KEGG   ORTHOLOGY: K22896
Entry
K22896                      KO                                     

Name
vnfD
Definition
vanadium-dependent nitrogenase alpha chain [EC:1.18.6.2]
Pathway
ko00910  Nitrogen metabolism
ko01100  Metabolic pathways
Module
M00175  Nitrogen fixation, nitrogen => ammonia
Brite
KEGG Orthology (KO) [BR:ko00001]
 09100 Metabolism
  09102 Energy metabolism
   00910 Nitrogen metabolism
    K22896  vnfD; vanadium-dependent nitrogenase alpha chain
Enzymes [BR:ko01000]
 1. Oxidoreductases
  1.18  Acting on iron-sulfur proteins as donors
   1.18.6  With dinitrogen as acceptor
    1.18.6.2  vanadium-dependent nitrogenase
     K22896  vnfD; vanadium-dependent nitrogenase alpha chain
Other DBs
RN: R12084
COG: COG2710
Genes
AVN: Avin_02610(vnfD)
AVL: AvCA_02610(vnfD)
AVD: AvCA6_02610(vnfD)
ACX: Achr_2530(vnfD)
MMOB: F6R98_01760(vnfD)
RPA: RPA1378(vnfD)
RVA: Rvan_0514
MBRY: B1812_06630
MHEY: H2LOC_000360(vnfD)
MPAR: F7D14_08705(vnfD)
ABS: AZOBR_p350020(nifD)
CKL: CKL_1747(vnfD)
CKR: CKR_1620
CPAS: Clopa_3473
CPAT: CLPA_c14260(vnfD)
CPAE: CPAST_c14260(vnfD)
MANA: MAMMFC1_00449(vnfD_2)
AVA: Ava_4026
ANN: EH233_18390(vnfD)
MBAR: MSBR2_1062
MBAK: MSBR3_1011
MAC: MA_1216(vnfD)
 » show all
Reference
PMID:2345152
  Authors
Joerger RD, Loveless TM, Pau RN, Mitchenall LA, Simon BH, Bishop PE
  Title
Nucleotide sequences and mutational analysis of the structural genes for nitrogenase 2 of Azotobacter vinelandii.
  Journal
J Bacteriol 172:3400-8 (1990)
DOI:10.1128/jb.172.6.3400-3408.1990
  Sequence

KEGG   ORTHOLOGY: K22897
Entry
K22897                      KO                                     

Name
vnfK
Definition
vanadium-dependent nitrogenase beta chain [EC:1.18.6.2]
Pathway
ko00910  Nitrogen metabolism
ko01100  Metabolic pathways
Module
M00175  Nitrogen fixation, nitrogen => ammonia
Brite
KEGG Orthology (KO) [BR:ko00001]
 09100 Metabolism
  09102 Energy metabolism
   00910 Nitrogen metabolism
    K22897  vnfK; vanadium-dependent nitrogenase beta chain
Enzymes [BR:ko01000]
 1. Oxidoreductases
  1.18  Acting on iron-sulfur proteins as donors
   1.18.6  With dinitrogen as acceptor
    1.18.6.2  vanadium-dependent nitrogenase
     K22897  vnfK; vanadium-dependent nitrogenase beta chain
Other DBs
RN: R12084
COG: COG2710
Genes
AVN: Avin_02590(vnfK)
AVL: AvCA_02590(vnfK)
AVD: AvCA6_02590(vnfK)
ACX: Achr_2510(vnfK)
RPA: RPA1380(vnfK)
RVA: Rvan_0516
MBRY: B1812_06640
ABS: AZOBR_p350022(nifK)
PDU: PDUR_11800
CKL: CKL_1745(vnfK)
CKR: CKR_1618
CPAS: Clopa_3471
CPAT: CLPA_c14280(vnfK)
CPAE: CPAST_c14280(vnfK)
AVA: Ava_4027
ANN: EH233_18385(vnfK)
MBAR: MSBR2_1060
MBAK: MSBR3_1013
MAC: MA_1218(vnfK)
 » show all
Reference
PMID:2345152
  Authors
Joerger RD, Loveless TM, Pau RN, Mitchenall LA, Simon BH, Bishop PE
  Title
Nucleotide sequences and mutational analysis of the structural genes for nitrogenase 2 of Azotobacter vinelandii.
  Journal
J Bacteriol 172:3400-8 (1990)
DOI:10.1128/jb.172.6.3400-3408.1990
  Sequence

