of the semiquinone is observed
H66Y
-
mutant lacking heme bL but having heme bH, the heme reduction by menadiol is abolished
H66Y
-
mutant lacking the distal heme bD, no EPR signal of the semiquinone is observed
H66Y
-
mutant lacks the distal heme bD, no EPR signal of the semiquinone is observed
K86A
-
mutant has a lower plumbagin:nitrate oxidoreductase activity than the wild-type enzyme, 10/s compared with 68/s, respectively
K86A
-
mutation dramatically reduces the rate of oxidation of both menaquinol and ubiquinol analogues
K86A
-
the mutation close to heme bD leads to the loss of the EPR signal of the semiquinone, although both hemes are present, the substitution dramatically reduces the rate of oxidation of both mena and ubiquinol analogues
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
freezing in liquid nitrogen may be repeated up to six times, with a reduction of 20% of the activity
-
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OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
the enzyme is remarkably resistant to air inactivation since only 2-5% of the activity is lost after a 1 h treatment
-
697691
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4°C, the purified preparation can be stored up to three days without inactivation
-
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene cluster NarGHI, overexpression in Escherichia coli strain LCB79
gene narG in the narGHI gene cluster
gene narG in the narGHI gene cluster
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
nitrate reductase A is synthesized optimally at NO3- concentrations of 10 mM or above
nitrate reductase A is synthesized optimally at NO3- concentrations of 10 mM or above
nitrate reductase A is synthesized optimally at NO3- concentrations of 10 mM or above
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Ballard, A.L.; Ferguson, S.J.
Respiratory nitrate reductase from Paracoccus denitrificans. Evidence for two b-type haems in the gamma subunit and properties of a water-soluble active enzyme containing alpha and beta subunits
Eur. J. Biochem.
174
207-212
1988
Paracoccus denitrificans
brenda
Morpeth, F.F.; Boxer, D.H.
Kinetic analysis of respiratory nitrate reductase from Escherichia coli K12
Biochemistry
24
40-46
1985
Escherichia coli
brenda
Anderson, L.J.; Richardson, D.J.; Butt, J.N.
Catalytic protein film voltammetry from a respiratory nitrate reductase provides evidence for complex electrochemical modulation of enzyme activity
Biochemistry
40
11294-11307
2001
Paracoccus pantotrophus
brenda
Rothery, R.A.; Bertero, M.G.; Cammack, R.; Palak, M.; Blasco, F.; Strynadka, N.C.; Weiner, J.H.
The catalytic subunit of Escherichia coli nitrate reductase A contains a novel [4Fe-4S] cluster with a high-spin ground state
Biochemistry
43
5324-5333
2004
Escherichia coli
brenda
Pinho, D.; Besson, S.; Silva, P.J.; de Castro, B.; Moura, I.
Isolation and spectroscopic characterization of the membrane-bound nitrate reductase from Pseudomonas chlororaphis DSM 50135
Biochim. Biophys. Acta
1723
151-162
2005
Pseudomonas chlororaphis
brenda
Bertero, M.G.; Rothery, R.A.; Boroumand, N.; Palak, M.; Blasco, F.; Ginet, N.; Weiner, J.H.; Strynadka, N.C.
Structural and biochemical characterization of a quinol binding site of Escherichia coli nitrate reductase A
J. Biol. Chem.
280
14836-14843
2005
Escherichia coli
brenda
Vergnes, A.; Pommier, J.; Toci, R.; Blasco, F.; Giordano, G.; Magalon, A.
NarJ chaperone binds on two distinct sites of the aponitrate reductase of Escherichia coli to coordinate molybdenum cofactor insertion and assembly
J. Biol. Chem.
281
2170-2176
2006
Escherichia coli
brenda
Bonnefoy, V.; Demoss, J.A.
Nitrate reductases in Escherichia coli
Antonie van Leeuwenhoek
66
47-56
1994
Escherichia coli
brenda
Enoch, H.G.; Lester, R.L.
Role of a novel cytochrome b-containing nitrate reductase and quinone in invitro reconstruction of formate-nitrate reductase activity of E. coli
Biochem. Biophys. Res. Commun.
61
1234-1241
1974
Escherichia coli
brenda
Rothery, R.A.; Chatterjee, I.; Kiema, G.; McDermott, M.T.; Weiner, J.H.
Hydroxylated naphthoquinones as substrates for Escherichia coli anaerobic reductases
Biochem. J.
332
35-41
1998
Escherichia coli
brenda
Guigliarelli, B.; Magalon, A.; Asso, M.; Bertrand, P.; Frixon, C.; Giordano, G.; Blasco, F.
Complete coordination of the four Fe-S centers of the beta subunit from Escherichia coli nitrate reductase. Physiological, biochemical, and EPR characterization of site-directed mutants lacking the highest or lowest potential [4Fe-4S] clusters
Biochemistry
35
4828-4836
1996
Escherichia coli (P11349 and P09152 and P11350), Escherichia coli
brenda
Zhao, Z.; Rothery, R.A.; Weiner, J.H.
