MetaCyc Polypeptide: [FeMo]-nitrogenase complex dinitrogenase component β subunit

Gene: nifK Accession Number: G-12734 (MetaCyc)

Species: Anabaena variabilis

Component of:
[FeMo]-nitrogenase complex dinitrogenase component
[FeMo]-nitrogenase complex (extended summary available)

This subunit is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation.

Unification Links: Protein Model Portal:Q44486, SMR:Q44486, String:240292.Ava_4249, UniProt:Q44486

Relationship Links: Entrez-Nucleotide:Homolog:AAA64711.1, InterPro:IN-FAMILY:IPR000318, InterPro:IN-FAMILY:IPR000510, InterPro:IN-FAMILY:IPR005976, InterPro:IN-FAMILY:IPR024564, Pfam:IN-FAMILY:PF00148, Pfam:IN-FAMILY:PF11844, Prosite:IN-FAMILY:PS00090, Prosite:IN-FAMILY:PS00699

Gene-Reaction Schematic

Gene-Reaction Schematic

Created 01-Apr-2011 by Weerasinghe D, SRI International

Subunit of: [FeMo]-nitrogenase complex dinitrogenase component

Species: Anabaena variabilis

Subunit composition of [FeMo]-nitrogenase complex dinitrogenase component = [NifK]2[NifD]2
         [FeMo]-nitrogenase complex dinitrogenase component β subunit = NifK (summary available)
         [FeMo]-nitrogenase complex dinitrogenase component α subunit = NifD (summary available)

Component of: [FeMo]-nitrogenase complex (extended summary available)

Subunit of: [FeMo]-nitrogenase complex

Synonyms: Mo-dependent nitrogenase complex

Species: Anabaena variabilis

Subunit composition of [FeMo]-nitrogenase complex = [(NifK)2(NifD)2][(NifH)2]
         [FeMo]-nitrogenase complex dinitrogenase component = (NifK)2(NifD)2
                 [FeMo]-nitrogenase complex dinitrogenase component β subunit = NifK (summary available)
                 [FeMo]-nitrogenase complex dinitrogenase component α subunit = NifD (summary available)
         [FeMo]-nitrogenase complex reductase component = (NifH)2 (summary available)
                 [FeMo]-nitrogenase complex reductase component monomer = NifH


Organisms capable of reducing dinitrogen gas to ammonia are known as diazotrophs. The reduction is catalyzed by the nitrogenase enzyme system, which employs ATP to drive this difficult process at atmospheric pressure and ambient temperatures. The process requires some of the most complex metal clusters observed in biology [Byer15].

Nitrogenase enzyme complexes consist of two oxygen-sensitive metalloprotein components [Richards94]. The first component is a heteromeric complex that contains two types of unique cofactors: a an [8Fe-7S] cluster known as the P-cluster is located at each αβ-subunit interface, and a second metal-containing cofactor is located within each α-subunit. The second component, dinitrogenase reductase (also known as the Fe protein), is a homodimeric protein with a binding site for ATP hydrolysis in each subunit and a single [4Fe4S] cluster bridging the two subunits. The [4Fe4S] cluster transfers electrons from an external electron donor (a ferredoxin or a flavodoxin, depending on the species) to the second component, dinitrogenase [OrmeJohnson92]. Ferrerdoxin-dependent enzymes are classified as EC and flavodoxin-dependent enzymes are classified as EC

Three types of nitrogenase systems have been described based on the metal content of the second cofactor (they also differ in their protein structures). Type I contains a molybedenum and iron cofactor ( [FeMo]-cofactor), type II contains vanadium and iron cofactor ([FeV]-cofactor) and type III contains only iron ([FeFe]-cofactor). Different genes and gene products are associated with the different types [Eady96].

All diazotrophic organisms sequenced to date encode an [FeMo]-nitrogenase, but some also have one or two alternative forms.

During catalysis, electrons are transferred from the [4Fe-4S] cluster in the reductase component to the P-cluster in the dinitrogenase protein, and ultimately to the second metal cofactor, where N2 is reduced. With each electron transfer the two components associate and dissociate, in what is named the "Fe protein cycle" [Duyvis98].