KEGG   ORTHOLOGY: K22898
Entry
K22898                      KO                                     

Name
vnfG
Definition
vanadium nitrogenase delta subunit [EC:1.18.6.2]
Pathway
ko00910  Nitrogen metabolism
ko01100  Metabolic pathways
Module
M00175  Nitrogen fixation, nitrogen => ammonia
Brite
KEGG Orthology (KO) [BR:ko00001]
 09100 Metabolism
  09102 Energy metabolism
   00910 Nitrogen metabolism
    K22898  vnfG; vanadium nitrogenase delta subunit
Enzymes [BR:ko01000]
 1. Oxidoreductases
  1.18  Acting on iron-sulfur proteins as donors
   1.18.6  With dinitrogen as acceptor
    1.18.6.2  vanadium-dependent nitrogenase
     K22898  vnfG; vanadium nitrogenase delta subunit
Other DBs
RN: R12084
Genes
AVN: Avin_02600(vnfG)
AVL: AvCA_02600(vnfG)
AVD: AvCA6_02600(vnfG)
ACX: Achr_2520(vnfG)
MMOB: F6R98_01755(vnfG)
RPA: RPA1379(vnfG)
RVA: Rvan_0515
MBRY: B1812_06635
MHEY: H2LOC_000355(vnfG)
MPAR: F7D14_08710(vnfG)
ABS: AZOBR_p350021(vnfG)
CKL: CKL_1746(vnfG)
CKR: CKR_1619
CPAS: Clopa_3472
MANA: MAMMFC1_00448(vnfG)
AVA: Ava_4026
ANN: EH233_18390(vnfD)
MBAR: MSBR2_1061
MBAK: MSBR3_1012
MAC: MA_1217(vnfG)
 » show all
Reference
PMID:2345152
  Authors
Joerger RD, Loveless TM, Pau RN, Mitchenall LA, Simon BH, Bishop PE
  Title
Nucleotide sequences and mutational analysis of the structural genes for nitrogenase 2 of Azotobacter vinelandii.
  Journal
J Bacteriol 172:3400-8 (1990)
DOI:10.1128/jb.172.6.3400-3408.1990
  Sequence

KEGG   ORTHOLOGY: K22899
Entry
K22899                      KO                                     

Name
vnfH
Definition
vanadium nitrogenase iron protein
Pathway
ko00910  Nitrogen metabolism
ko01100  Metabolic pathways
Module
M00175  Nitrogen fixation, nitrogen => ammonia
Brite
KEGG Orthology (KO) [BR:ko00001]
 09100 Metabolism
  09102 Energy metabolism
   00910 Nitrogen metabolism
    K22899  vnfH; vanadium nitrogenase iron protein
Other DBs
RN: R12084
COG: COG1348
Genes
AVN: Avin_02660(vnfH)
AVL: AvCA_02660(vnfH)
AVD: AvCA6_02660(vnfH)
ACX: Achr_2560(vnfH)
RPA: RPA1376(vnfH)
MBRY: B1812_06620
PDU: PDUR_11785(nifH)
CKL: CKL_1748(vnfH)
CKR: CKR_1621
CPAS: Clopa_3474
CPAT: CLPA_c14350(nifH4)
CPAE: CPAST_c14350(nifH4)
MBAR: MSBR2_1065
MAC: MA_1205(anfH) MA_1213(vnfH)
 » show all
Reference
PMID:2345152
  Authors
Joerger RD, Loveless TM, Pau RN, Mitchenall LA, Simon BH, Bishop PE
  Title
Nucleotide sequences and mutational analysis of the structural genes for nitrogenase 2 of Azotobacter vinelandii.
  Journal
J Bacteriol 172:3400-8 (1990)
DOI:10.1128/jb.172.6.3400-3408.1990
  Sequence

