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MetaCyc Enzyme: Fe-only nitrogenase

Synonyms: iron-iron nitrogenase

Species: Azotobacter vinelandii

Subunit composition of Fe-only nitrogenase = [AnfG]2[AnfK]2[AnfD]2[AnfH]2
         Dinitrogenase 3 subunit delta = AnfG (summary available)
         Dinitrogenase 3 subunit beta = AnfK (summary available)
         Dinitrogenase 3 subunit alpha = AnfD (summary available)
         nitrogenase reductase subunit = AnfH (summary available)

Summary:
Background

The reduction of nitrogen to ammonia and the production of H2 is catalyzed by the nitrogenase enzyme system in diazotrophs. The enzyme complex consists of two oxygen-sensitive metalloproteins [Richards94]. The dinitrogenase reductase is a Fe protein containing a single [4Fe4S] center which acts as a specific ATP-dependent electron donor, transferring electrons from the external electron donor (a ferredoxin or a flavoprotein) to the second protein, dinitrogenase [OrmeJohnson92]. Dinitrogenase can be a [FeFe], [MoFe] or [VFe] protein, with two types of redox centers, two P clusters and two metal containing cofactor centers.

About this Enzyme

An alternative nitrogenase lacking both Mo and V was first isolated in Azotobacter vinelandii and has also been characterized in other diazotrophs including the phototrophic purple bacterium Rhodobacter capsulatus. It is encoded by the anfHDGKOR operon under the control of the anfA transcriptional activator. The transcription of anfA is regulated by ammonium and traces of Mo [Kutsche96]. The anfO gene product is essential for Fe-nitrogenase dependent nitrogen reduction to ammonia and H2.

Component I of the Fe-nitrogenase is an α2β2δ2 hexameric protein. The Fe-nitrogenase complex has a higher rate of H2 evolving activity than the Mo enzyme [Schneider91]. Under optimal conditions for nitrogen reduction, the amount of H2 produced is almost two fold compared to the Mo nitrogenase [Sicking05].

Gene-Reaction Schematic: ?

Credits:
Created 11-Apr-2011 by Weerasinghe D , SRI International


Enzymatic reaction of: nitrogenase

EC Number: 1.18.6.1

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

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.

In Pathways: nitrogen fixation

Summary:
Requires Mg2+. 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, with two molecules of ATP and ferredoxin, generates an electron. The electron is transferred to the other protein, dinitrogenase (molybdoferredoxin). Dinitrogenase is a molybdenum-iron protein that reduces dinitrogen in three successive two-electron reductions from nitrogen to diimine to hydrazine to two molecules of ammonia. The molybdenum may be replaced by vanadium or iron. The reduction is initiated by formation of hydrogen in stoichiometric amounts. Acetylene is reduced to ethylene (but only very slowly to ethane), azide to nitrogen and ammonia, and cyanide to methane and ammonia. In the absence of a suitable substrate, hydrogen is slowly formed. Ferredoxin may be replaced by flavodoxin.

Cofactors or Prosthetic Groups: Mg2+


Subunit of Fe-only nitrogenase: Dinitrogenase 3 subunit delta

Synonyms: AnfG, Nitrogenase iron-iron protein delta chain, Nitrogenase component I

Gene: anfG Accession Number: G-12782 (MetaCyc)

Molecular Weight: 15.3 kD (from nucleotide sequence)

Unification Links: UniProt:P16268

Relationship Links: InterPro:IN-FAMILY:IPR004349 , InterPro:IN-FAMILY:IPR014278 , Pfam:IN-FAMILY:PF03139 , ProDom:IN-FAMILY:PD006096

Summary:
This subunit forms a hexamer of two alpha two beta and two delta chains which is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation.

Citations: [Joerger89]


Subunit of Fe-only nitrogenase: Dinitrogenase 3 subunit beta

Synonyms: AnfK, Nitrogenase iron-iron protein beta chain, Nitrogenase component I

Gene: anfK Accession Number: G-12781 (MetaCyc)

Molecular Weight: 51.0 kD (from nucleotide sequence)

Unification Links: Protein Model Portal:P16267 , UniProt:P16267

Relationship Links: InterPro:IN-FAMILY:IPR000318 , InterPro:IN-FAMILY:IPR000510 , InterPro:IN-FAMILY:IPR014280 , Pfam:IN-FAMILY:PF00148 , Prosite:IN-FAMILY:PS00090 , Prosite:IN-FAMILY:PS00699

Summary:
This subunit forms a hexamer of two alpha two beta and two delta chains which is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation.

