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Information on EC 1.18.6.2 - vanadium-dependent nitrogenase
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1.18.6.2 vanadium-dependent nitrogenaseIUBMB Comments
Requires Mg2+. This enzyme, originally isolated from the bacterium Azotobacter vinelandii, is a complex of two components (namely dinitrogen reductase and dinitrogenase). Dinitrogen reductase is a [4Fe-4S] protein, which, in the presence of ATP, transfers an electron from ferredoxin to the dinitrogenase component. Dinitrogenase is a vanadium-iron protein that reduces dinitrogen to two molecules of ammonia in three successive two-electron reductions via diazine and hydrazine. Compared with molybdenum-depedent nitrogenase (EC 1.18.6.1), this enzyme produces more dihydrogen and consumes more ATP per dinitrogen molecule being reduced. Unlike EC 1.18.6.1, this enzyme can also use CO as substrate, producing ethene, ethane and propane [7,9].
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Word Map
- 1.18.6.2
- molybdenum
- vinelandii
- azotobacter
- anabaena
- variabilis
- mo
- acetylene
- ethane
-
nitrogen-fixing
- nitrogenases
-
heterocystous
- ethylene
-
heterotrophic
- cyanobacterium
-
v-dependent
- v-nitrogenase
-
diazotrophic
- analysis
The enzyme appears in viruses and cellular organisms
Reaction Schemes
12
+
12
+
+
40
+
40
=
12
+
3
+
2
+
40
+
40
Synonyms
vnfdg, vanadium-dependent nitrogenase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
vnfD
VnfDG
vnfG
vnfK
VnfY
vnfD
-
-
-
-
vnfD
alpha-chain
vnfG
-
-
-
-
vnfG
delta-chain
vnfK
-
-
-
-
vnfK
beta-chain
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
12 reduced ferredoxin + 12 H+ + N2 + 40 ATP + 40 H2O = 12 oxidized ferredoxin + 3 H2 + 2 NH3 + 40 ADP + 40 phosphate
-
-
-
-
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PATHWAY SOURCE
PATHWAYS
KEGG
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SYSTEMATIC NAME
IUBMB Comments
ferredoxin:dinitrogen oxidoreductase (ATP-hydrolysing, vanadium-dependent)
Requires Mg2+. This enzyme, originally isolated from the bacterium Azotobacter vinelandii, is a complex of two components (namely dinitrogen reductase and dinitrogenase). Dinitrogen reductase is a [4Fe-4S] protein, which, in the presence of ATP, transfers an electron from ferredoxin to the dinitrogenase component. Dinitrogenase is a vanadium-iron protein that reduces dinitrogen to two molecules of ammonia in three successive two-electron reductions via diazine and hydrazine. Compared with molybdenum-depedent nitrogenase (EC 1.18.6.1), this enzyme produces more dihydrogen and consumes more ATP per dinitrogen molecule being reduced. Unlike EC 1.18.6.1, this enzyme can also use CO as substrate, producing ethene, ethane and propane [7,9].
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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
12 reduced ferredoxin + 12 H+ + N2 + 40 ATP + 40 H2O
12 oxidized ferredoxin + 3 H2 + 2 NH3 + 40 ADP + 40 phosphate
12 reduced ferredoxin + 12 H+ + N2 + 40 ATP + 40 H2O
12 oxidized ferredoxin + 3 H2 + 2 NH3 + 40 ADP + 40 phosphate
-
-
-
-
?
12 reduced ferredoxin + 12 H+ + N2 + 40 ATP + 40 H2O
12 oxidized ferredoxin + 3 H2 + 2 NH3 + 40 ADP + 40 phosphate
-
-
-
?
12 reduced ferredoxin + 12 H+ + N2 + 40 ATP + 40 H2O
12 oxidized ferredoxin + 3 H2 + 2 NH3 + 40 ADP + 40 phosphate
-
-
-
?
12 reduced ferredoxin + 12 H+ + N2 + 40 ATP + 40 H2O
12 oxidized ferredoxin + 3 H2 + 2 NH3 + 40 ADP + 40 phosphate
-
-
-
-
?
additional information
?