Effects of site-directed mutations on heme reduction in Escherichia coli nitrate reductase A by menaquinol: a stopped-flow study
Biochemistry
42
14225-14233
2003
Escherichia coli
brenda
Zhao, Z.; Rothery, R.A.; Weiner, J.H.
Transient kinetic studies of heme reduction in Escherichia coli nitrate reductase A (NarGHI) by menaquinol
Biochemistry
42
5403-5413
2003
Escherichia coli
brenda
Lanciano, P.; Magalon, A.; Bertrand, P.; Guigliarelli, B.; Grimaldi, S.
High-stability semiquinone intermediate in nitrate reductase A (NarGHI) from Escherichia coli is located in a quinol oxidation site close to heme bD
Biochemistry
46
5323-5329
2007
Escherichia coli
brenda
Berks, B.C.; Ferguson, S.J.; Moir, J.W.; Richardson, D.J.
Enzymes and associated electron transport systems that catalyse the respiratory reduction of nitrogen oxides and oxyanions.
Biochim. Biophys. Acta
1232
97-173
1995
Escherichia coli
brenda
Vergnes, A.; Gouffi-Belhabich, K.; Blasco, F.; Giordano, G.; Magalon, A.J.
Involvement of the molybdenum cofactor biosynthetic machinery in the maturation of the Escherichia coli nitrate reductase A
Biol. Chem.
279
41398-41403
2004
Escherichia coli
brenda
Blasco, F.; Guigliarelli, B.; Magalon, A.; Asso, M.; Giordano, G.; Rothery, RA.
The coordination and function of the redox centres of the membrane-bound nitrate reductases
Cell. Mol. Life Sci.
58
179-193
2001
Escherichia coli
brenda
Iobbi, C.; Santini, C.L.; Bonnefoy, V.; Giordano, G.
Biochemical and immunological evidence for a second nitrate reductase in Escherichia coli K12
Eur. J. Biochem.
168
451-459
1987
Escherichia coli K-12
brenda
Iobbi-Nivol, C.; Santini, C.L.; Blasco, F.; Giordano, G.
Purification and further characterization of the second nitrate reductase of Escherichia coli K12
Eur. J. Biochem.
188
679-687
1990
Escherichia coli
brenda
Guigliarelli, B.; Asso, M.; More, C.; Augier, V.; Blasco, F.; Pommier, J.; Giordano, G.; Bertrand, P.
EPR and redox characterization of iron-sulfur centers in nitrate reductases A and Z from Escherichia coli. Evidence for a high-potential and a low-potential class and their relevance in the electron-transfer mechanism
Eur. J. Biochem.
207
61-68
1992
Escherichia coli
brenda
Giordani, R.; Buc, J.
Evidence for two different electron transfer pathways in the same enzyme, nitrate reductase A from Escherichia coli
Eur. J. Biochem.
271
2400-2407
2004
Escherichia coli
brenda
Uchimura, H.; Enjoji, H.; Seki, T.; Taguchi, A.; Takaya, N.; Shoun, H.
Nitrate reductase-formate dehydrogenase couple involved in the fungal denitrification by Fusarium oxysporum
J. Biochem.
131
579-586
2002
Fusarium oxysporum
brenda
Blasco, F.; Iobbi, C.; Giordano, G.; Chippaux, M.; Bonnefoy, V.
Nitrate reductase of Escherichia coli: completion of the nucleotide sequence of the nar operon and reassessment of the role of the alpha and beta subunits in iron binding and electron transfer
Mol. Gen. Genet.
218
249-256
1989
Escherichia coli (P09152 and P11349 and P0AF26)
brenda
Chang, L.; Wie, L.I.; Audia, J.P.; Morton, R.A.; Schellhorn, H.E.
Expression of the Escherichia coli NRZ nitrate reductase is highly growth phase dependent and is controlled by RpoS, the alternative vegetative sigma factor
Mol. Microbiol.
34
756-766
1999
Escherichia coli
brenda
Cava, F.; Zafra, O.; Berenguer, J.
A cytochrome c containing nitrate reductase plays a role in electron transport for denitrification in Thermus thermophilus without involvement of the bc respiratory complex
Mol. Microbiol.
70
507-518
2008
Thermus thermophilus
brenda
Bertero, M.G.; Rothery, R.A.; Palak, M.; Hou, C.; Lim, D.; Blasco, F.; Weiner, J.H.; Strynadka, N.C.
Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A
Nat. Struct. Biol.
10
681-687
2003
Escherichia coli, Escherichia coli (P11349 and P09152 and P11350)
brenda
Rothery, R.A.; Bertero, M.G.; Spreter, T.; Bouromand, N.; Strynadka, N.C.; Weiner, J.H.