Citations: [Joerger89]


Subunit of Fe-only nitrogenase: Dinitrogenase 3 subunit alpha

Synonyms: AnfD, Nitrogenase molybdenum-iron protein alpha chain

Gene: anfD Accession Number: G-12780 (MetaCyc)

Molecular Weight: 55.2 kD (from nucleotide sequence)

Unification Links: DIP:DIP-6252N , Mint:MINT-1508543 , Protein Model Portal:P07328 , SMR:P07328 , UniProt:P07328

Relationship Links: InterPro:IN-FAMILY:IPR000318 , InterPro:IN-FAMILY:IPR000510 , InterPro:IN-FAMILY:IPR005972 , InterPro:IN-FAMILY:IPR010143 , PDB:Structure:1FP4 , PDB:Structure:1G20 , PDB:Structure:1G21 , PDB:Structure:1L5H , PDB:Structure:1M1N , PDB:Structure:1M1Y , PDB:Structure:1M34 , PDB:Structure:1N2C , PDB:Structure:2AFH , PDB:Structure:2AFI , PDB:Structure:2AFK , PDB:Structure:2MIN , PDB:Structure:3K1A , PDB:Structure:3MIN , PDB:Structure:3U7Q , Pfam:IN-FAMILY:PF00148 , Prosite:IN-FAMILY:PS00090 , Prosite:IN-FAMILY:PS00699

Summary:
This subunit forms a hexamer of two alpha two beta and two delta chains which is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation.

Citations: [Joerger89]


Subunit of Fe-only nitrogenase: nitrogenase reductase subunit

Synonyms: AnfH, Nitrogenase Fe protein 1, Nitrogenase component II

Gene: anfH Accession Number: G-12779 (MetaCyc)

Molecular Weight: 31.5 kD (from nucleotide sequence)

Unification Links: Protein Model Portal:P00459 , SMR:P00459 , UniProt:P00459

Relationship Links: InterPro:IN-FAMILY:IPR000392 , InterPro:IN-FAMILY:IPR005977 , InterPro:IN-FAMILY:IPR027417 , Panther:IN-FAMILY:PTHR13696:SF32 , PDB:Structure:1DE0 , PDB:Structure:1FP6 , PDB:Structure:1G1M , PDB:Structure:1G5P , PDB:Structure:1G20 , PDB:Structure:1G21 , PDB:Structure:1M1Y , PDB:Structure:1M34 , PDB:Structure:1N2C , PDB:Structure:1NIP , PDB:Structure:1RW4 , PDB:Structure:1XCP , PDB:Structure:1XD8 , PDB:Structure:1XD9 , PDB:Structure:1XDB , PDB:Structure:2AFH , PDB:Structure:2AFI , PDB:Structure:2AFK , PDB:Structure:2C8V , PDB:Structure:2NIP , Pfam:IN-FAMILY:PF00142 , Prints:IN-FAMILY:PR00091 , Prosite:IN-FAMILY:PS00692 , Prosite:IN-FAMILY:PS00746 , Prosite:IN-FAMILY:PS51026

Summary:
This subunit is a homodimer associated with the molybdenum-iron nitrogenase component 2 and binds 1 4Fe-4S cluster per dimer.

Citations: [Jacobson89]


References

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

Jacobson89: Jacobson MR, Brigle KE, Bennett LT, Setterquist RA, Wilson MS, Cash VL, Beynon J, Newton WE, Dean DR (1989). "Physical and genetic map of the major nif gene cluster from Azotobacter vinelandii." J Bacteriol 171(2);1017-27. PMID: 2644218

Joerger89: Joerger RD, Jacobson MR, Premakumar R, Wolfinger ED, Bishop PE (1989). "Nucleotide sequence and mutational analysis of the structural genes (anfHDGK) for the second alternative nitrogenase from Azotobacter vinelandii." J Bacteriol 171(2);1075-86. PMID: 2644222

Kutsche96: Kutsche M, Leimkuhler S, Angermuller S, Klipp W (1996). "Promoters controlling expression of the alternative nitrogenase and the molybdenum uptake system in Rhodobacter capsulatus are activated by NtrC, independent of sigma54, and repressed by molybdenum." J Bacteriol 178(7);2010-7. PMID: 8606177

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

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

Schneider91: Schneider K, Muller A, Schramm U, Klipp W (1991). "Demonstration of a molybdenum- and vanadium-independent nitrogenase in a nifHDK-deletion mutant of Rhodobacter capsulatus." Eur J Biochem 195(3);653-61. PMID: 1999188

Sicking05: Sicking C, Brusch M, Lindackers A, Riedel KU, Schubert B, Isakovic N, Krall C, Klipp W, Drepper T, Schneider K, Masepohl B (2005). "Identification of two new genes involved in diazotrophic growth via the alternative Fe-only nitrogenase in the phototrophic purple bacterium Rhodobacter capsulatus." J Bacteriol 187(1);92-8. PMID: 15601692

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
Page generated by SRI International Pathway Tools version 18.5 on Sun Dec 21, 2014, BIOCYC13A.