-
enzym also forms ethane continuously at a rate of 2.1% of that of ethylene
-
-
?
additional information
?
-
-
enzym also forms ethane continuously at a rate of 2.1% of that of ethylene
-
-
?
additional information
?
-
enzym also forms ethane continuously at a rate of 2.1% of that of ethylene
-
-
?
additional information
?
-
-
enzym also forms ethane continuously at a rate of 2.1% of that of ethylene
-
-
?
additional information
?
-
the efficiency of ATP hydrolysis coupled to substrate reduction (ATP/2e ratio) is 4.87 at 30°C during the reduction of protons to H2 and 7.16 during the reduction of N2
-
-
?
additional information
?
-
the efficiency of ATP hydrolysis coupled to substrate reduction (ATP/2e ratio) is 4.87 at 30°C during the reduction of protons to H2 and 7.16 during the reduction of N2
-
-
?
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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
12 reduced ferredoxin + 12 H+ + N2 + 40 ATP + 40 H2O
12 oxidized ferredoxin + 3 H2 + 2 NH3 + 40 ADP + 40 phosphate
12 reduced ferredoxin + 12 H+ + N2 + 40 ATP + 40 H2O
12 oxidized ferredoxin + 3 H2 + 2 NH3 + 40 ADP + 40 phosphate
-
-
-
?
12 reduced ferredoxin + 12 H+ + N2 + 40 ATP + 40 H2O
12 oxidized ferredoxin + 3 H2 + 2 NH3 + 40 ADP + 40 phosphate
-
-
-
?
additional information
?
-
the efficiency of ATP hydrolysis coupled to substrate reduction (ATP/2e ratio) is 4.87 at 30°C during the reduction of protons to H2 and 7.16 during the reduction of N2
-
-
?
additional information
?
-
the efficiency of ATP hydrolysis coupled to substrate reduction (ATP/2e ratio) is 4.87 at 30°C during the reduction of protons to H2 and 7.16 during the reduction of N2
-
-
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Iron
Vanadium
contains 2 mol of vanadium and 23 mol of iron per mol of protein
Iron
contains 2 mol of vanadium and 23 mol of iron per mol of protein
Iron
-
enhanced low-temperature activity of vanadium-dependent nitrogenase is associated with the Fe protein of V nitrogenase
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
H2
-
CO-reduction by V-nitrogenase is inhibited by the addition of increasing amounts of H2
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
over the temperature range 30-45 degrees C the apparent Km for the reduction of N2 is the same, but increases from 30 to 58 kPa of N2
-
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
1211
evolution of H2 under argon atmosphere, pH not specified in the publication, temperature not specified in the publication
337
formation of NH3, pH not specified in the publication, temperature not specified in the publication
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
45 - 50
on increasing the temperature from 45 degrees C to 50 degrees C, little change occurrs in the rate of reduction of protons to H2. The rate of N2H4 production increases, but the rate of NH3 formation decreases 7fold. This selective loss of the ability to reduce N2 to NH3 is reversible
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
P15332 i.e. subunit VnfD, P15334 i.e. subunit VnfK, P15333 i.e. subunit VnfG
UniProt
brenda
P15332 i.e. subunit VnfD, P15334 i.e. subunit VnfK, P15333 i.e. subunit VnfG
UniProt
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
additional information
additional information
the vnf genes are strongly transcribed in cultures grown either in Mo-free medium, or in W-containing medium, and also weakly in Mo-containing medium
brenda
additional information
-
the vnf genes are strongly transcribed in cultures grown either in Mo-free medium, or in W-containing medium, and also weakly in Mo-containing medium
brenda
additional information
-
the vnf genes are strongly transcribed in cultures grown either in Mo-free medium, or in W-containing medium, and also weakly in Mo-containing medium
-
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
physiological function
a deletion in the VnfD, VnfG and VnfK gene cluster prevents V-dependent nitrogen fixation. A strain defective in both V-nitrogenase and Mo-nitrogenase (EC 1.18.6.1) structural genes shows no residual nitrogen fixing capacity
physiological function
-