Protein crystallography reveals a role for the FS0 cluster of Escherichia coli nitrate reductase A (NarGHI) in enzyme maturation
J. Biol. Chem.
285
8801-8807
2010
Escherichia coli (P09152), Escherichia coli, Escherichia coli LCB79 (P09152)
brenda
Rowley, G.; Hensen, D.; Felgate, H.; Arkenberg, A.; Appia-Ayme, C.; Prior, K.; Harrington, C.; Field, S.J.; Butt, J.N.; Baggs, E.; Richardson, D.J.
Resolving the contributions of the membrane-bound and periplasmic nitrate reductase systems to nitric oxide and nitrous oxide production in Salmonella enterica serovar Typhimurium
Biochem. J.
441
755-762
2012
Salmonella enterica subsp. enterica serovar Typhimurium (A0A0H3N903), Salmonella enterica subsp. enterica serovar Typhimurium, Salmonella enterica subsp. enterica serovar Typhimurium SL1344 (A0A0H3N903)
brenda
Fischer, M.; Alderson, J.; Van Keulen, G.; White, J.; Sawers, R.
The obligate aerobe Streptomyces coelicolor A3(2) synthesizes three active respiratory nitrate reductases
Microbiology
156
3166-3179
2010
Streptomyces coelicolor, Streptomyces coelicolor A3(2)
brenda
Moebius, K.; Arias-Cartin, R.; Breckau, D.; Haennig, A.L.; Riedmann, K.; Biedendieck, R.; Schroeder, S.; Becher, D.; Magalon, A.; Moser, J.; Jahn, M.; Jahn, D.
Heme biosynthesis is coupled to electron transport chains for energy generation
Proc. Natl. Acad. Sci. USA
107
10436-10441
2010
Escherichia coli
brenda
Fedor, J.; Rothery, R.; Weiner, J.
A new paradigm for electron transfer through Escherichia coli nitrate reductase A
Biochemistry
53
4549-4556
2014
Escherichia coli (P09152), Escherichia coli (P11349), Escherichia coli (P11350), Escherichia coli
brenda
Rendon, J.; Pilet, E.; Fahs, Z.; Seduk, F.; Sylvi, L.; Hajj Chehade, M.; Pierrel, F.; Guigliarelli, B.; Magalon, A.; Grimaldi, S.
Demethylmenaquinol is a substrate of Escherichia coli nitrate reductase A (NarGHI) and forms a stable semiquinone intermediate at the NarGHI quinol oxidation site
Biochim. Biophys. Acta
1847
739-747
2015
Escherichia coli (P09152), Escherichia coli (P11349), Escherichia coli (P11350), Escherichia coli
brenda
Vazquez-Torres, A.; Baeumler, A.J.
Nitrate, nitrite and nitric oxide reductases from the last universal common ancestor to modern bacterial pathogens
Curr. Opin. Microbiol.
29
1-8
2016
Escherichia coli (P09152), Mycobacterium tuberculosis (P9WJQ3), Salmonella enterica subsp. enterica serovar Typhimurium (Q8ZP37), Mycobacterium tuberculosis H37Rv (P9WJQ3)
brenda
Seif Eddine, M.; Biaso, F.; Rendon, J.; Pilet, E.; Guigliarelli, B.; Magalon, A.; Grimaldi, S.
1,2H hyperfine spectroscopy and DFT modeling unveil the demethylmenasemiquinone binding mode to E. coli nitrate reductase A (NarGHI)
Biochim. Biophys. Acta Bioenerg.
1861
148203
2020
Escherichia coli
brenda
Falke, D.; Biefel, B.; Haase, A.; Franke, S.; Fischer, M.; Gary Sawers, R.
Activity of spore-specific respiratory nitrate reductase 1 of Streptomyces coelicolor A3(2) requires a functional cytochrome bcc-aa3 oxidase supercomplex
J. Bacteriol.
201
e00104
2019
Streptomyces coelicolor (O86717 and O86716 and O86714 and O86715), Streptomyces coelicolor A3(2) (O86717 and O86716 and O86714 and O86715)
brenda
Pinchbeck, B.J.; Soriano-Laguna, M.J.; Sullivan, M.J.; Luque-Almagro, V.M.; Rowley, G.; Ferguson, S.J.; Roldan, M.D.; Richardson, D.J.; Gates, A.J.
A dual functional redox enzyme maturation protein for respiratory and assimilatory nitrate reductases in bacteria
Mol. Microbiol.
111
1592-1603
2019
Paracoccus denitrificans (A1B9V6), Paracoccus denitrificans Pd 1222 (A1B9V6)
brenda
Cardoso, N.C.; Papadopoulos, A.O.; Kana, B.D.
Mycobacterium smegmatis does not display functional redundancy in nitrate reductase enzymes
PLoS ONE
16
e0245745
2021
Mycolicibacterium smegmatis (A0R2J8), Mycolicibacterium smegmatis ATCC 700084 (A0R2J8)
brenda
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