About this Enzyme

Anabaena variabilis expresses two Mo-dependent nitrogenases, the nif1 gene cluster encoded enzyme functions only in heterocysts, while the nif2 gene cluster encoded enzyme functions in both vegetative cells and heterocysts [Rao02]. The nif1 enzyme functions under both aerobic and anaerobic conditions while the nif2 enzyme is strictly anaerobic.

Citations: [Tamagnini02]

Created 01-Apr-2011 by Weerasinghe D, SRI International

Enzymatic reaction of: nitrogenase

Inferred from experiment

EC Number:

8 reduced ferredoxins + N2 + 16 ATP + 16 H2O → 8 oxidized ferredoxins + 2 ammonium + 16 ADP + 16 phosphate + H2 + 6 H+

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

In Pathways: nitrogen fixation I (ferredoxin)

It is composed of two proteins that can be separated but are both required for nitrogenase activity.

Dinitrogen reductase is a [4Fe-4S] protein, which for every two molecules of ATP, transfers an electron from the external electron donor ferredoxin, to dinitrogenase.

Dinitrogenase is a molybdenum-iron protein that breaks apart the atoms of nitrogen. It reduces dinitrogen in three successive two-electron reductions from nitrogen to diimine to hydrazine to two molecules of ammonia. The reduction is initiated by formation of hydrogen in stoichiometric amounts. The complex can also reduce acetylene to ethylene and very slowly to ethane, azide to nitrogen and ammonia, and cyanide to methane and ammonia. Ferredoxin may be replaced by flavodoxin.

The molybdenum in the enzyme can be replaced by vanadium or iron.

Cofactors or Prosthetic Groups: iron-molybdenum cofactor, an [8Fe-7S] cluster, Mg2+


Byer15: Byer AS, Shepard EM, Peters JW, Broderick JB (2015). "Radical S-adenosyl-L-methionine chemistry in the synthesis of hydrogenase and nitrogenase metal cofactors." J Biol Chem 290(7);3987-94. PMID: 25477518

Duyvis98: Duyvis MG, Wassink H, Haaker H (1998). "Nitrogenase of Azotobacter vinelandii: kinetic analysis of the Fe protein redox cycle." Biochemistry 37(50);17345-54. PMID: 9860849

Eady72: Eady RR, Smith BE, Cook KA, Postgate JR (1972). "Nitrogenase of Klebsiella pneumoniae. Purification and properties of the component proteins." Biochem J 1972;128(3);655-75. PMID: 4344006

Eady96: Eady RR (1996). "Structureminus signFunction Relationships of Alternative Nitrogenases." Chem Rev 96(7);3013-3030. PMID: 11848850

OrmeJohnson92: Orme-Johnson WH (1992). "Nitrogenase structure: where to now?." Science 257(5077);1639-40. PMID: 1529351

Park06: Park YJ, Yoo CB, Choi SY, Lee HB (2006). "Purifications and characterizations of a ferredoxin and its related 2-oxoacid:ferredoxin oxidoreductase from the hyperthermophilic archaeon, Sulfolobus solfataricus P1." J Biochem Mol Biol 39(1);46-54. PMID: 16466637

Rao02: Rao K. K, Cammack R (2002). "Hydrogen as a FuelProducing hydrogen as a fuel." Learning from Nature.

Richards94: Richards AJ, Lowe DJ, Richards RL, Thomson AJ, Smith BE (1994). "Electron-paramagnetic-resonance and magnetic-circular-dichroism studies of the binding of cyanide and thiols to the thiols to the iron-molybdenum cofactor from Klebsiella pneumoniae nitrogenase." Biochem J 297 ( Pt 2);373-8. PMID: 8297344

Tamagnini02: Tamagnini P, Axelsson R, Lindberg P, Oxelfelt F, Wunschiers R, Lindblad P (2002). "Hydrogenases and hydrogen metabolism of cyanobacteria." Microbiol Mol Biol Rev 66(1);1-20, table of contents. PMID: 11875125

Vandecasteele70: Vandecasteele JP, Burris RH (1970). "Purification and properties of the constituents of the nitrogenase complex from Clostridium pasteurianum." J Bacteriol 1970;101(3);794-801. PMID: 5438048

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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