KEGG   ENZYME: 1.18.6.2
Entry
EC 1.18.6.2                 Enzyme                                 

Name
vanadium-dependent nitrogenase;
vnfD (gene name);
vnfG (gene name);
vnfK (gene name)
Class
Oxidoreductases;
Acting on iron-sulfur proteins as donors;
With dinitrogen as acceptor
Sysname
ferredoxin:dinitrogen oxidoreductase (ATP-hydrolysing, vanadium-dependent)
Reaction(IUBMB)
12 reduced ferredoxin + 12 H+ + N2 + 40 ATP + 40 H2O = 12 oxidized ferredoxin + 3 H2 + 2 NH3 + 40 ADP + 40 phosphate [RN:R12084]
Reaction(KEGG)
R12084
Substrate
reduced ferredoxin [CPD:C00138];
H+ [CPD:C00080];
N2 [CPD:C00697];
ATP [CPD:C00002];
H2O [CPD:C00001]
Product
oxidized ferredoxin [CPD:C00139];
H2 [CPD:C00282];
NH3 [CPD:C00014];
ADP [CPD:C00008];
phosphate [CPD:C00009]
Comment
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].
History
EC 1.18.6.2 created 2018
Pathway
ec00910  Nitrogen metabolism
ec01100  Metabolic pathways
Orthology
K22896  vanadium-dependent nitrogenase alpha chain
K22897  vanadium-dependent nitrogenase beta chain
K22898  vanadium nitrogenase delta subunit
Genes
AVN: Avin_02590(vnfK) Avin_02600(vnfG) Avin_02610(vnfD)
AVL: AvCA_02590(vnfK) AvCA_02600(vnfG) AvCA_02610(vnfD)
AVD: AvCA6_02590(vnfK) AvCA6_02600(vnfG) AvCA6_02610(vnfD)
ACX: Achr_2510(vnfK) Achr_2520(vnfG) Achr_2530(vnfD)
MMOB: F6R98_01755(vnfG) F6R98_01760(vnfD)
RPA: RPA1378(vnfD) RPA1379(vnfG) RPA1380(vnfK)
RVA: Rvan_0514 Rvan_0515 Rvan_0516
MBRY: B1812_06630 B1812_06635 B1812_06640
MHEY: H2LOC_000355(vnfG) H2LOC_000360(vnfD)
MPAR: F7D14_08705(vnfD) F7D14_08710(vnfG)
ABS: AZOBR_p350020(nifD) AZOBR_p350021(vnfG) AZOBR_p350022(nifK)
CKL: CKL_1745(vnfK) CKL_1746(vnfG) CKL_1747(vnfD)
MANA: MAMMFC1_00448(vnfG) MAMMFC1_00449(vnfD_2)
ANN: EH233_18385(vnfK) EH233_18390(vnfD)
MAC: MA_1216(vnfD) MA_1217(vnfG) MA_1218(vnfK)
 » show all
Reference
1  [PMID:2851977]
  Authors
Eady RR, Richardson TH, Miller RW, Hawkins M, Lowe DJ
  Title
The vanadium nitrogenase of Azotobacter chroococcum. Purification and properties  of the Fe protein.
  Journal
Biochem J 256:189-96 (1988)
DOI:10.1042/bj2560189
Reference
2  [PMID:3223922]
  Authors
Miller RW, Eady RR
  Title
Molybdenum and vanadium nitrogenases of Azotobacter chroococcum. Low temperature  favours N2 reduction by vanadium nitrogenase.
  Journal
Biochem J 256:429-32 (1988)
DOI:10.1042/bj2560429
Reference
3  [PMID:2784670]
  Authors
Thorneley RN, Bergstrom NH, Eady RR, Lowe DJ
  Title
Vanadium nitrogenase of Azotobacter chroococcum. MgATP-dependent electron transfer within the protein complex.
  Journal
Biochem J 257:789-94 (1989)
DOI:10.1042/bj2570789
Reference
4  [PMID:1336937]
  Authors
Dilworth MJ, Eldridge ME, Eady RR
  Title
Correction for creatine interference with the direct indophenol measurement of NH3 in steady-state nitrogenase assays.
  Journal
Anal Biochem 207:6-10 (1992)
DOI:10.1016/0003-2697(92)90491-O
Reference
5  [PMID:8424785]
  Authors
Dilworth MJ, Eldridge ME, Eady RR
  Title
The molybdenum and vanadium nitrogenases of Azotobacter chroococcum: effect of elevated temperature on N2 reduction.
  Journal
Biochem J 289 ( Pt 2):395-400 (1993)
DOI:10.1042/bj2890395
Reference
6
  Authors
Eady, R.R.
  Title
Current status of structure function relationships of vanadium nitrogenase.
  Journal
Coordinat Chem Rev 237:23-30 (2003)
Reference
7  [PMID:20689010]
  Authors
Lee CC, Hu Y, Ribbe MW
  Title
Vanadium nitrogenase reduces CO.
  Journal
Science 329:642 (2010)
DOI:10.1126/science.1191455
Reference
8  [PMID:21538750]
  Authors
Lee CC, Hu Y, Ribbe MW
  Title
Tracing the hydrogen source of hydrocarbons formed by vanadium nitrogenase.
  Journal
Angew Chem Int Ed Engl 50:5545-7 (2011)
DOI:10.1002/anie.201100869
Reference
9  [PMID:28692069]
  Authors
Sippel D, Einsle O
  Title
The structure of vanadium nitrogenase reveals an unusual bridging ligand.
  Journal
Nat Chem Biol 13:956-960 (2017)
DOI:10.1038/nchembio.2428
Other DBs
ExplorEnz - The Enzyme Database: 1.18.6.2
IUBMB Enzyme Nomenclature: 1.18.6.2
ExPASy - ENZYME nomenclature database: 1.18.6.2
BRENDA, the Enzyme Database: 1.18.6.2

KEGG   REACTION: R12084
Entry
R12084                      Reaction                               

Name
ferredoxin:dinitrogen oxidoreductase (ATP-hydrolysing, vanadium-dependent)
Definition
12 Reduced ferredoxin + 12 H+ + Nitrogen + 40 ATP + 40 H2O <=> 12 Oxidized ferredoxin + 3 Hydrogen + 2 Ammonia + 40 ADP + 40 Orthophosphate
Equation
12 C00138 + 12 C00080 + C00697 + 40 C00002 + 40 C00001 <=> 12 C00139 + 3 C00282 + 2 C00014 + 40 C00008 + 40 C00009
Reaction class
RC02891  C00014_C00697
Enzyme
Pathway
rn00910  Nitrogen metabolism
rn01100  Metabolic pathways
Module
M00175  Nitrogen fixation, nitrogen => ammonia
Orthology
K22896  vanadium-dependent nitrogenase alpha chain [EC:1.18.6.2]
K22897  vanadium-dependent nitrogenase beta chain [EC:1.18.6.2]
K22898  vanadium nitrogenase delta subunit [EC:1.18.6.2]
K22899  vanadium nitrogenase iron protein
Other DBs
RHEA: 55543

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