a nifB mutant lacking a small Fe-S cluster that is a precursor of FeMo-co, is unable to grow diazotrophically, even in presence of vanadium, in the absence of molybdenum
physiological function
an insertion mutant in VnfY has 10fold less V-containing nitrogenase activity and exhibits a greatly diminished level of V label incorporation into the V-dependent dinitrogenase when compared to the wild-type. VnfY is involved in the biosynthesis or insertion of FeV-co into the V-containing dinitrogenase
physiological function
-
a deletion in the VnfD, VnfG and VnfK gene cluster prevents V-dependent nitrogen fixation. A strain defective in both V-nitrogenase and Mo-nitrogenase (EC 1.18.6.1) structural genes shows no residual nitrogen fixing capacity
-
physiological function
-
an insertion mutant in VnfY has 10fold less V-containing nitrogenase activity and exhibits a greatly diminished level of V label incorporation into the V-dependent dinitrogenase when compared to the wild-type. VnfY is involved in the biosynthesis or insertion of FeV-co into the V-containing dinitrogenase
-
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). C1DI21_AZOVD
Azotobacter vinelandii (strain DJ / ATCC BAA-1303)
161
0
17172
TrEMBL
-
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
?
x * 53793, subunit VnfD, x * 52724, subunit VnfK, x * 13274, subunit vnfG, calculated
?
-
x * 53793, subunit VnfD, x * 52724, subunit VnfK, x * 13274, subunit vnfG, calculated
-
dimer
2 * 32000, SDS-PAGE, isolated iron-subunit
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
to 1.35 A resolution. The protein contains an additional alpha-helical subunit not present in molybdenum nitrogenase. The FeV cofactor (FeVco) is a [V:7Fe:8S:C] cluster with a homocitrate ligand to vanadium. It lacks one sulfide ion compared to FeMoco that is replaced by a bridging ligand, likely a my-1,3-carbonate. It fits into a pocket within the protein that is obstructed in molybdenum nitrogenase
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
protocols to isolate unmodified vanadium nitrogenase from molybdenum-depleted, actively nitrogen-fixing wild-type cells
-
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
expression of vanadium-containing nitrogenase when under molybdenum deficiency
genes for the three subunits vnJD (alpha), vnfG (delta) and vnfK (beta) are contiguous and form an operon whose transcription is repressed in response to ammonia
expression of vanadium-containing nitrogenase when under molybdenum deficiency
expression of vanadium-containing nitrogenase when under molybdenum deficiency
-
-
genes for the three subunits vnJD (alpha), vnfG (delta) and vnfK (beta) are contiguous and form an operon whose transcription is repressed in response to ammonia
genes for the three subunits vnJD (alpha), vnfG (delta) and vnfK (beta) are contiguous and form an operon whose transcription is repressed in response to ammonia
-
-
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
analysis
analysis
development of A method for removing other compounds which inhibit color development and for compensating for the interference produced by creatine. ThE method avoids time-consuming microdiffusion and routinely makes available the efficiency of ATP hydrolysis coupled to substrate reduction (ATP/2e ratio) with N2 as a reducible substrate
analysis
-
development of A method for removing other compounds which inhibit color development and for compensating for the interference produced by creatine. ThE method avoids time-consuming microdiffusion and routinely makes available the efficiency of ATP hydrolysis coupled to substrate reduction (ATP/2e ratio) with N2 as a reducible substrate
-
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Dilworth, M.; Eldridge, M.; Eady, R.
Correction for creatine interference with the direct indophenol measurement of NH3 in steady-state nitrogenase assays
Anal. Biochem.
207
6-10
1992
Azotobacter chroococcum (P15332 and P15334 and P15333), Azotobacter chroococcum MCD1 (P15332 and P15334 and P15333)
brenda
Lee, C.; Hu, Y.; Ribbe, M.
Tracing the hydrogen source of hydrocarbons formed by vanadium nitrogenase
Angew. Chem. Int. Ed. Engl.
50
5545-5547
2011
Azotobacter vinelandii
brenda
Boison, G.; Steingen, C.; Stal, L.J.; Bothe, H.
The rice field cyanobacteria Anabaena azotica and Anabaena sp. CH1 express vanadium-dependent nitrogenase
Arch. Microbiol.
186
367-376
2006
Anabaena azotica (Q6TFK2), Anabaena azotica, Anabaena azotica FACHB-118 (Q6TFK2), Anabaena azotica FACHB-118
brenda
Eady, R.; Robson, R.; Richardson, T.; Miller, R.; Hawkins, M.
The vanadium nitrogenase of Azotobacter chroococcum. Purification and properties of the VFe protein
Biochem. J.
244
197-207
1987
Azotobacter chroococcum (P15332 and P15334 and P15333), Azotobacter chroococcum MCD1 (P15332 and P15334 and P15333)
brenda
Eady, R.; Richardson, T.; Miller, R.; Hawkins, M.; Lowe, D.
The vanadium nitrogenase of Azotobacter chroococcum. Purification and properties of the Fe protein
Biochem. J.
256
189-196
1988
Azotobacter chroococcum (P15332 and P15334 and P15333), Azotobacter chroococcum MCD1 (P15332 and P15334 and P15333)
brenda
Miller, R.; Eady, R.
Molybdenum and vanadium nitrogenases of Azotobacter chroococcum. Low temperature favours N2 reduction by vanadium nitrogenase
Biochem. J.
256
429-432
1988
Azotobacter chroococcum
brenda
Thorneley, R.; Bergström, N.; Eady, R.; Lowe, D.
Vanadium nitrogenase of Azotobacter chroococcum. MgATP-dependent electron transfer within the protein complex
Biochem. J.
257
789-794
1989
Azotobacter chroococcum (P15332 and P15334 and P15333), Azotobacter chroococcum MCD1 (P15332 and P15334 and P15333)
brenda
Dilworth, M.; Eldridge, M.; Eady, R.
The molybdenum and vanadium nltrogenases of Azotobacter chroococcum Effect of elevated temperature on N2 reduction
Biochem. J.
289
395-400
1993
Azotobacter chroococcum (P15332 and P15334 and P15333), Azotobacter chroococcum MCD1 (P15332 and P15334 and P15333)
brenda
Robson, R.; Woodley, P.; Pau, R.; Eady, R.
Structural genes for the vanadium nitrogenase from Azotobacter chroococcum
EMBO J.
8
1217-1224
1989
Azotobacter chroococcum (P15332 and P15334 and P15333), Azotobacter chroococcum MCD1 (P15332 and P15334 and P15333)
brenda
Lyons, E.M.; Thiel, T.
Characterization of nifB, nifS, and nifU genes in the cyanobacterium Anabaena variabilis NifB is required for the vanadium-dependent nitrogenase
J. Bacteriol.
177
1570-1575
1995
Trichormus variabilis
brenda
Ruettimann-Johnson, C.; Rubio, L.; Dean, D.; Ludden, P.
VnfY is required for full activity of the vanadium-containing dinitrogenase in Azotobacter vinelandii
J. Bacteriol.
185
2383-2386
2003
Azotobacter vinelandii (C1DI21), Azotobacter vinelandii DJ (C1DI21)
brenda
Sippel, D.; Schlesier, J.; Rohde, M.; Trncik, C.; Decamps, L.; Djurdjevic, I.; Spatzal, T.; Andrade, S.L.; Einsle, O.
Production and isolation of vanadium nitrogenase from Azotobacter vinelandii by molybdenum depletion
J. Biol. Inorg. Chem.
22
161-168
2017
Azotobacter vinelandii
brenda
Sippel, D.; Einsle, O.
The structure of vanadium nitrogenase reveals an unusual bridging ligand
Nat. Chem. Biol.
13
956-960
2017
Azotobacter vinelandii (P16855)
brenda
Lee, C.; Hu, Y.; Ribbe, M.
Vanadium nitrogenase reduces CO
Science
329
642
2010
Azotobacter vinelandii
brenda
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